From 57b3496af147a53a8f9883381887413823663369 Mon Sep 17 00:00:00 2001 From: frehburg <43171336+frehburg@users.noreply.github.com> Date: Tue, 15 Oct 2024 16:19:37 +0000 Subject: [PATCH] =?UTF-8?q?Deploying=20to=20gh-pages=20from=20@=20BIH-CEI/?= =?UTF-8?q?phenopacket=5Fmapper@73c8c5ab95500f68cd33dcf84422e8409d923ce1?= =?UTF-8?q?=20=F0=9F=9A=80?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- .../phenopacket_mapper/utils/io/read_xml.html | 20 ++++++++++++++++++ .../apidocs/phenopacket_mapper.utils.io.html | 1 + .../phenopacket_mapper.utils.io.read_xml.html | 5 +++++ latest/genindex.html | 2 ++ latest/objects.inv | Bin 3733 -> 3746 bytes latest/searchindex.js | 2 +- 6 files changed, 29 insertions(+), 1 deletion(-) diff --git a/latest/_modules/phenopacket_mapper/utils/io/read_xml.html b/latest/_modules/phenopacket_mapper/utils/io/read_xml.html index cfb9410..c33d5d6 100644 --- a/latest/_modules/phenopacket_mapper/utils/io/read_xml.html +++ b/latest/_modules/phenopacket_mapper/utils/io/read_xml.html @@ -136,6 +136,25 @@

Source code for phenopacket_mapper.utils.io.read_xml

return dict_ +
+[docs] +def remove_at_symbols(dict_: Dict) -> Dict: + if isinstance(dict_, dict): + new_dict = {} + for k, v in dict_.items(): + if k.startswith("@"): + k = k[1:] + if isinstance(v, list): + new_dict[k] = [remove_at_symbols(item) for item in v] + else: + new_dict[k] = remove_at_symbols(v) + + return new_dict + else: + return dict_
+ + +
[docs] def parse_xml(file: IOBase) -> Dict: @@ -143,6 +162,7 @@

Source code for phenopacket_mapper.utils.io.read_xml

dict_ = xmltodict.parse(file.read()) print(f"{dict_=}, {type(dict_)=}") dict_ = _post_process_xml_dict(dict_) + dict_ = remove_at_symbols(dict_) return dict_
diff --git a/latest/apidocs/phenopacket_mapper.utils.io.html b/latest/apidocs/phenopacket_mapper.utils.io.html index af1e71e..d7f54a6 100644 --- a/latest/apidocs/phenopacket_mapper.utils.io.html +++ b/latest/apidocs/phenopacket_mapper.utils.io.html @@ -231,6 +231,7 @@

Submodulesphenopacket_mapper.utils.io.read_xml module diff --git a/latest/apidocs/phenopacket_mapper.utils.io.read_xml.html b/latest/apidocs/phenopacket_mapper.utils.io.read_xml.html index 4d1963e..f49dd11 100644 --- a/latest/apidocs/phenopacket_mapper.utils.io.read_xml.html +++ b/latest/apidocs/phenopacket_mapper.utils.io.read_xml.html @@ -83,6 +83,11 @@ phenopacket_mapper.utils.io.read_xml.read_xml(path: str | Path | IOBase, encoding='utf-8') → Dict[source]
+
+
+phenopacket_mapper.utils.io.read_xml.remove_at_symbols(dict_: Dict) → Dict[source]
+
+
phenopacket_mapper.utils.io.read_xml.parse_xml(file: IOBase) → Dict[source]
diff --git a/latest/genindex.html b/latest/genindex.html index 8e77a7b..aae3c08 100644 --- a/latest/genindex.html +++ b/latest/genindex.html @@ -1304,6 +1304,8 @@

R

  • (in module phenopacket_mapper.utils.io.read_xml)
    • +
  • remove_at_symbols() (in module phenopacket_mapper.utils.io.read_xml) +
  • remove_duplicates() (phenopacket_mapper.data_standards.value_set.ValueSet method)
      diff --git a/latest/objects.inv b/latest/objects.inv index c496fb185fa53bf514049d0f84e2ae518e0ce6eb..d6bc60830d21ff505b264cc1974b9520446df4b2 100644 GIT binary patch delta 3651 zcmV-J4!rS|9iknOf`84Dq5l z#5p&<tOd?_eUd4K+ZTPXCEm$xBy3&Kxz1#qMy3&W zavL>D6fe=xO=xv0u4GdsoT`UB4u?MW7a;OtS@=98C!W087FAK4p13YXRLf{=9A}yQ z%+u&ooHd-J(SMg5`U?uj+AOO09~!e(t^?NC#%1)Hod3h)hhOdIr$&GIzHJ}3hFa?S z3Yx3Zwf6i}|Ni*PAiQh&CQ9vB$5`>GsWQNIMIpU=o&Hjlr#Mip&a}eT>s);InjQTS zDRY%XNq1d>2ZSrWzyrlKKU4$AO-^b+?VI!+p^6!-gPKL@pSrdGUHfRSbV#Pp zU*XDlNV!TXQP!b`*g;vOfdzv-pbU~`5+N!cx}>V)iFg)C9KKn9Gus^DuAElx&~McR zF6W_=pQA$FL-~^)Ec6+C{}F#F+=RP~ARFBTN{DT63U%-%If*EA3!Op~yunT?3fX?A z5Pt@5&XbCIZ{1T+_-yPG=zcfaB!5ayJdZus(r$S4SZBNCZG#;?0B)iKnLiZfV8X)< z$DN{{#^q%uI`MGbs0Wx{Ja+&H{G>4z5BspO&~5^b9#1^!9-4RW;}@;F%>FvgfA zY{1E1CmHm4t`iMD0es?hpuSrlx+j`Y1%I=LpQ}qlmX*}!>T4#1YS^*g$ewr{=;_$1 ziI-CyvRccEYbpI?sKS-!EPF@m_Ag66MU9cu9bLdWP>blTUj$F zHcvdY$azRjp=9*ezkKs;AkCAWn}uskqZYRNbk*6mWzZg!i=wG{xRP4Eu(g}Z!hepY z0p-G$(C)1ToBC+MO4jn&JV$2W(ck4|AYsK5S)}1=*6M|A%`=Y!s|73HFV)YLY|7mq zIW9WEr>vcB=hcsnoHubp*sy*7k*?ZbNyRCTa*Ni-P z?9Ys?(J|2r6cht4R+^dx6GQFGatY=0=@i=3r#Bcgl9p}3yo+QozC@YY#llT{WZ7zC0e7JphI+|wpK z3r*4sEf+o+hL{JPBty%CN}i!bK_}IC;>=>u;3MAPz+=E086$)I=NSI_G%IO@JS6KD zgglsKFhUI64S)~?zidVbLzHMhM}$Z}AcnvuB~asF0|=>kkTHcj;57HXz!Av~boz8D z5QI$F?H5WEWV!?)3O0#i4}TOyY6T$~76{(k^K5&lUAapxO9 zU8pD)MWOer6l%jt9e9;iB1%#UlHM1RsZWoHqxxKO_jf&S)siy`_pc4^S9p%d?Hg2q za=0u%lq@cV!C#sv^A7<)kOPQRM`i>1tK;$lak}^FaCEtX{tVcxL9Ft<>K>U%h!nn8 zsnOYm2x+Q3Lw^Kp#(yDJ`ChG#%RR=qUyH!9Y(v(626{G8-}d#I0n2)g54I z06&jAwE~s{^ShvH!k&r&`YQ#cNACs5j=wryhNkG)4TF%baNQH6d))9sG+u9U(gXT5 z;eM2ufy9%l6eZ6@;k-uNo$u0dhAmCN)563EtTNw51q%*;VYFu$ZY_Bm1V|92BB`-e z&^p1?gLSY%g@3D&5f>Eba-m}@#=1dO&Betk8?t)FbXTyNTDWi6wI{n2)}HteS@WZm zukA?d{P-{ufp|Z}X&SYub_vg%ocG0WqO9iUD zku9hq$9Ddex={C%C8}&NjVQ{d23L7&1*&XoaXYIBa#c_u=0=;#GBF`!49oQDYH;oqxUg_d(+qhyx&Z$=P*7+ zU*Z5bCdmfARna@~t&PEfcM6097Xrxcw7m%~Y)fGpX&z&XssecFpY=qp4mCoEBAAr4 z`G13$hP}A(ZQIU#!Q0cz}TQh6^e5+~I7yjn81xiDRx_ZJO zBCfeGfY&7h<8c6iqwDj z&3=%sTU%FT;d`IBs@PfCR#r^a>G%2odp9_|eAU{pA09ujia+y;7YTp3 zuDRxDg{<|tVr~A4Uv3E;^jDF2Oj2DMX$hgR3Q2-Rp>9=I9Kc{kb0n||<^E@t65XHoD18Az^#`Z@el2=v7RqcVd zG`>l=qU8qJ-Bvsh=cYFS7dqQ`(|`0fN3fNjW@FpF9Xk5T53aYbzWi>Ko$!>Lcpm$a z-f-wxiknQ(>Yltq%d0^1UqNFqO*pWLfAu5n;uD#piWgh=OGw^`o2}Svrpf9#e6w14REO9$|M=Rwu@gRU1-gxPk#Yd$b3r5 zz01P^)E=YEu*T#CI9*#}5WQ{GF74cnY@A@rZY8mAUwF%`Vi>|SshBw_I9JC3G~-@L zLuK2(-C=Iztik{{(ixc_!*)UXd`LIkNjfCEnP0ix&w6JzP8vus#Llv9-|iIw>t8dg zZ5-zw)>~Y{aDhCdm{{iE9e=>nFUSFjCaZDGNx^|?l5*=vw8*$++sV8Rz4=;Rt`F5L z8NS9b&b~CTdwJm2UT|ka`787&TaeuEG&<%Yh8HR29 z2Ec%BpleAb%)vW=XGov`B2BX=n41O^%tY$@aCNcr%t^tOY7(Ii!CHifGdB%)unO?V zv5Zh*+tKQ-!vP@h+=tdNPMcBi0c(F6dhAoUMcgriY5D;VF;4!>)A(BkR`w=GLW6mI zQM&+8f7)^MCj+YbF@LXy=J^-kYFr+}@c0!CTNXGxnijAwxE*-Lz{;-V^KdZ;@mj1H zb5`0W1TGeAt`Q8;K-+i6We5=v!kK2VV)4QYQKa17aI^TxGo#rZwf;Vsj}OCX7qHP8 zzw<1SdQMVHHrkzJ_GNtk`_F$B(>9HHYj68o+keu|R2^rT{eR`{iO=D9Cq5j}W_6{x zlcm{kyfYh)JmlsUxF}?Ke%F0rZ9dvyJX_pc>e1xF#|OdQdLjAMVDYZA_}CwM7^!Vw zJf8Iwy_nJrApqlI4@a%#Kl{HQ6pyRqG*z<4?5R)o`$y9=8^x>Wr4i{g&TMqp+Wbo& zU_ZA9#x`GHW<1ZMpI%;>wmTVEo%ik6EM{iUo7vx$76p5+KTLFI3GC7E4;BE`2N zEL5CF)i=fBw8ODZldtTF@4goA?p99udsv4b^H?UvXOx6hC4au#bh+j05bIAtYCZ;8 zm`dY2tm{%eHnrsN|Dy(gLTlKISop+h={SCEm$xpln_6xlZyh4ooBN z!`d6e{#Dvb9aO1;qLfeS)pH>az-1#g%}SpvZ&c<=pY&Olm3g>v z9Bz1YPg$Ow(#m&vVZ%L((EtDE)J{_P=W%?UfGE z^!dwQ84t0nqEZ#LuOW6&RO7b8Q08BPEWd^FXFXWxGvxjw{!+N{cNsx8x*3!R+u$7P;7xKCQRo&rhbVZ1omCXF z{eR9O4Bnh)6-95|b5LM5_8D})A8nF9L`Rv1$hEX99uezo*Su}8!w0}kbRhGG%p8oQ zzu~x3)YG`MNK_~8uN(CM(~IW@0G^*Trs94dHWu2A$I;_KM%_d6?tT2Mb(7g&r|tQX zqm%VG`RgRTKF@Wc-Y0+$vi8(>>qGZM>^HJU8G3p; zwrcA6So^HjqLf-nKN(j3O8G^__0dxyy*wwGClhZsjaEz_D*XvQiKQWlMFqpc`M(i@|QAi zirpVM&N|+wtevj!?aEHq<21RG^fX28VVTHOW_9IR z^|h9nhxuwR=&ir@iuPfkU5^YZ_kZ|e2IW$w`Dgtc(iDl=)R&c4?a>C#-qYsUZ3VGk zGxC7gpBY<|W1<%*BnDcnG&c(+h8oLq4&}pi3T=w%4aSTmCUgM6E0d!`Ss-X(cvu8< z#3(_K7&}T)CP$G{#2MmADe~0FQi`_!&K(TJMUHD{56I!Iv!*7iEJ!E_EPqKXyhOC8 zO@0=hq!(T;dNK?%4>?JOmxq)*!;3;rszKt+V$k3t-rxW+;EjxlLH=_LygtuL8Y2(O zx&tuJswvICz! zUkU^x6LtHA6NQ*A!H7alqJP)}g^*goh(k@d*aL+t4TF)5AvuGOhL&Ey&%u&(umcuH zIO+~qZ{qoaHEm%ZqUPpT8!5$sli&@_eYw&hSYd8H_2o&OU`2T&(_eHb370xC`GOUL zn3BQE@)qul#PkhD22xT78wWYngN=li07Awfg=uoBzmeN6Ye**>&40}w064-w*&uFw zLGm6C5hQt+K5_0IxP#4rt7!N(^MJwLt1Z-cv2f|X{lc`2CO*GESC$0 zo+8FZLP;Crf}qWExhQzj%eZK`QqK5zsA*_!B<8>F$9_UvWNg6x;3L}kcr%KlUkD`76eSfq!g!EQpWa3s5!0HaL zG=QJSomv6QLHS+KHDRQphyKbziRirm+3{D8=buK+g8&JFSVc9p z3R)+Wdaw>wsDEfRGU9>)oiB81#aK6_syVw@Wg}M4nC=2rQ!DokyY^(4!rBx6k=ODu z&tKY+*7@;aBm(h%2;(?tQ|%&|IL8Z9#L}>QiSsX+7r`&3s-=1IfrQh$ibbW=)7C&0 zr|dCMSpa!`#AOfe9c9&;(t9rBkU1#*Y;P<=kK7ZD(0_N4SVM|Mw_fGmm8Z7uop@%q zL~t9-FGE~aS2?VdDt9lLKG(#A{U$@`b=ax6yFVPmEKX$GRf2ZK6OtnjQ*9T$%Dz;f z${X2&DspUxuhfM)PL`>%!89r>ni^c?tre)Ut;O}MBFI%ag>X|h^>Pcz@o8;<#J?-s zw7%7=eSbw+Th~c3Z)!~UwPv9Hdp2qBpNP_o6}P19j>>DgTdmQr19zFOtApC7w*)oO zU^P(&7Hy{OB+7MxqZF%Mh0fg&-hA2+-g?G}(*38(&XVJj?y86#KDM1Fc@)I*DQuD& z>VMmLVKyVH0I@(Zwsh|f6DvZ=mg*a_C1hE2Vt)iFoHa1>3NweYuOkW`Pr=$7vfv=w ze)nMAJmnSMc(C%Y6a-D_j$p?(Jt9T75oWCjHx-ur;&h4_i&EzUVivEl?gp($(V!k#NoV0ld^XZ%oW} zdxGkcFHX|cIBpn*mcUg#I5PgK6H-;Q4pyj$Rk9gqYb~p~G@EGcn|cBj!>VIu>|PCX z!xaih@mD!608HLVIZX z_=}vB-nb0aVLRUAUpnb%EGhVkNX2^kk@ zs4{?}IsKZf_2*R1E{Zvb@-z*z7(_9#+yI)YxUv1&sOY7t!?H%;Esd`du4uVIcDEG- z;@tEq;6i5`Z<=G~2)6S3Xky#9Lw`qK`PK9G{gdC1QUo5NqfA2_=@o~LrMSujt?tQ- ztWX7-{}h>kX~Ka`5Gsze3lbELDk!$@=ZMgVu;YTvrk_>C9oWn1~`;qX)=9Y+Ql!HF0|$oQ@|B6Oi3lWJQ6^S7=LAkH6|3` zbZtpM^tMsE+;2Csah9vNmPx*S;Vn~pVF=UAUg4zRTpb6{jC&;)RBZcphq;nC3Ip88 zDHJ${?Sk}4iEg-)oJ4Uo$#J`%_0DXtGLT>hU=`cG-75mtzh+k3ILZbb0(nM( zslvfKfTv%O0}@SENx>$MPq~J<5iBN}NEkeYFn}$1B33%jKMyQDGXm!`&01$YN zp>>SY794!Q+Mk9VV+yy3I~Fia9Pkk1glC?{-wLoYnw$s?=Eb6R0ibx=arCDEs^XYe zL-X(jxEPlwC_K2LQGd$`ELJR@Wu~%N+8b^XKFY*sc1Nwh59Z_DaM~GcbjBYtiE=$BsdF*fofP(s zc>nv)e=DJF8uRMh_6M*3qMcQBm?ZY+uO~i-+s$*%^Bcb&z@{?Oe>Z3E-}q^IcFlx7G47#Dju zYAyfS|9w}r?Lj I4>mOmqUqTc0RR91 diff --git a/latest/searchindex.js b/latest/searchindex.js index ffa8889..43a18cc 100644 --- a/latest/searchindex.js +++ b/latest/searchindex.js @@ -1 +1 @@ -Search.setIndex({"alltitles": {"API reference": [[0, null]], "About": [[58, "about"]], "Anaconda": [[59, "anaconda"], [59, "id2"]], "Contents:": [[58, null], [62, null]], "Create a Data Model in Code": [[63, null]], "Creating a virtual environment": [[59, "creating-a-virtual-environment"]], "Features": [[60, "features"]], "Indices and tables": [[58, "indices-and-tables"]], "Installation": [[59, null]], "Installing Git": [[59, "installing-git"]], "Installing Java": [[59, "installing-java"]], "Installing Python": [[59, "installing-python"]], "Installing the Phenopacket Mapper": [[59, "installing-the-phenopacket-mapper"]], "Introduction": [[60, null]], "Motivation": [[60, "motivation"]], "Phenopackets": [[60, "phenopackets"]], "Publications": [[60, "publications"]], "Quickstart": [[61, null]], "Read a Data Model from a File": [[64, null]], "Resources": [[60, "resources"]], "Standard Python": [[59, "standard-python"], [59, "id1"]], "Submodules": [[2, "submodules"], [7, "submodules"], [12, "submodules"], [18, "submodules"], [23, "submodules"], [27, "submodules"], [32, "submodules"], [36, "submodules"], [39, "submodules"], [46, "submodules"], [56, "submodules"]], "Subpackages": [[1, "subpackages"], [12, "subpackages"], [36, "subpackages"]], "TLDR": [[60, "tldr"]], "User Guides": [[62, null]], "Using pip": [[59, "using-pip"]], "Welcome to Phenopacket Mapper\u2019s documentation!": [[58, null]], "What are Phenopackets?": [[60, "what-are-phenopackets"]], "Why Phenopackets?": [[60, "why-phenopackets"]], "[WIP] Local installation": [[59, "wip-local-installation"]], "phenopacket_mapper package": [[1, null]], "phenopacket_mapper.api_requests package": [[2, null]], "phenopacket_mapper.api_requests.api_request_super_class module": [[3, null]], "phenopacket_mapper.api_requests.get module": [[4, null]], "phenopacket_mapper.api_requests.hpo_api_request module": [[5, null]], "phenopacket_mapper.api_requests.orpha_api_request module": [[6, null]], "phenopacket_mapper.cli package": [[7, null]], "phenopacket_mapper.cli.main module": [[8, null]], "phenopacket_mapper.cli.mapping_command module": [[9, null]], "phenopacket_mapper.cli.quickstart_command module": [[10, null]], "phenopacket_mapper.cli.validate_command module": [[11, null]], "phenopacket_mapper.data_standards package": [[12, null]], "phenopacket_mapper.data_standards.DataModel2PhenopacketSchema module": [[13, null]], "phenopacket_mapper.data_standards.cardinality module": [[14, null]], "phenopacket_mapper.data_standards.code module": [[15, null]], "phenopacket_mapper.data_standards.code_system module": [[16, null]], "phenopacket_mapper.data_standards.data_model module": [[17, null]], "phenopacket_mapper.data_standards.data_models package": [[18, null]], "phenopacket_mapper.data_standards.data_models.erdri_cds module": [[19, null]], "phenopacket_mapper.data_standards.data_models.rarelink_datamodel module": [[20, null]], "phenopacket_mapper.data_standards.date module": [[21, null]], "phenopacket_mapper.data_standards.value_set module": [[22, null]], "phenopacket_mapper.mapping package": [[23, null]], "phenopacket_mapper.mapping.map_field module": [[24, null]], "phenopacket_mapper.mapping.mapper module": [[25, null]], "phenopacket_mapper.mapping.phenopacket_building_block module": [[26, null]], "phenopacket_mapper.pipeline package": [[27, null]], "phenopacket_mapper.pipeline.input module": [[28, null]], "phenopacket_mapper.pipeline.mapper module": [[29, null]], "phenopacket_mapper.pipeline.output module": [[30, null]], "phenopacket_mapper.pipeline.validate module": [[31, null]], "phenopacket_mapper.preprocessing package": [[32, null]], "phenopacket_mapper.preprocessing.preprocess module": [[33, null]], "phenopacket_mapper.preprocessing.preprocess_dict module": [[34, null]], "phenopacket_mapper.preprocessing.preprocess_method module": [[35, null]], "phenopacket_mapper.utils package": [[36, null]], "phenopacket_mapper.utils.create_ipynb_in_code module": [[37, null]], "phenopacket_mapper.utils.get_field_name module": [[38, null]], "phenopacket_mapper.utils.io package": [[39, null]], "phenopacket_mapper.utils.io.data_reader module": [[40, null]], "phenopacket_mapper.utils.io.input module": [[41, null]], "phenopacket_mapper.utils.io.output module": [[42, null]], "phenopacket_mapper.utils.io.read_json module": [[43, null]], "phenopacket_mapper.utils.io.read_xml module": [[44, null]], "phenopacket_mapper.utils.pandas_utils module": [[45, null]], "phenopacket_mapper.utils.parsing package": [[46, null]], "phenopacket_mapper.utils.parsing.get_codesystem_by_namespace_prefix module": [[47, null]], "phenopacket_mapper.utils.parsing.parse_coding module": [[48, null]], "phenopacket_mapper.utils.parsing.parse_data_type module": [[49, null]], "phenopacket_mapper.utils.parsing.parse_date module": [[50, null]], "phenopacket_mapper.utils.parsing.parse_ordinal module": [[51, null]], "phenopacket_mapper.utils.parsing.parse_primitive_data_value module": [[52, null]], "phenopacket_mapper.utils.parsing.parse_value module": [[53, null]], "phenopacket_mapper.utils.parsing.parse_value_set module": [[54, null]], "phenopacket_mapper.utils.str_to_valid_id module": [[55, null]], "phenopacket_mapper.validate package": [[56, null]], "phenopacket_mapper.validate.validate module": [[57, null]]}, "docnames": ["apidocs/modules", "apidocs/phenopacket_mapper", "apidocs/phenopacket_mapper.api_requests", "apidocs/phenopacket_mapper.api_requests.api_request_super_class", "apidocs/phenopacket_mapper.api_requests.get", "apidocs/phenopacket_mapper.api_requests.hpo_api_request", "apidocs/phenopacket_mapper.api_requests.orpha_api_request", "apidocs/phenopacket_mapper.cli", "apidocs/phenopacket_mapper.cli.main", "apidocs/phenopacket_mapper.cli.mapping_command", "apidocs/phenopacket_mapper.cli.quickstart_command", "apidocs/phenopacket_mapper.cli.validate_command", "apidocs/phenopacket_mapper.data_standards", "apidocs/phenopacket_mapper.data_standards.DataModel2PhenopacketSchema", "apidocs/phenopacket_mapper.data_standards.cardinality", "apidocs/phenopacket_mapper.data_standards.code", "apidocs/phenopacket_mapper.data_standards.code_system", "apidocs/phenopacket_mapper.data_standards.data_model", "apidocs/phenopacket_mapper.data_standards.data_models", "apidocs/phenopacket_mapper.data_standards.data_models.erdri_cds", "apidocs/phenopacket_mapper.data_standards.data_models.rarelink_datamodel", "apidocs/phenopacket_mapper.data_standards.date", "apidocs/phenopacket_mapper.data_standards.value_set", "apidocs/phenopacket_mapper.mapping", "apidocs/phenopacket_mapper.mapping.map_field", "apidocs/phenopacket_mapper.mapping.mapper", "apidocs/phenopacket_mapper.mapping.phenopacket_building_block", "apidocs/phenopacket_mapper.pipeline", "apidocs/phenopacket_mapper.pipeline.input", "apidocs/phenopacket_mapper.pipeline.mapper", "apidocs/phenopacket_mapper.pipeline.output", "apidocs/phenopacket_mapper.pipeline.validate", "apidocs/phenopacket_mapper.preprocessing", "apidocs/phenopacket_mapper.preprocessing.preprocess", "apidocs/phenopacket_mapper.preprocessing.preprocess_dict", "apidocs/phenopacket_mapper.preprocessing.preprocess_method", "apidocs/phenopacket_mapper.utils", "apidocs/phenopacket_mapper.utils.create_ipynb_in_code", "apidocs/phenopacket_mapper.utils.get_field_name", "apidocs/phenopacket_mapper.utils.io", "apidocs/phenopacket_mapper.utils.io.data_reader", "apidocs/phenopacket_mapper.utils.io.input", "apidocs/phenopacket_mapper.utils.io.output", "apidocs/phenopacket_mapper.utils.io.read_json", "apidocs/phenopacket_mapper.utils.io.read_xml", "apidocs/phenopacket_mapper.utils.pandas_utils", "apidocs/phenopacket_mapper.utils.parsing", "apidocs/phenopacket_mapper.utils.parsing.get_codesystem_by_namespace_prefix", "apidocs/phenopacket_mapper.utils.parsing.parse_coding", "apidocs/phenopacket_mapper.utils.parsing.parse_data_type", "apidocs/phenopacket_mapper.utils.parsing.parse_date", "apidocs/phenopacket_mapper.utils.parsing.parse_ordinal", "apidocs/phenopacket_mapper.utils.parsing.parse_primitive_data_value", "apidocs/phenopacket_mapper.utils.parsing.parse_value", "apidocs/phenopacket_mapper.utils.parsing.parse_value_set", "apidocs/phenopacket_mapper.utils.str_to_valid_id", "apidocs/phenopacket_mapper.validate", "apidocs/phenopacket_mapper.validate.validate", "index", "installation", "introduction", "quickstart", "user_guides", "user_guides/create_data_model_in_code", "user_guides/read_data_model_from_file"], "envversion": {"sphinx": 64, "sphinx.domains.c": 3, "sphinx.domains.changeset": 1, "sphinx.domains.citation": 1, "sphinx.domains.cpp": 9, "sphinx.domains.index": 1, "sphinx.domains.javascript": 3, "sphinx.domains.math": 2, "sphinx.domains.python": 4, "sphinx.domains.rst": 2, "sphinx.domains.std": 2, "sphinx.ext.intersphinx": 1, "sphinx.ext.viewcode": 1}, "filenames": ["apidocs/modules.rst", "apidocs/phenopacket_mapper.rst", "apidocs/phenopacket_mapper.api_requests.rst", "apidocs/phenopacket_mapper.api_requests.api_request_super_class.rst", "apidocs/phenopacket_mapper.api_requests.get.rst", "apidocs/phenopacket_mapper.api_requests.hpo_api_request.rst", "apidocs/phenopacket_mapper.api_requests.orpha_api_request.rst", "apidocs/phenopacket_mapper.cli.rst", "apidocs/phenopacket_mapper.cli.main.rst", "apidocs/phenopacket_mapper.cli.mapping_command.rst", "apidocs/phenopacket_mapper.cli.quickstart_command.rst", "apidocs/phenopacket_mapper.cli.validate_command.rst", "apidocs/phenopacket_mapper.data_standards.rst", "apidocs/phenopacket_mapper.data_standards.DataModel2PhenopacketSchema.rst", "apidocs/phenopacket_mapper.data_standards.cardinality.rst", "apidocs/phenopacket_mapper.data_standards.code.rst", "apidocs/phenopacket_mapper.data_standards.code_system.rst", "apidocs/phenopacket_mapper.data_standards.data_model.rst", "apidocs/phenopacket_mapper.data_standards.data_models.rst", "apidocs/phenopacket_mapper.data_standards.data_models.erdri_cds.rst", "apidocs/phenopacket_mapper.data_standards.data_models.rarelink_datamodel.rst", "apidocs/phenopacket_mapper.data_standards.date.rst", "apidocs/phenopacket_mapper.data_standards.value_set.rst", "apidocs/phenopacket_mapper.mapping.rst", "apidocs/phenopacket_mapper.mapping.map_field.rst", "apidocs/phenopacket_mapper.mapping.mapper.rst", "apidocs/phenopacket_mapper.mapping.phenopacket_building_block.rst", "apidocs/phenopacket_mapper.pipeline.rst", "apidocs/phenopacket_mapper.pipeline.input.rst", "apidocs/phenopacket_mapper.pipeline.mapper.rst", "apidocs/phenopacket_mapper.pipeline.output.rst", "apidocs/phenopacket_mapper.pipeline.validate.rst", "apidocs/phenopacket_mapper.preprocessing.rst", "apidocs/phenopacket_mapper.preprocessing.preprocess.rst", "apidocs/phenopacket_mapper.preprocessing.preprocess_dict.rst", "apidocs/phenopacket_mapper.preprocessing.preprocess_method.rst", "apidocs/phenopacket_mapper.utils.rst", "apidocs/phenopacket_mapper.utils.create_ipynb_in_code.rst", "apidocs/phenopacket_mapper.utils.get_field_name.rst", "apidocs/phenopacket_mapper.utils.io.rst", "apidocs/phenopacket_mapper.utils.io.data_reader.rst", "apidocs/phenopacket_mapper.utils.io.input.rst", "apidocs/phenopacket_mapper.utils.io.output.rst", "apidocs/phenopacket_mapper.utils.io.read_json.rst", "apidocs/phenopacket_mapper.utils.io.read_xml.rst", "apidocs/phenopacket_mapper.utils.pandas_utils.rst", "apidocs/phenopacket_mapper.utils.parsing.rst", "apidocs/phenopacket_mapper.utils.parsing.get_codesystem_by_namespace_prefix.rst", "apidocs/phenopacket_mapper.utils.parsing.parse_coding.rst", "apidocs/phenopacket_mapper.utils.parsing.parse_data_type.rst", "apidocs/phenopacket_mapper.utils.parsing.parse_date.rst", "apidocs/phenopacket_mapper.utils.parsing.parse_ordinal.rst", "apidocs/phenopacket_mapper.utils.parsing.parse_primitive_data_value.rst", "apidocs/phenopacket_mapper.utils.parsing.parse_value.rst", "apidocs/phenopacket_mapper.utils.parsing.parse_value_set.rst", "apidocs/phenopacket_mapper.utils.str_to_valid_id.rst", "apidocs/phenopacket_mapper.validate.rst", "apidocs/phenopacket_mapper.validate.validate.rst", "index.rst", "installation.rst", "introduction.rst", "quickstart.rst", "user_guides.rst", "user_guides/create_data_model_in_code.rst", "user_guides/read_data_model_from_file.rst"], "indexentries": {"add_code_cell() (phenopacket_mapper.utils.create_ipynb_in_code.notebookbuilder method)": [[37, "phenopacket_mapper.utils.create_ipynb_in_code.NotebookBuilder.add_code_cell", false]], "add_code_cell() (phenopacket_mapper.utils.notebookbuilder method)": [[36, "phenopacket_mapper.utils.NotebookBuilder.add_code_cell", false]], "add_markdown_cell() (phenopacket_mapper.utils.create_ipynb_in_code.notebookbuilder method)": [[37, "phenopacket_mapper.utils.create_ipynb_in_code.NotebookBuilder.add_markdown_cell", false]], "add_markdown_cell() (phenopacket_mapper.utils.notebookbuilder method)": [[36, "phenopacket_mapper.utils.NotebookBuilder.add_markdown_cell", false]], "api_base_url (phenopacket_mapper.api_requests.hpo_api_request.hpoapirequest attribute)": [[5, "phenopacket_mapper.api_requests.hpo_api_request.HPOAPIRequest.api_base_url", false]], "api_base_url (phenopacket_mapper.api_requests.hpoapirequest attribute)": [[2, "phenopacket_mapper.api_requests.HPOAPIRequest.api_base_url", false]], "api_base_url (phenopacket_mapper.api_requests.orpha_api_request.orphaapirequest attribute)": [[6, "phenopacket_mapper.api_requests.orpha_api_request.OrphaAPIRequest.api_base_url", false]], "api_base_url (phenopacket_mapper.api_requests.orphaapirequest attribute)": [[2, "phenopacket_mapper.api_requests.OrphaAPIRequest.api_base_url", false]], "apirequestsuperclass (class in phenopacket_mapper.api_requests)": [[2, "phenopacket_mapper.api_requests.APIRequestSuperClass", false]], "apirequestsuperclass (class in phenopacket_mapper.api_requests.api_request_super_class)": [[3, "phenopacket_mapper.api_requests.api_request_super_class.APIRequestSuperClass", false]], "cardinality (class in phenopacket_mapper.data_standards)": [[12, "phenopacket_mapper.data_standards.Cardinality", false]], "cardinality (class in phenopacket_mapper.data_standards.cardinality)": [[14, "phenopacket_mapper.data_standards.cardinality.Cardinality", false]], "cardinality (phenopacket_mapper.data_standards.data_model.datafield attribute)": [[17, "phenopacket_mapper.data_standards.data_model.DataField.cardinality", false]], "cardinality (phenopacket_mapper.data_standards.data_model.datasection attribute)": [[17, "phenopacket_mapper.data_standards.data_model.DataSection.cardinality", false]], "cardinality (phenopacket_mapper.data_standards.data_model.orgroup attribute)": [[17, "phenopacket_mapper.data_standards.data_model.OrGroup.cardinality", false]], "cardinality (phenopacket_mapper.data_standards.datafield attribute)": [[12, "phenopacket_mapper.data_standards.DataField.cardinality", false]], "cardinality (phenopacket_mapper.data_standards.datasection attribute)": [[12, "phenopacket_mapper.data_standards.DataSection.cardinality", false]], "cardinality (phenopacket_mapper.data_standards.orgroup attribute)": [[12, "phenopacket_mapper.data_standards.OrGroup.cardinality", false]], "check_fields_adheres_to_phenopacket_allowed_values() (phenopacket_mapper.mapping.mapper.phenopacketmapper method)": [[25, "phenopacket_mapper.mapping.mapper.PhenopacketMapper.check_fields_adheres_to_phenopacket_allowed_values", false]], "check_fields_adheres_to_phenopacket_allowed_values() (phenopacket_mapper.mapping.phenopacketmapper method)": [[23, "phenopacket_mapper.mapping.PhenopacketMapper.check_fields_adheres_to_phenopacket_allowed_values", false]], "check_fields_adheres_to_phenopacket_allowed_values() (phenopacket_mapper.phenopacketmapper method)": [[1, "phenopacket_mapper.PhenopacketMapper.check_fields_adheres_to_phenopacket_allowed_values", false]], "code (phenopacket_mapper.data_standards.code.coding attribute)": [[15, "phenopacket_mapper.data_standards.code.Coding.code", false]], "code (phenopacket_mapper.data_standards.coding attribute)": [[12, "phenopacket_mapper.data_standards.Coding.code", false]], "codeableconcept (class in phenopacket_mapper.data_standards)": [[12, "phenopacket_mapper.data_standards.CodeableConcept", false]], "codeableconcept (class in phenopacket_mapper.data_standards.code)": [[15, "phenopacket_mapper.data_standards.code.CodeableConcept", false]], "codesystem (class in phenopacket_mapper.data_standards)": [[12, "phenopacket_mapper.data_standards.CodeSystem", false]], "codesystem (class in phenopacket_mapper.data_standards.code_system)": [[16, "phenopacket_mapper.data_standards.code_system.CodeSystem", false]], "coding (class in phenopacket_mapper.data_standards)": [[12, "phenopacket_mapper.data_standards.Coding", false]], "coding (class in phenopacket_mapper.data_standards.code)": [[15, "phenopacket_mapper.data_standards.code.Coding", false]], "coding (phenopacket_mapper.data_standards.code.codeableconcept attribute)": [[15, "phenopacket_mapper.data_standards.code.CodeableConcept.coding", false]], "coding (phenopacket_mapper.data_standards.codeableconcept attribute)": [[12, "phenopacket_mapper.data_standards.CodeableConcept.coding", false]], "compliance (phenopacket_mapper.data_standards.data_model.datamodelinstance attribute)": [[17, "phenopacket_mapper.data_standards.data_model.DataModelInstance.compliance", false]], "compliance (phenopacket_mapper.data_standards.datamodelinstance attribute)": [[12, "phenopacket_mapper.data_standards.DataModelInstance.compliance", false]], "data (phenopacket_mapper.data_standards.data_model.dataset attribute)": [[17, "phenopacket_mapper.data_standards.data_model.DataSet.data", false]], "data (phenopacket_mapper.data_standards.dataset attribute)": [[12, "phenopacket_mapper.data_standards.DataSet.data", false]], "data_frame (phenopacket_mapper.data_standards.data_model.dataset property)": [[17, "phenopacket_mapper.data_standards.data_model.DataSet.data_frame", false]], "data_frame (phenopacket_mapper.data_standards.dataset property)": [[12, "phenopacket_mapper.data_standards.DataSet.data_frame", false]], "data_model (phenopacket_mapper.data_standards.data_model.datamodelinstance attribute)": [[17, "phenopacket_mapper.data_standards.data_model.DataModelInstance.data_model", false]], "data_model (phenopacket_mapper.data_standards.data_model.dataset attribute)": [[17, "phenopacket_mapper.data_standards.data_model.DataSet.data_model", false]], "data_model (phenopacket_mapper.data_standards.datamodelinstance attribute)": [[12, "phenopacket_mapper.data_standards.DataModelInstance.data_model", false]], "data_model (phenopacket_mapper.data_standards.dataset attribute)": [[12, "phenopacket_mapper.data_standards.DataSet.data_model", false]], "data_model_name (phenopacket_mapper.data_standards.data_model.datamodel attribute)": [[17, "phenopacket_mapper.data_standards.data_model.DataModel.data_model_name", false]], "data_model_name (phenopacket_mapper.data_standards.datamodel attribute)": [[12, "phenopacket_mapper.data_standards.DataModel.data_model_name", false]], "data_model_name (phenopacket_mapper.datamodel attribute)": [[1, "phenopacket_mapper.DataModel.data_model_name", false]], "datafield (class in phenopacket_mapper.data_standards)": [[12, "phenopacket_mapper.data_standards.DataField", false]], "datafield (class in phenopacket_mapper.data_standards.data_model)": [[17, "phenopacket_mapper.data_standards.data_model.DataField", false]], "datafieldvalue (class in phenopacket_mapper.data_standards)": [[12, "phenopacket_mapper.data_standards.DataFieldValue", false]], "datafieldvalue (class in phenopacket_mapper.data_standards.data_model)": [[17, "phenopacket_mapper.data_standards.data_model.DataFieldValue", false]], "datamodel (class in phenopacket_mapper)": [[1, "phenopacket_mapper.DataModel", false]], "datamodel (class in phenopacket_mapper.data_standards)": [[12, "phenopacket_mapper.data_standards.DataModel", false]], "datamodel (class in phenopacket_mapper.data_standards.data_model)": [[17, "phenopacket_mapper.data_standards.data_model.DataModel", false]], "datamodel2phenopacketschema (class in phenopacket_mapper.data_standards.datamodel2phenopacketschema)": [[13, "phenopacket_mapper.data_standards.DataModel2PhenopacketSchema.DataModel2PhenopacketSchema", false]], "datamodelinstance (class in phenopacket_mapper.data_standards)": [[12, "phenopacket_mapper.data_standards.DataModelInstance", false]], "datamodelinstance (class in phenopacket_mapper.data_standards.data_model)": [[17, "phenopacket_mapper.data_standards.data_model.DataModelInstance", false]], "datareader (class in phenopacket_mapper.utils.io)": [[39, "phenopacket_mapper.utils.io.DataReader", false]], "datareader (class in phenopacket_mapper.utils.io.data_reader)": [[40, "phenopacket_mapper.utils.io.data_reader.DataReader", false]], "datasection (class in phenopacket_mapper.data_standards)": [[12, "phenopacket_mapper.data_standards.DataSection", false]], "datasection (class in phenopacket_mapper.data_standards.data_model)": [[17, "phenopacket_mapper.data_standards.data_model.DataSection", false]], "dataset (class in phenopacket_mapper.data_standards)": [[12, "phenopacket_mapper.data_standards.DataSet", false]], "dataset (class in phenopacket_mapper.data_standards.data_model)": [[17, "phenopacket_mapper.data_standards.data_model.DataSet", false]], "date (class in phenopacket_mapper.data_standards)": [[12, "phenopacket_mapper.data_standards.Date", false]], "date (class in phenopacket_mapper.data_standards.date)": [[21, "phenopacket_mapper.data_standards.date.Date", false]], "day (phenopacket_mapper.data_standards.date attribute)": [[12, "phenopacket_mapper.data_standards.Date.day", false]], "day (phenopacket_mapper.data_standards.date.date attribute)": [[21, "phenopacket_mapper.data_standards.date.Date.day", false]], "day_str (phenopacket_mapper.data_standards.date attribute)": [[12, "phenopacket_mapper.data_standards.Date.day_str", false]], "day_str (phenopacket_mapper.data_standards.date.date attribute)": [[21, "phenopacket_mapper.data_standards.date.Date.day_str", false]], "description (phenopacket_mapper.data_standards.data_model.datafield attribute)": [[17, "phenopacket_mapper.data_standards.data_model.DataField.description", false]], "description (phenopacket_mapper.data_standards.data_model.orgroup attribute)": [[17, "phenopacket_mapper.data_standards.data_model.OrGroup.description", false]], "description (phenopacket_mapper.data_standards.datafield attribute)": [[12, "phenopacket_mapper.data_standards.DataField.description", false]], "description (phenopacket_mapper.data_standards.orgroup attribute)": [[12, "phenopacket_mapper.data_standards.OrGroup.description", false]], "description (phenopacket_mapper.data_standards.value_set.valueset attribute)": [[22, "phenopacket_mapper.data_standards.value_set.ValueSet.description", false]], "description (phenopacket_mapper.data_standards.valueset attribute)": [[12, "phenopacket_mapper.data_standards.ValueSet.description", false]], "display (phenopacket_mapper.data_standards.code.coding attribute)": [[15, "phenopacket_mapper.data_standards.code.Coding.display", false]], "display (phenopacket_mapper.data_standards.coding attribute)": [[12, "phenopacket_mapper.data_standards.Coding.display", false]], "elements (phenopacket_mapper.data_standards.value_set.valueset attribute)": [[22, "phenopacket_mapper.data_standards.value_set.ValueSet.elements", false]], "elements (phenopacket_mapper.data_standards.valueset attribute)": [[12, "phenopacket_mapper.data_standards.ValueSet.elements", false]], "extend() (phenopacket_mapper.data_standards.value_set.valueset method)": [[22, "phenopacket_mapper.data_standards.value_set.ValueSet.extend", false]], "extend() (phenopacket_mapper.data_standards.valueset method)": [[12, "phenopacket_mapper.data_standards.ValueSet.extend", false]], "field (phenopacket_mapper.data_standards.data_model.datafieldvalue attribute)": [[17, "phenopacket_mapper.data_standards.data_model.DataFieldValue.field", false]], "field (phenopacket_mapper.data_standards.datafieldvalue attribute)": [[12, "phenopacket_mapper.data_standards.DataFieldValue.field", false]], "fields (phenopacket_mapper.data_standards.data_model.datamodel attribute)": [[17, "phenopacket_mapper.data_standards.data_model.DataModel.fields", false]], "fields (phenopacket_mapper.data_standards.data_model.datasection attribute)": [[17, "phenopacket_mapper.data_standards.data_model.DataSection.fields", false]], "fields (phenopacket_mapper.data_standards.data_model.orgroup attribute)": [[17, "phenopacket_mapper.data_standards.data_model.OrGroup.fields", false]], "fields (phenopacket_mapper.data_standards.datamodel attribute)": [[12, "phenopacket_mapper.data_standards.DataModel.fields", false]], "fields (phenopacket_mapper.data_standards.datasection attribute)": [[12, "phenopacket_mapper.data_standards.DataSection.fields", false]], "fields (phenopacket_mapper.data_standards.orgroup attribute)": [[12, "phenopacket_mapper.data_standards.OrGroup.fields", false]], "fields (phenopacket_mapper.datamodel attribute)": [[1, "phenopacket_mapper.DataModel.fields", false]], "formatted_string() (phenopacket_mapper.data_standards.date method)": [[12, "phenopacket_mapper.data_standards.Date.formatted_string", false]], "formatted_string() (phenopacket_mapper.data_standards.date.date method)": [[21, "phenopacket_mapper.data_standards.date.Date.formatted_string", false]], "from_datetime() (phenopacket_mapper.data_standards.date static method)": [[12, "phenopacket_mapper.data_standards.Date.from_datetime", false]], "from_datetime() (phenopacket_mapper.data_standards.date.date static method)": [[21, "phenopacket_mapper.data_standards.date.Date.from_datetime", false]], "from_file() (phenopacket_mapper.data_standards.data_model.datamodel static method)": [[17, "phenopacket_mapper.data_standards.data_model.DataModel.from_file", false]], "from_file() (phenopacket_mapper.data_standards.datamodel static method)": [[12, "phenopacket_mapper.data_standards.DataModel.from_file", false]], "from_file() (phenopacket_mapper.datamodel static method)": [[1, "phenopacket_mapper.DataModel.from_file", false]], "from_iso_8601() (phenopacket_mapper.data_standards.date static method)": [[12, "phenopacket_mapper.data_standards.Date.from_iso_8601", false]], "from_iso_8601() (phenopacket_mapper.data_standards.date.date static method)": [[21, "phenopacket_mapper.data_standards.date.Date.from_iso_8601", false]], "get() (in module phenopacket_mapper.api_requests)": [[2, "phenopacket_mapper.api_requests.get", false]], "get() (in module phenopacket_mapper.api_requests.get)": [[4, "phenopacket_mapper.api_requests.get.get", false]], "get() (phenopacket_mapper.api_requests.api_request_super_class.apirequestsuperclass method)": [[3, "phenopacket_mapper.api_requests.api_request_super_class.APIRequestSuperClass.get", false]], "get() (phenopacket_mapper.api_requests.apirequestsuperclass method)": [[2, "phenopacket_mapper.api_requests.APIRequestSuperClass.get", false]], "get() (phenopacket_mapper.api_requests.hpo_api_request.hpoapirequest method)": [[5, "phenopacket_mapper.api_requests.hpo_api_request.HPOAPIRequest.get", false]], "get() (phenopacket_mapper.api_requests.hpoapirequest method)": [[2, "phenopacket_mapper.api_requests.HPOAPIRequest.get", false]], "get() (phenopacket_mapper.api_requests.orpha_api_request.orphaapirequest method)": [[6, "phenopacket_mapper.api_requests.orpha_api_request.OrphaAPIRequest.get", false]], "get() (phenopacket_mapper.api_requests.orphaapirequest method)": [[2, "phenopacket_mapper.api_requests.OrphaAPIRequest.get", false]], "get_codesystem_by_namespace_prefx() (in module phenopacket_mapper.utils.parsing)": [[46, "phenopacket_mapper.utils.parsing.get_codesystem_by_namespace_prefx", false]], "get_codesystem_by_namespace_prefx() (in module phenopacket_mapper.utils.parsing.get_codesystem_by_namespace_prefix)": [[47, "phenopacket_mapper.utils.parsing.get_codesystem_by_namespace_prefix.get_codesystem_by_namespace_prefx", false]], "get_field() (phenopacket_mapper.data_standards.data_model.datamodel method)": [[17, "phenopacket_mapper.data_standards.data_model.DataModel.get_field", false]], "get_field() (phenopacket_mapper.data_standards.datamodel method)": [[12, "phenopacket_mapper.data_standards.DataModel.get_field", false]], "get_field() (phenopacket_mapper.datamodel method)": [[1, "phenopacket_mapper.DataModel.get_field", false]], "get_field_ids() (phenopacket_mapper.data_standards.data_model.datamodel method)": [[17, "phenopacket_mapper.data_standards.data_model.DataModel.get_field_ids", false]], "get_field_ids() (phenopacket_mapper.data_standards.datamodel method)": [[12, "phenopacket_mapper.data_standards.DataModel.get_field_ids", false]], "get_field_ids() (phenopacket_mapper.datamodel method)": [[1, "phenopacket_mapper.DataModel.get_field_ids", false]], "get_field_name() (in module phenopacket_mapper.utils.get_field_name)": [[38, "phenopacket_mapper.utils.get_field_name.get_field_name", false]], "handle_file_extension() (phenopacket_mapper.utils.io.data_reader.datareader method)": [[40, "phenopacket_mapper.utils.io.data_reader.DataReader.handle_file_extension", false]], "handle_file_extension() (phenopacket_mapper.utils.io.datareader method)": [[39, "phenopacket_mapper.utils.io.DataReader.handle_file_extension", false]], "head() (phenopacket_mapper.data_standards.data_model.dataset method)": [[17, "phenopacket_mapper.data_standards.data_model.DataSet.head", false]], "head() (phenopacket_mapper.data_standards.dataset method)": [[12, "phenopacket_mapper.data_standards.DataSet.head", false]], "height (phenopacket_mapper.data_standards.data_model.dataset property)": [[17, "phenopacket_mapper.data_standards.data_model.DataSet.height", false]], "height (phenopacket_mapper.data_standards.dataset property)": [[12, "phenopacket_mapper.data_standards.DataSet.height", false]], "hour (phenopacket_mapper.data_standards.date attribute)": [[12, "phenopacket_mapper.data_standards.Date.hour", false]], "hour (phenopacket_mapper.data_standards.date.date attribute)": [[21, "phenopacket_mapper.data_standards.date.Date.hour", false]], "hour_str (phenopacket_mapper.data_standards.date attribute)": [[12, "phenopacket_mapper.data_standards.Date.hour_str", false]], "hour_str (phenopacket_mapper.data_standards.date.date attribute)": [[21, "phenopacket_mapper.data_standards.date.Date.hour_str", false]], "hpoapirequest (class in phenopacket_mapper.api_requests)": [[2, "phenopacket_mapper.api_requests.HPOAPIRequest", false]], "hpoapirequest (class in phenopacket_mapper.api_requests.hpo_api_request)": [[5, "phenopacket_mapper.api_requests.hpo_api_request.HPOAPIRequest", false]], "id (phenopacket_mapper.data_standards.data_model.datafield attribute)": [[17, "phenopacket_mapper.data_standards.data_model.DataField.id", false]], "id (phenopacket_mapper.data_standards.data_model.datasection attribute)": [[17, "phenopacket_mapper.data_standards.data_model.DataSection.id", false]], "id (phenopacket_mapper.data_standards.data_model.orgroup attribute)": [[17, "phenopacket_mapper.data_standards.data_model.OrGroup.id", false]], "id (phenopacket_mapper.data_standards.datafield attribute)": [[12, "phenopacket_mapper.data_standards.DataField.id", false]], "id (phenopacket_mapper.data_standards.datasection attribute)": [[12, "phenopacket_mapper.data_standards.DataSection.id", false]], "id (phenopacket_mapper.data_standards.orgroup attribute)": [[12, "phenopacket_mapper.data_standards.OrGroup.id", false]], "iri_prefix (phenopacket_mapper.data_standards.code_system.codesystem attribute)": [[16, "phenopacket_mapper.data_standards.code_system.CodeSystem.iri_prefix", false]], "iri_prefix (phenopacket_mapper.data_standards.codesystem attribute)": [[12, "phenopacket_mapper.data_standards.CodeSystem.iri_prefix", false]], "iso_8601_datestring() (phenopacket_mapper.data_standards.date method)": [[12, "phenopacket_mapper.data_standards.Date.iso_8601_datestring", false]], "iso_8601_datestring() (phenopacket_mapper.data_standards.date.date method)": [[21, "phenopacket_mapper.data_standards.date.Date.iso_8601_datestring", false]], "load_data() (phenopacket_mapper.data_standards.data_model.datamodel method)": [[17, "phenopacket_mapper.data_standards.data_model.DataModel.load_data", false]], "load_data() (phenopacket_mapper.data_standards.datamodel method)": [[12, "phenopacket_mapper.data_standards.DataModel.load_data", false]], "load_data() (phenopacket_mapper.datamodel method)": [[1, "phenopacket_mapper.DataModel.load_data", false]], "load_data_using_data_model() (in module phenopacket_mapper.utils.io)": [[39, "phenopacket_mapper.utils.io.load_data_using_data_model", false]], "load_data_using_data_model() (in module phenopacket_mapper.utils.io.input)": [[41, "phenopacket_mapper.utils.io.input.load_data_using_data_model", false]], "load_data_using_data_model() (phenopacket_mapper.data_standards.data_model.datamodel static method)": [[17, "phenopacket_mapper.data_standards.data_model.DataModel.load_data_using_data_model", false]], "load_data_using_data_model() (phenopacket_mapper.data_standards.datamodel static method)": [[12, "phenopacket_mapper.data_standards.DataModel.load_data_using_data_model", false]], "load_data_using_data_model() (phenopacket_mapper.datamodel static method)": [[1, "phenopacket_mapper.DataModel.load_data_using_data_model", false]], "loc_default() (in module phenopacket_mapper.utils)": [[36, "phenopacket_mapper.utils.loc_default", false]], "loc_default() (in module phenopacket_mapper.utils.pandas_utils)": [[45, "phenopacket_mapper.utils.pandas_utils.loc_default", false]], "map() (phenopacket_mapper.mapping.mapper.phenopacketmapper method)": [[25, "phenopacket_mapper.mapping.mapper.PhenopacketMapper.map", false]], "map() (phenopacket_mapper.mapping.phenopacket_building_block.phenopacketbuildingblock method)": [[26, "phenopacket_mapper.mapping.phenopacket_building_block.PhenopacketBuildingBlock.map", false]], "map() (phenopacket_mapper.mapping.phenopacketbuildingblock method)": [[23, "phenopacket_mapper.mapping.PhenopacketBuildingBlock.map", false]], "map() (phenopacket_mapper.mapping.phenopacketmapper method)": [[23, "phenopacket_mapper.mapping.PhenopacketMapper.map", false]], "map() (phenopacket_mapper.phenopacketmapper method)": [[1, "phenopacket_mapper.PhenopacketMapper.map", false]], "map_single() (in module phenopacket_mapper.mapping)": [[23, "phenopacket_mapper.mapping.map_single", false]], "map_single() (in module phenopacket_mapper.mapping.phenopacket_building_block)": [[26, "phenopacket_mapper.mapping.phenopacket_building_block.map_single", false]], "max (phenopacket_mapper.data_standards.cardinality attribute)": [[12, "phenopacket_mapper.data_standards.Cardinality.max", false]], "max (phenopacket_mapper.data_standards.cardinality.cardinality attribute)": [[14, "phenopacket_mapper.data_standards.cardinality.Cardinality.max", false]], "min (phenopacket_mapper.data_standards.cardinality attribute)": [[12, "phenopacket_mapper.data_standards.Cardinality.min", false]], "min (phenopacket_mapper.data_standards.cardinality.cardinality attribute)": [[14, "phenopacket_mapper.data_standards.cardinality.Cardinality.min", false]], "minute (phenopacket_mapper.data_standards.date attribute)": [[12, "phenopacket_mapper.data_standards.Date.minute", false]], "minute (phenopacket_mapper.data_standards.date.date attribute)": [[21, "phenopacket_mapper.data_standards.date.Date.minute", false]], "minute_str (phenopacket_mapper.data_standards.date attribute)": [[12, "phenopacket_mapper.data_standards.Date.minute_str", false]], "minute_str (phenopacket_mapper.data_standards.date.date attribute)": [[21, "phenopacket_mapper.data_standards.date.Date.minute_str", false]], "module": [[1, "module-phenopacket_mapper", false], [2, "module-phenopacket_mapper.api_requests", false], [3, "module-phenopacket_mapper.api_requests.api_request_super_class", false], [4, "module-phenopacket_mapper.api_requests.get", false], [5, "module-phenopacket_mapper.api_requests.hpo_api_request", false], [6, "module-phenopacket_mapper.api_requests.orpha_api_request", false], [7, "module-phenopacket_mapper.cli", false], [12, "module-phenopacket_mapper.data_standards", false], [13, "module-phenopacket_mapper.data_standards.DataModel2PhenopacketSchema", false], [14, "module-phenopacket_mapper.data_standards.cardinality", false], [15, "module-phenopacket_mapper.data_standards.code", false], [16, "module-phenopacket_mapper.data_standards.code_system", false], [17, "module-phenopacket_mapper.data_standards.data_model", false], [18, "module-phenopacket_mapper.data_standards.data_models", false], [19, "module-phenopacket_mapper.data_standards.data_models.erdri_cds", false], [21, "module-phenopacket_mapper.data_standards.date", false], [22, "module-phenopacket_mapper.data_standards.value_set", false], [23, "module-phenopacket_mapper.mapping", false], [24, "module-phenopacket_mapper.mapping.map_field", false], [25, "module-phenopacket_mapper.mapping.mapper", false], [26, "module-phenopacket_mapper.mapping.phenopacket_building_block", false], [27, "module-phenopacket_mapper.pipeline", false], [32, "module-phenopacket_mapper.preprocessing", false], [33, "module-phenopacket_mapper.preprocessing.preprocess", false], [34, "module-phenopacket_mapper.preprocessing.preprocess_dict", false], [35, "module-phenopacket_mapper.preprocessing.preprocess_method", false], [36, "module-phenopacket_mapper.utils", false], [37, "module-phenopacket_mapper.utils.create_ipynb_in_code", false], [38, "module-phenopacket_mapper.utils.get_field_name", false], [39, "module-phenopacket_mapper.utils.io", false], [40, "module-phenopacket_mapper.utils.io.data_reader", false], [41, "module-phenopacket_mapper.utils.io.input", false], [42, "module-phenopacket_mapper.utils.io.output", false], [43, "module-phenopacket_mapper.utils.io.read_json", false], [44, "module-phenopacket_mapper.utils.io.read_xml", false], [45, "module-phenopacket_mapper.utils.pandas_utils", false], [46, "module-phenopacket_mapper.utils.parsing", false], [47, "module-phenopacket_mapper.utils.parsing.get_codesystem_by_namespace_prefix", false], [48, "module-phenopacket_mapper.utils.parsing.parse_coding", false], [49, "module-phenopacket_mapper.utils.parsing.parse_data_type", false], [50, "module-phenopacket_mapper.utils.parsing.parse_date", false], [51, "module-phenopacket_mapper.utils.parsing.parse_ordinal", false], [52, "module-phenopacket_mapper.utils.parsing.parse_primitive_data_value", false], [53, "module-phenopacket_mapper.utils.parsing.parse_value", false], [54, "module-phenopacket_mapper.utils.parsing.parse_value_set", false], [55, "module-phenopacket_mapper.utils.str_to_valid_id", false], [56, "module-phenopacket_mapper.validate", false], [57, "module-phenopacket_mapper.validate.validate", false]], "month (phenopacket_mapper.data_standards.date attribute)": [[12, "phenopacket_mapper.data_standards.Date.month", false]], "month (phenopacket_mapper.data_standards.date.date attribute)": [[21, "phenopacket_mapper.data_standards.date.Date.month", false]], "month_str (phenopacket_mapper.data_standards.date attribute)": [[12, "phenopacket_mapper.data_standards.Date.month_str", false]], "month_str (phenopacket_mapper.data_standards.date.date attribute)": [[21, "phenopacket_mapper.data_standards.date.Date.month_str", false]], "name (phenopacket_mapper.data_standards.code_system.codesystem attribute)": [[16, "phenopacket_mapper.data_standards.code_system.CodeSystem.name", false]], "name (phenopacket_mapper.data_standards.codesystem attribute)": [[12, "phenopacket_mapper.data_standards.CodeSystem.name", false]], "name (phenopacket_mapper.data_standards.data_model.datafield attribute)": [[17, "phenopacket_mapper.data_standards.data_model.DataField.name", false]], "name (phenopacket_mapper.data_standards.data_model.datasection attribute)": [[17, "phenopacket_mapper.data_standards.data_model.DataSection.name", false]], "name (phenopacket_mapper.data_standards.data_model.orgroup attribute)": [[17, "phenopacket_mapper.data_standards.data_model.OrGroup.name", false]], "name (phenopacket_mapper.data_standards.datafield attribute)": [[12, "phenopacket_mapper.data_standards.DataField.name", false]], "name (phenopacket_mapper.data_standards.datasection attribute)": [[12, "phenopacket_mapper.data_standards.DataSection.name", false]], "name (phenopacket_mapper.data_standards.orgroup attribute)": [[12, "phenopacket_mapper.data_standards.OrGroup.name", false]], "name (phenopacket_mapper.data_standards.value_set.valueset attribute)": [[22, "phenopacket_mapper.data_standards.value_set.ValueSet.name", false]], "name (phenopacket_mapper.data_standards.valueset attribute)": [[12, "phenopacket_mapper.data_standards.ValueSet.name", false]], "namespace_prefix (phenopacket_mapper.data_standards.code_system.codesystem attribute)": [[16, "phenopacket_mapper.data_standards.code_system.CodeSystem.namespace_prefix", false]], "namespace_prefix (phenopacket_mapper.data_standards.codesystem attribute)": [[12, "phenopacket_mapper.data_standards.CodeSystem.namespace_prefix", false]], "notebookbuilder (class in phenopacket_mapper.utils)": [[36, "phenopacket_mapper.utils.NotebookBuilder", false]], "notebookbuilder (class in phenopacket_mapper.utils.create_ipynb_in_code)": [[37, "phenopacket_mapper.utils.create_ipynb_in_code.NotebookBuilder", false]], "orgroup (class in phenopacket_mapper.data_standards)": [[12, "phenopacket_mapper.data_standards.OrGroup", false]], "orgroup (class in phenopacket_mapper.data_standards.data_model)": [[17, "phenopacket_mapper.data_standards.data_model.OrGroup", false]], "orphaapirequest (class in phenopacket_mapper.api_requests)": [[2, "phenopacket_mapper.api_requests.OrphaAPIRequest", false]], "orphaapirequest (class in phenopacket_mapper.api_requests.orpha_api_request)": [[6, "phenopacket_mapper.api_requests.orpha_api_request.OrphaAPIRequest", false]], "parse_bool() (in module phenopacket_mapper.utils.parsing)": [[46, "phenopacket_mapper.utils.parsing.parse_bool", false]], "parse_bool() (in module phenopacket_mapper.utils.parsing.parse_primitive_data_value)": [[52, "phenopacket_mapper.utils.parsing.parse_primitive_data_value.parse_bool", false]], "parse_coding() (in module phenopacket_mapper.utils.parsing)": [[46, "phenopacket_mapper.utils.parsing.parse_coding", false]], "parse_coding() (in module phenopacket_mapper.utils.parsing.parse_coding)": [[48, "phenopacket_mapper.utils.parsing.parse_coding.parse_coding", false]], "parse_coding() (phenopacket_mapper.data_standards.code.coding static method)": [[15, "phenopacket_mapper.data_standards.code.Coding.parse_coding", false]], "parse_coding() (phenopacket_mapper.data_standards.coding static method)": [[12, "phenopacket_mapper.data_standards.Coding.parse_coding", false]], "parse_data_type() (in module phenopacket_mapper.data_standards.data_models)": [[18, "phenopacket_mapper.data_standards.data_models.parse_data_type", false]], "parse_data_type() (in module phenopacket_mapper.utils.parsing)": [[46, "phenopacket_mapper.utils.parsing.parse_data_type", false]], "parse_data_type() (in module phenopacket_mapper.utils.parsing.parse_data_type)": [[49, "phenopacket_mapper.utils.parsing.parse_data_type.parse_data_type", false]], "parse_date() (in module phenopacket_mapper.utils.parsing)": [[46, "phenopacket_mapper.utils.parsing.parse_date", false]], "parse_date() (in module phenopacket_mapper.utils.parsing.parse_date)": [[50, "phenopacket_mapper.utils.parsing.parse_date.parse_date", false]], "parse_date() (phenopacket_mapper.data_standards.date static method)": [[12, "phenopacket_mapper.data_standards.Date.parse_date", false]], "parse_date() (phenopacket_mapper.data_standards.date.date static method)": [[21, "phenopacket_mapper.data_standards.date.Date.parse_date", false]], "parse_float() (in module phenopacket_mapper.utils.parsing)": [[46, "phenopacket_mapper.utils.parsing.parse_float", false]], "parse_float() (in module phenopacket_mapper.utils.parsing.parse_primitive_data_value)": [[52, "phenopacket_mapper.utils.parsing.parse_primitive_data_value.parse_float", false]], "parse_int() (in module phenopacket_mapper.utils.parsing)": [[46, "phenopacket_mapper.utils.parsing.parse_int", false]], "parse_int() (in module phenopacket_mapper.utils.parsing.parse_primitive_data_value)": [[52, "phenopacket_mapper.utils.parsing.parse_primitive_data_value.parse_int", false]], "parse_ordinal() (in module phenopacket_mapper.utils.parsing)": [[46, "phenopacket_mapper.utils.parsing.parse_ordinal", false]], "parse_ordinal() (in module phenopacket_mapper.utils.parsing.parse_ordinal)": [[51, "phenopacket_mapper.utils.parsing.parse_ordinal.parse_ordinal", false]], "parse_primitive_data_value() (in module phenopacket_mapper.utils.parsing)": [[46, "phenopacket_mapper.utils.parsing.parse_primitive_data_value", false]], "parse_primitive_data_value() (in module phenopacket_mapper.utils.parsing.parse_primitive_data_value)": [[52, "phenopacket_mapper.utils.parsing.parse_primitive_data_value.parse_primitive_data_value", false]], "parse_single_data_type() (in module phenopacket_mapper.utils.parsing)": [[46, "phenopacket_mapper.utils.parsing.parse_single_data_type", false]], "parse_single_data_type() (in module phenopacket_mapper.utils.parsing.parse_data_type)": [[49, "phenopacket_mapper.utils.parsing.parse_data_type.parse_single_data_type", false]], "parse_value() (in module phenopacket_mapper.utils.parsing)": [[46, "phenopacket_mapper.utils.parsing.parse_value", false]], "parse_value() (in module phenopacket_mapper.utils.parsing.parse_value)": [[53, "phenopacket_mapper.utils.parsing.parse_value.parse_value", false]], "parse_value_set() (in module phenopacket_mapper.utils.parsing)": [[46, "phenopacket_mapper.utils.parsing.parse_value_set", false]], "parse_value_set() (in module phenopacket_mapper.utils.parsing.parse_value_set)": [[54, "phenopacket_mapper.utils.parsing.parse_value_set.parse_value_set", false]], "parse_value_set() (phenopacket_mapper.data_standards.value_set.valueset static method)": [[22, "phenopacket_mapper.data_standards.value_set.ValueSet.parse_value_set", false]], "parse_value_set() (phenopacket_mapper.data_standards.valueset static method)": [[12, "phenopacket_mapper.data_standards.ValueSet.parse_value_set", false]], "parse_xml() (in module phenopacket_mapper.utils.io)": [[39, "phenopacket_mapper.utils.io.parse_xml", false]], "parse_xml() (in module phenopacket_mapper.utils.io.read_xml)": [[44, "phenopacket_mapper.utils.io.read_xml.parse_xml", false]], "phenopacket_mapper": [[1, "module-phenopacket_mapper", false]], "phenopacket_mapper.api_requests": [[2, "module-phenopacket_mapper.api_requests", false]], "phenopacket_mapper.api_requests.api_request_super_class": [[3, "module-phenopacket_mapper.api_requests.api_request_super_class", false]], "phenopacket_mapper.api_requests.get": [[4, "module-phenopacket_mapper.api_requests.get", false]], "phenopacket_mapper.api_requests.hpo_api_request": [[5, "module-phenopacket_mapper.api_requests.hpo_api_request", false]], "phenopacket_mapper.api_requests.orpha_api_request": [[6, "module-phenopacket_mapper.api_requests.orpha_api_request", false]], "phenopacket_mapper.cli": [[7, "module-phenopacket_mapper.cli", false]], "phenopacket_mapper.data_standards": [[12, "module-phenopacket_mapper.data_standards", false]], "phenopacket_mapper.data_standards.cardinality": [[14, "module-phenopacket_mapper.data_standards.cardinality", false]], "phenopacket_mapper.data_standards.code": [[15, "module-phenopacket_mapper.data_standards.code", false]], "phenopacket_mapper.data_standards.code_system": [[16, "module-phenopacket_mapper.data_standards.code_system", false]], "phenopacket_mapper.data_standards.data_model": [[17, "module-phenopacket_mapper.data_standards.data_model", false]], "phenopacket_mapper.data_standards.data_models": [[18, "module-phenopacket_mapper.data_standards.data_models", false]], "phenopacket_mapper.data_standards.data_models.erdri_cds": [[19, "module-phenopacket_mapper.data_standards.data_models.erdri_cds", false]], "phenopacket_mapper.data_standards.datamodel2phenopacketschema": [[13, "module-phenopacket_mapper.data_standards.DataModel2PhenopacketSchema", false]], "phenopacket_mapper.data_standards.date": [[21, "module-phenopacket_mapper.data_standards.date", false]], "phenopacket_mapper.data_standards.value_set": [[22, "module-phenopacket_mapper.data_standards.value_set", false]], "phenopacket_mapper.mapping": [[23, "module-phenopacket_mapper.mapping", false]], "phenopacket_mapper.mapping.map_field": [[24, "module-phenopacket_mapper.mapping.map_field", false]], "phenopacket_mapper.mapping.mapper": [[25, "module-phenopacket_mapper.mapping.mapper", false]], "phenopacket_mapper.mapping.phenopacket_building_block": [[26, "module-phenopacket_mapper.mapping.phenopacket_building_block", false]], "phenopacket_mapper.pipeline": [[27, "module-phenopacket_mapper.pipeline", false]], "phenopacket_mapper.preprocessing": [[32, "module-phenopacket_mapper.preprocessing", false]], "phenopacket_mapper.preprocessing.preprocess": [[33, "module-phenopacket_mapper.preprocessing.preprocess", false]], "phenopacket_mapper.preprocessing.preprocess_dict": [[34, "module-phenopacket_mapper.preprocessing.preprocess_dict", false]], "phenopacket_mapper.preprocessing.preprocess_method": [[35, "module-phenopacket_mapper.preprocessing.preprocess_method", false]], "phenopacket_mapper.utils": [[36, "module-phenopacket_mapper.utils", false]], "phenopacket_mapper.utils.create_ipynb_in_code": [[37, "module-phenopacket_mapper.utils.create_ipynb_in_code", false]], "phenopacket_mapper.utils.get_field_name": [[38, "module-phenopacket_mapper.utils.get_field_name", false]], "phenopacket_mapper.utils.io": [[39, "module-phenopacket_mapper.utils.io", false]], "phenopacket_mapper.utils.io.data_reader": [[40, "module-phenopacket_mapper.utils.io.data_reader", false]], "phenopacket_mapper.utils.io.input": [[41, "module-phenopacket_mapper.utils.io.input", false]], "phenopacket_mapper.utils.io.output": [[42, "module-phenopacket_mapper.utils.io.output", false]], "phenopacket_mapper.utils.io.read_json": [[43, "module-phenopacket_mapper.utils.io.read_json", false]], "phenopacket_mapper.utils.io.read_xml": [[44, "module-phenopacket_mapper.utils.io.read_xml", false]], "phenopacket_mapper.utils.pandas_utils": [[45, "module-phenopacket_mapper.utils.pandas_utils", false]], "phenopacket_mapper.utils.parsing": [[46, "module-phenopacket_mapper.utils.parsing", false]], "phenopacket_mapper.utils.parsing.get_codesystem_by_namespace_prefix": [[47, "module-phenopacket_mapper.utils.parsing.get_codesystem_by_namespace_prefix", false]], "phenopacket_mapper.utils.parsing.parse_coding": [[48, "module-phenopacket_mapper.utils.parsing.parse_coding", false]], "phenopacket_mapper.utils.parsing.parse_data_type": [[49, "module-phenopacket_mapper.utils.parsing.parse_data_type", false]], "phenopacket_mapper.utils.parsing.parse_date": [[50, "module-phenopacket_mapper.utils.parsing.parse_date", false]], "phenopacket_mapper.utils.parsing.parse_ordinal": [[51, "module-phenopacket_mapper.utils.parsing.parse_ordinal", false]], "phenopacket_mapper.utils.parsing.parse_primitive_data_value": [[52, "module-phenopacket_mapper.utils.parsing.parse_primitive_data_value", false]], "phenopacket_mapper.utils.parsing.parse_value": [[53, "module-phenopacket_mapper.utils.parsing.parse_value", false]], "phenopacket_mapper.utils.parsing.parse_value_set": [[54, "module-phenopacket_mapper.utils.parsing.parse_value_set", false]], "phenopacket_mapper.utils.str_to_valid_id": [[55, "module-phenopacket_mapper.utils.str_to_valid_id", false]], "phenopacket_mapper.validate": [[56, "module-phenopacket_mapper.validate", false]], "phenopacket_mapper.validate.validate": [[57, "module-phenopacket_mapper.validate.validate", false]], "phenopacketbuildingblock (class in phenopacket_mapper.mapping)": [[23, "phenopacket_mapper.mapping.PhenopacketBuildingBlock", false]], "phenopacketbuildingblock (class in phenopacket_mapper.mapping.phenopacket_building_block)": [[26, "phenopacket_mapper.mapping.phenopacket_building_block.PhenopacketBuildingBlock", false]], "phenopacketmapper (class in phenopacket_mapper)": [[1, "phenopacket_mapper.PhenopacketMapper", false]], "phenopacketmapper (class in phenopacket_mapper.mapping)": [[23, "phenopacket_mapper.mapping.PhenopacketMapper", false]], "phenopacketmapper (class in phenopacket_mapper.mapping.mapper)": [[25, "phenopacket_mapper.mapping.mapper.PhenopacketMapper", false]], "preprocess() (in module phenopacket_mapper.preprocessing)": [[32, "phenopacket_mapper.preprocessing.preprocess", false]], "preprocess() (in module phenopacket_mapper.preprocessing.preprocess)": [[33, "phenopacket_mapper.preprocessing.preprocess.preprocess", false]], "preprocess() (phenopacket_mapper.data_standards.data_model.dataset method)": [[17, "phenopacket_mapper.data_standards.data_model.DataSet.preprocess", false]], "preprocess() (phenopacket_mapper.data_standards.dataset method)": [[12, "phenopacket_mapper.data_standards.DataSet.preprocess", false]], "preprocess_dict() (in module phenopacket_mapper.preprocessing)": [[32, "phenopacket_mapper.preprocessing.preprocess_dict", false]], "preprocess_dict() (in module phenopacket_mapper.preprocessing.preprocess_dict)": [[34, "phenopacket_mapper.preprocessing.preprocess_dict.preprocess_dict", false]], "preprocess_method() (in module phenopacket_mapper.preprocessing)": [[32, "phenopacket_mapper.preprocessing.preprocess_method", false]], "preprocess_method() (in module phenopacket_mapper.preprocessing.preprocess_method)": [[35, "phenopacket_mapper.preprocessing.preprocess_method.preprocess_method", false]], "protobuf_timestamp() (phenopacket_mapper.data_standards.date method)": [[12, "phenopacket_mapper.data_standards.Date.protobuf_timestamp", false]], "protobuf_timestamp() (phenopacket_mapper.data_standards.date.date method)": [[21, "phenopacket_mapper.data_standards.date.Date.protobuf_timestamp", false]], "read_data_model() (in module phenopacket_mapper.utils.io)": [[39, "phenopacket_mapper.utils.io.read_data_model", false]], "read_data_model() (in module phenopacket_mapper.utils.io.input)": [[41, "phenopacket_mapper.utils.io.input.read_data_model", false]], "read_json() (in module phenopacket_mapper.utils.io)": [[39, "phenopacket_mapper.utils.io.read_json", false]], "read_json() (in module phenopacket_mapper.utils.io.read_json)": [[43, "phenopacket_mapper.utils.io.read_json.read_json", false]], "read_phenopacket_from_json() (in module phenopacket_mapper.utils.io)": [[39, "phenopacket_mapper.utils.io.read_phenopacket_from_json", false]], "read_phenopacket_from_json() (in module phenopacket_mapper.utils.io.input)": [[41, "phenopacket_mapper.utils.io.input.read_phenopacket_from_json", false]], "read_phenopackets() (in module phenopacket_mapper.utils.io)": [[39, "phenopacket_mapper.utils.io.read_phenopackets", false]], "read_phenopackets() (in module phenopacket_mapper.utils.io.input)": [[41, "phenopacket_mapper.utils.io.input.read_phenopackets", false]], "read_validate() (in module phenopacket_mapper.validate)": [[56, "phenopacket_mapper.validate.read_validate", false]], "read_validate() (in module phenopacket_mapper.validate.validate)": [[57, "phenopacket_mapper.validate.validate.read_validate", false]], "read_xml() (in module phenopacket_mapper.utils.io)": [[39, "phenopacket_mapper.utils.io.read_xml", false]], "read_xml() (in module phenopacket_mapper.utils.io.read_xml)": [[44, "phenopacket_mapper.utils.io.read_xml.read_xml", false]], "remove_duplicates() (phenopacket_mapper.data_standards.value_set.valueset method)": [[22, "phenopacket_mapper.data_standards.value_set.ValueSet.remove_duplicates", false]], "remove_duplicates() (phenopacket_mapper.data_standards.valueset method)": [[12, "phenopacket_mapper.data_standards.ValueSet.remove_duplicates", false]], "required (phenopacket_mapper.data_standards.data_model.datafield attribute)": [[17, "phenopacket_mapper.data_standards.data_model.DataField.required", false]], "required (phenopacket_mapper.data_standards.data_model.datasection attribute)": [[17, "phenopacket_mapper.data_standards.data_model.DataSection.required", false]], "required (phenopacket_mapper.data_standards.data_model.orgroup attribute)": [[17, "phenopacket_mapper.data_standards.data_model.OrGroup.required", false]], "required (phenopacket_mapper.data_standards.datafield attribute)": [[12, "phenopacket_mapper.data_standards.DataField.required", false]], "required (phenopacket_mapper.data_standards.datasection attribute)": [[12, "phenopacket_mapper.data_standards.DataSection.required", false]], "required (phenopacket_mapper.data_standards.orgroup attribute)": [[12, "phenopacket_mapper.data_standards.OrGroup.required", false]], "resources (phenopacket_mapper.data_standards.data_model.datamodel attribute)": [[17, "phenopacket_mapper.data_standards.data_model.DataModel.resources", false]], "resources (phenopacket_mapper.data_standards.datamodel attribute)": [[12, "phenopacket_mapper.data_standards.DataModel.resources", false]], "resources (phenopacket_mapper.data_standards.value_set.valueset property)": [[22, "phenopacket_mapper.data_standards.value_set.ValueSet.resources", false]], "resources (phenopacket_mapper.data_standards.valueset property)": [[12, "phenopacket_mapper.data_standards.ValueSet.resources", false]], "resources (phenopacket_mapper.datamodel attribute)": [[1, "phenopacket_mapper.DataModel.resources", false]], "row_no (phenopacket_mapper.data_standards.data_model.datafieldvalue attribute)": [[17, "phenopacket_mapper.data_standards.data_model.DataFieldValue.row_no", false]], "row_no (phenopacket_mapper.data_standards.data_model.datamodelinstance attribute)": [[17, "phenopacket_mapper.data_standards.data_model.DataModelInstance.row_no", false]], "row_no (phenopacket_mapper.data_standards.datafieldvalue attribute)": [[12, "phenopacket_mapper.data_standards.DataFieldValue.row_no", false]], "row_no (phenopacket_mapper.data_standards.datamodelinstance attribute)": [[12, "phenopacket_mapper.data_standards.DataModelInstance.row_no", false]], "second (phenopacket_mapper.data_standards.date attribute)": [[12, "phenopacket_mapper.data_standards.Date.second", false]], "second (phenopacket_mapper.data_standards.date.date attribute)": [[21, "phenopacket_mapper.data_standards.date.Date.second", false]], "second_str (phenopacket_mapper.data_standards.date attribute)": [[12, "phenopacket_mapper.data_standards.Date.second_str", false]], "second_str (phenopacket_mapper.data_standards.date.date attribute)": [[21, "phenopacket_mapper.data_standards.date.Date.second_str", false]], "set_version() (phenopacket_mapper.data_standards.code_system.codesystem method)": [[16, "phenopacket_mapper.data_standards.code_system.CodeSystem.set_version", false]], "set_version() (phenopacket_mapper.data_standards.codesystem method)": [[12, "phenopacket_mapper.data_standards.CodeSystem.set_version", false]], "specification (phenopacket_mapper.data_standards.data_model.datafield attribute)": [[17, "phenopacket_mapper.data_standards.data_model.DataField.specification", false]], "specification (phenopacket_mapper.data_standards.datafield attribute)": [[12, "phenopacket_mapper.data_standards.DataField.specification", false]], "str_to_valid_id() (in module phenopacket_mapper.utils)": [[36, "phenopacket_mapper.utils.str_to_valid_id", false]], "str_to_valid_id() (in module phenopacket_mapper.utils.str_to_valid_id)": [[55, "phenopacket_mapper.utils.str_to_valid_id.str_to_valid_id", false]], "synonyms (phenopacket_mapper.data_standards.code_system.codesystem attribute)": [[16, "phenopacket_mapper.data_standards.code_system.CodeSystem.synonyms", false]], "synonyms (phenopacket_mapper.data_standards.codesystem attribute)": [[12, "phenopacket_mapper.data_standards.CodeSystem.synonyms", false]], "system (phenopacket_mapper.data_standards.code.coding attribute)": [[15, "phenopacket_mapper.data_standards.code.Coding.system", false]], "system (phenopacket_mapper.data_standards.coding attribute)": [[12, "phenopacket_mapper.data_standards.Coding.system", false]], "text (phenopacket_mapper.data_standards.code.codeableconcept attribute)": [[15, "phenopacket_mapper.data_standards.code.CodeableConcept.text", false]], "text (phenopacket_mapper.data_standards.code.coding attribute)": [[15, "phenopacket_mapper.data_standards.code.Coding.text", false]], "text (phenopacket_mapper.data_standards.codeableconcept attribute)": [[12, "phenopacket_mapper.data_standards.CodeableConcept.text", false]], "text (phenopacket_mapper.data_standards.coding attribute)": [[12, "phenopacket_mapper.data_standards.Coding.text", false]], "url (phenopacket_mapper.data_standards.code_system.codesystem attribute)": [[16, "phenopacket_mapper.data_standards.code_system.CodeSystem.url", false]], "url (phenopacket_mapper.data_standards.codesystem attribute)": [[12, "phenopacket_mapper.data_standards.CodeSystem.url", false]], "validate() (in module phenopacket_mapper.validate)": [[56, "phenopacket_mapper.validate.validate", false]], "validate() (in module phenopacket_mapper.validate.validate)": [[57, "phenopacket_mapper.validate.validate.validate", false]], "validate() (phenopacket_mapper.data_standards.data_model.datafieldvalue method)": [[17, "phenopacket_mapper.data_standards.data_model.DataFieldValue.validate", false]], "validate() (phenopacket_mapper.data_standards.data_model.datamodelinstance method)": [[17, "phenopacket_mapper.data_standards.data_model.DataModelInstance.validate", false]], "validate() (phenopacket_mapper.data_standards.datafieldvalue method)": [[12, "phenopacket_mapper.data_standards.DataFieldValue.validate", false]], "validate() (phenopacket_mapper.data_standards.datamodelinstance method)": [[12, "phenopacket_mapper.data_standards.DataModelInstance.validate", false]], "validate() (phenopacket_mapper.validate.validate.validator method)": [[57, "phenopacket_mapper.validate.validate.Validator.validate", false]], "validator (class in phenopacket_mapper.validate.validate)": [[57, "phenopacket_mapper.validate.validate.Validator", false]], "value (phenopacket_mapper.data_standards.data_model.datafieldvalue attribute)": [[17, "phenopacket_mapper.data_standards.data_model.DataFieldValue.value", false]], "value (phenopacket_mapper.data_standards.datafieldvalue attribute)": [[12, "phenopacket_mapper.data_standards.DataFieldValue.value", false]], "values (phenopacket_mapper.data_standards.data_model.datamodelinstance attribute)": [[17, "phenopacket_mapper.data_standards.data_model.DataModelInstance.values", false]], "values (phenopacket_mapper.data_standards.datamodelinstance attribute)": [[12, "phenopacket_mapper.data_standards.DataModelInstance.values", false]], "valueset (class in phenopacket_mapper.data_standards)": [[12, "phenopacket_mapper.data_standards.ValueSet", false]], "valueset (class in phenopacket_mapper.data_standards.value_set)": [[22, "phenopacket_mapper.data_standards.value_set.ValueSet", false]], "version (phenopacket_mapper.data_standards.code_system.codesystem attribute)": [[16, "phenopacket_mapper.data_standards.code_system.CodeSystem.version", false]], "version (phenopacket_mapper.data_standards.codesystem attribute)": [[12, "phenopacket_mapper.data_standards.CodeSystem.version", false]], "width (phenopacket_mapper.data_standards.data_model.dataset property)": [[17, "phenopacket_mapper.data_standards.data_model.DataSet.width", false]], "width (phenopacket_mapper.data_standards.dataset property)": [[12, "phenopacket_mapper.data_standards.DataSet.width", false]], "write() (in module phenopacket_mapper.utils.io)": [[39, "phenopacket_mapper.utils.io.write", false]], "write() (in module phenopacket_mapper.utils.io.output)": [[42, "phenopacket_mapper.utils.io.output.write", false]], "write_to_file() (phenopacket_mapper.utils.create_ipynb_in_code.notebookbuilder method)": [[37, "phenopacket_mapper.utils.create_ipynb_in_code.NotebookBuilder.write_to_file", false]], "write_to_file() (phenopacket_mapper.utils.notebookbuilder method)": [[36, "phenopacket_mapper.utils.NotebookBuilder.write_to_file", false]], "year (phenopacket_mapper.data_standards.date attribute)": [[12, "phenopacket_mapper.data_standards.Date.year", false]], "year (phenopacket_mapper.data_standards.date.date attribute)": [[21, "phenopacket_mapper.data_standards.date.Date.year", false]], "year_str (phenopacket_mapper.data_standards.date attribute)": [[12, "phenopacket_mapper.data_standards.Date.year_str", false]], "year_str (phenopacket_mapper.data_standards.date.date attribute)": [[21, "phenopacket_mapper.data_standards.date.Date.year_str", false]]}, "objects": {"": [[1, 0, 0, "-", "phenopacket_mapper"]], "phenopacket_mapper": [[1, 1, 1, "", "DataModel"], [1, 1, 1, "", "PhenopacketMapper"], [2, 0, 0, "-", "api_requests"], [7, 0, 0, "-", "cli"], [12, 0, 0, "-", "data_standards"], [23, 0, 0, "-", "mapping"], [27, 0, 0, "-", "pipeline"], [32, 0, 0, "-", "preprocessing"], [36, 0, 0, "-", "utils"], [56, 0, 0, "-", "validate"]], "phenopacket_mapper.DataModel": [[1, 2, 1, "", "data_model_name"], [1, 2, 1, "", "fields"], [1, 3, 1, "", "from_file"], [1, 3, 1, "", "get_field"], [1, 3, 1, "", "get_field_ids"], [1, 3, 1, "", "load_data"], [1, 3, 1, "", "load_data_using_data_model"], [1, 2, 1, "", "resources"]], "phenopacket_mapper.PhenopacketMapper": [[1, 3, 1, "", "check_fields_adheres_to_phenopacket_allowed_values"], [1, 3, 1, "", "map"]], "phenopacket_mapper.api_requests": [[2, 1, 1, "", "APIRequestSuperClass"], [2, 1, 1, "", "HPOAPIRequest"], [2, 1, 1, "", "OrphaAPIRequest"], [3, 0, 0, "-", "api_request_super_class"], [4, 0, 0, "-", "get"], [5, 0, 0, "-", "hpo_api_request"], [6, 0, 0, "-", "orpha_api_request"]], "phenopacket_mapper.api_requests.APIRequestSuperClass": [[2, 3, 1, "", "get"]], "phenopacket_mapper.api_requests.HPOAPIRequest": [[2, 2, 1, "", "api_base_url"], [2, 3, 1, "", "get"]], "phenopacket_mapper.api_requests.OrphaAPIRequest": [[2, 2, 1, "", "api_base_url"], [2, 3, 1, "", "get"]], "phenopacket_mapper.api_requests.api_request_super_class": [[3, 1, 1, "", "APIRequestSuperClass"]], "phenopacket_mapper.api_requests.api_request_super_class.APIRequestSuperClass": [[3, 3, 1, "", "get"]], "phenopacket_mapper.api_requests.get": [[4, 4, 1, "", "get"]], "phenopacket_mapper.api_requests.hpo_api_request": [[5, 1, 1, "", "HPOAPIRequest"]], "phenopacket_mapper.api_requests.hpo_api_request.HPOAPIRequest": [[5, 2, 1, "", "api_base_url"], [5, 3, 1, "", "get"]], "phenopacket_mapper.api_requests.orpha_api_request": [[6, 1, 1, "", "OrphaAPIRequest"]], "phenopacket_mapper.api_requests.orpha_api_request.OrphaAPIRequest": [[6, 2, 1, "", "api_base_url"], [6, 3, 1, "", "get"]], "phenopacket_mapper.data_standards": [[12, 1, 1, "", "Cardinality"], [12, 1, 1, "", "CodeSystem"], [12, 1, 1, "", "CodeableConcept"], [12, 1, 1, "", "Coding"], [12, 1, 1, "", "DataField"], [12, 1, 1, "", "DataFieldValue"], [12, 1, 1, "", "DataModel"], [13, 0, 0, "-", "DataModel2PhenopacketSchema"], [12, 1, 1, "", "DataModelInstance"], [12, 1, 1, "", "DataSection"], [12, 1, 1, "", "DataSet"], [12, 1, 1, "", "Date"], [12, 1, 1, "", "OrGroup"], [12, 1, 1, "", "ValueSet"], [14, 0, 0, "-", "cardinality"], [15, 0, 0, "-", "code"], [16, 0, 0, "-", "code_system"], [17, 0, 0, "-", "data_model"], [18, 0, 0, "-", "data_models"], [21, 0, 0, "-", "date"], [22, 0, 0, "-", "value_set"]], "phenopacket_mapper.data_standards.Cardinality": [[12, 2, 1, "", "max"], [12, 2, 1, "", "min"]], "phenopacket_mapper.data_standards.CodeSystem": [[12, 2, 1, "", "iri_prefix"], [12, 2, 1, "", "name"], [12, 2, 1, "", "namespace_prefix"], [12, 3, 1, "", "set_version"], [12, 2, 1, "", "synonyms"], [12, 2, 1, "", "url"], [12, 2, 1, "", "version"]], "phenopacket_mapper.data_standards.CodeableConcept": [[12, 2, 1, "", "coding"], [12, 2, 1, "", "text"]], "phenopacket_mapper.data_standards.Coding": [[12, 2, 1, "", "code"], [12, 2, 1, "", "display"], [12, 3, 1, "", "parse_coding"], [12, 2, 1, "", "system"], [12, 2, 1, "", "text"]], "phenopacket_mapper.data_standards.DataField": [[12, 2, 1, "", "cardinality"], [12, 2, 1, "", "description"], [12, 2, 1, "", "id"], [12, 2, 1, "", "name"], [12, 2, 1, "", "required"], [12, 2, 1, "", "specification"]], "phenopacket_mapper.data_standards.DataFieldValue": [[12, 2, 1, "", "field"], [12, 2, 1, "", "row_no"], [12, 3, 1, "", "validate"], [12, 2, 1, "", "value"]], "phenopacket_mapper.data_standards.DataModel": [[12, 2, 1, "", "data_model_name"], [12, 2, 1, "", "fields"], [12, 3, 1, "", "from_file"], [12, 3, 1, "", "get_field"], [12, 3, 1, "", "get_field_ids"], [12, 3, 1, "", "load_data"], [12, 3, 1, "", "load_data_using_data_model"], [12, 2, 1, "", "resources"]], "phenopacket_mapper.data_standards.DataModel2PhenopacketSchema": [[13, 1, 1, "", "DataModel2PhenopacketSchema"]], "phenopacket_mapper.data_standards.DataModelInstance": [[12, 2, 1, "", "compliance"], [12, 2, 1, "", "data_model"], [12, 2, 1, "", "row_no"], [12, 3, 1, "", "validate"], [12, 2, 1, "", "values"]], "phenopacket_mapper.data_standards.DataSection": [[12, 2, 1, "", "cardinality"], [12, 2, 1, "", "fields"], [12, 2, 1, "", "id"], [12, 2, 1, "", "name"], [12, 2, 1, "", "required"]], "phenopacket_mapper.data_standards.DataSet": [[12, 2, 1, "", "data"], [12, 5, 1, "", "data_frame"], [12, 2, 1, "", "data_model"], [12, 3, 1, "", "head"], [12, 5, 1, "", "height"], [12, 3, 1, "", "preprocess"], [12, 5, 1, "", "width"]], "phenopacket_mapper.data_standards.Date": [[12, 2, 1, "", "day"], [12, 2, 1, "", "day_str"], [12, 3, 1, "", "formatted_string"], [12, 3, 1, "", "from_datetime"], [12, 3, 1, "", "from_iso_8601"], [12, 2, 1, "", "hour"], [12, 2, 1, "", "hour_str"], [12, 3, 1, "", "iso_8601_datestring"], [12, 2, 1, "", "minute"], [12, 2, 1, "", "minute_str"], [12, 2, 1, "", "month"], [12, 2, 1, "", "month_str"], [12, 3, 1, "", "parse_date"], [12, 3, 1, "", "protobuf_timestamp"], [12, 2, 1, "", "second"], [12, 2, 1, "", "second_str"], [12, 2, 1, "", "year"], [12, 2, 1, "", "year_str"]], "phenopacket_mapper.data_standards.OrGroup": [[12, 2, 1, "", "cardinality"], [12, 2, 1, "", "description"], [12, 2, 1, "", "fields"], [12, 2, 1, "", "id"], [12, 2, 1, "", "name"], [12, 2, 1, "", "required"]], "phenopacket_mapper.data_standards.ValueSet": [[12, 2, 1, "", "description"], [12, 2, 1, "", "elements"], [12, 3, 1, "", "extend"], [12, 2, 1, "", "name"], [12, 3, 1, "", "parse_value_set"], [12, 3, 1, "", "remove_duplicates"], [12, 5, 1, "", "resources"]], "phenopacket_mapper.data_standards.cardinality": [[14, 1, 1, "", "Cardinality"]], "phenopacket_mapper.data_standards.cardinality.Cardinality": [[14, 2, 1, "", "max"], [14, 2, 1, "", "min"]], "phenopacket_mapper.data_standards.code": [[15, 1, 1, "", "CodeableConcept"], [15, 1, 1, "", "Coding"]], "phenopacket_mapper.data_standards.code.CodeableConcept": [[15, 2, 1, "", "coding"], [15, 2, 1, "", "text"]], "phenopacket_mapper.data_standards.code.Coding": [[15, 2, 1, "", "code"], [15, 2, 1, "", "display"], [15, 3, 1, "", "parse_coding"], [15, 2, 1, "", "system"], [15, 2, 1, "", "text"]], "phenopacket_mapper.data_standards.code_system": [[16, 1, 1, "", "CodeSystem"]], "phenopacket_mapper.data_standards.code_system.CodeSystem": [[16, 2, 1, "", "iri_prefix"], [16, 2, 1, "", "name"], [16, 2, 1, "", "namespace_prefix"], [16, 3, 1, "", "set_version"], [16, 2, 1, "", "synonyms"], [16, 2, 1, "", "url"], [16, 2, 1, "", "version"]], "phenopacket_mapper.data_standards.data_model": [[17, 1, 1, "", "DataField"], [17, 1, 1, "", "DataFieldValue"], [17, 1, 1, "", "DataModel"], [17, 1, 1, "", "DataModelInstance"], [17, 1, 1, "", "DataSection"], [17, 1, 1, "", "DataSet"], [17, 1, 1, "", "OrGroup"]], "phenopacket_mapper.data_standards.data_model.DataField": [[17, 2, 1, "", "cardinality"], [17, 2, 1, "", "description"], [17, 2, 1, "", "id"], [17, 2, 1, "", "name"], [17, 2, 1, "", "required"], [17, 2, 1, "", "specification"]], "phenopacket_mapper.data_standards.data_model.DataFieldValue": [[17, 2, 1, "", "field"], [17, 2, 1, "", "row_no"], [17, 3, 1, "", "validate"], [17, 2, 1, "", "value"]], "phenopacket_mapper.data_standards.data_model.DataModel": [[17, 2, 1, "", "data_model_name"], [17, 2, 1, "", "fields"], [17, 3, 1, "", "from_file"], [17, 3, 1, "", "get_field"], [17, 3, 1, "", "get_field_ids"], [17, 3, 1, "", "load_data"], [17, 3, 1, "", "load_data_using_data_model"], [17, 2, 1, "", "resources"]], "phenopacket_mapper.data_standards.data_model.DataModelInstance": [[17, 2, 1, "", "compliance"], [17, 2, 1, "", "data_model"], [17, 2, 1, "", "row_no"], [17, 3, 1, "", "validate"], [17, 2, 1, "", "values"]], "phenopacket_mapper.data_standards.data_model.DataSection": [[17, 2, 1, "", "cardinality"], [17, 2, 1, "", "fields"], [17, 2, 1, "", "id"], [17, 2, 1, "", "name"], [17, 2, 1, "", "required"]], "phenopacket_mapper.data_standards.data_model.DataSet": [[17, 2, 1, "", "data"], [17, 5, 1, "", "data_frame"], [17, 2, 1, "", "data_model"], [17, 3, 1, "", "head"], [17, 5, 1, "", "height"], [17, 3, 1, "", "preprocess"], [17, 5, 1, "", "width"]], "phenopacket_mapper.data_standards.data_model.OrGroup": [[17, 2, 1, "", "cardinality"], [17, 2, 1, "", "description"], [17, 2, 1, "", "fields"], [17, 2, 1, "", "id"], [17, 2, 1, "", "name"], [17, 2, 1, "", "required"]], "phenopacket_mapper.data_standards.data_models": [[19, 0, 0, "-", "erdri_cds"], [18, 4, 1, "", "parse_data_type"]], "phenopacket_mapper.data_standards.date": [[21, 1, 1, "", "Date"]], "phenopacket_mapper.data_standards.date.Date": [[21, 2, 1, "", "day"], [21, 2, 1, "", "day_str"], [21, 3, 1, "", "formatted_string"], [21, 3, 1, "", "from_datetime"], [21, 3, 1, "", "from_iso_8601"], [21, 2, 1, "", "hour"], [21, 2, 1, "", "hour_str"], [21, 3, 1, "", "iso_8601_datestring"], [21, 2, 1, "", "minute"], [21, 2, 1, "", "minute_str"], [21, 2, 1, "", "month"], [21, 2, 1, "", "month_str"], [21, 3, 1, "", "parse_date"], [21, 3, 1, "", "protobuf_timestamp"], [21, 2, 1, "", "second"], [21, 2, 1, "", "second_str"], [21, 2, 1, "", "year"], [21, 2, 1, "", "year_str"]], "phenopacket_mapper.data_standards.value_set": [[22, 1, 1, "", "ValueSet"]], "phenopacket_mapper.data_standards.value_set.ValueSet": [[22, 2, 1, "", "description"], [22, 2, 1, "", "elements"], [22, 3, 1, "", "extend"], [22, 2, 1, "", "name"], [22, 3, 1, "", "parse_value_set"], [22, 3, 1, "", "remove_duplicates"], [22, 5, 1, "", "resources"]], "phenopacket_mapper.mapping": [[23, 1, 1, "", "PhenopacketBuildingBlock"], [23, 1, 1, "", "PhenopacketMapper"], [24, 0, 0, "-", "map_field"], [23, 4, 1, "", "map_single"], [25, 0, 0, "-", "mapper"], [26, 0, 0, "-", "phenopacket_building_block"]], "phenopacket_mapper.mapping.PhenopacketBuildingBlock": [[23, 3, 1, "", "map"]], "phenopacket_mapper.mapping.PhenopacketMapper": [[23, 3, 1, "", "check_fields_adheres_to_phenopacket_allowed_values"], [23, 3, 1, "", "map"]], "phenopacket_mapper.mapping.mapper": [[25, 1, 1, "", "PhenopacketMapper"]], "phenopacket_mapper.mapping.mapper.PhenopacketMapper": [[25, 3, 1, "", "check_fields_adheres_to_phenopacket_allowed_values"], [25, 3, 1, "", "map"]], "phenopacket_mapper.mapping.phenopacket_building_block": [[26, 1, 1, "", "PhenopacketBuildingBlock"], [26, 4, 1, "", "map_single"]], "phenopacket_mapper.mapping.phenopacket_building_block.PhenopacketBuildingBlock": [[26, 3, 1, "", "map"]], "phenopacket_mapper.preprocessing": [[33, 0, 0, "-", "preprocess"], [34, 0, 0, "-", "preprocess_dict"], [35, 0, 0, "-", "preprocess_method"]], "phenopacket_mapper.preprocessing.preprocess": [[33, 4, 1, "", "preprocess"]], "phenopacket_mapper.preprocessing.preprocess_dict": [[34, 4, 1, "", "preprocess_dict"]], "phenopacket_mapper.preprocessing.preprocess_method": [[35, 4, 1, "", "preprocess_method"]], "phenopacket_mapper.utils": [[36, 1, 1, "", "NotebookBuilder"], [37, 0, 0, "-", "create_ipynb_in_code"], [38, 0, 0, "-", "get_field_name"], [39, 0, 0, "-", "io"], [36, 4, 1, "", "loc_default"], [45, 0, 0, "-", "pandas_utils"], [46, 0, 0, "-", "parsing"], [55, 0, 0, "-", "str_to_valid_id"]], "phenopacket_mapper.utils.NotebookBuilder": [[36, 3, 1, "", "add_code_cell"], [36, 3, 1, "", "add_markdown_cell"], [36, 3, 1, "", "write_to_file"]], "phenopacket_mapper.utils.create_ipynb_in_code": [[37, 1, 1, "", "NotebookBuilder"]], "phenopacket_mapper.utils.create_ipynb_in_code.NotebookBuilder": [[37, 3, 1, "", "add_code_cell"], [37, 3, 1, "", "add_markdown_cell"], [37, 3, 1, "", "write_to_file"]], "phenopacket_mapper.utils.get_field_name": [[38, 4, 1, "", "get_field_name"]], "phenopacket_mapper.utils.io": [[39, 1, 1, "", "DataReader"], [40, 0, 0, "-", "data_reader"], [41, 0, 0, "-", "input"], [39, 4, 1, "", "load_data_using_data_model"], [42, 0, 0, "-", "output"], [39, 4, 1, "", "parse_xml"], [39, 4, 1, "", "read_data_model"], [43, 0, 0, "-", "read_json"], [39, 4, 1, "", "read_phenopacket_from_json"], [39, 4, 1, "", "read_phenopackets"], [44, 0, 0, "-", "read_xml"], [39, 4, 1, "", "write"]], "phenopacket_mapper.utils.io.DataReader": [[39, 3, 1, "", "handle_file_extension"]], "phenopacket_mapper.utils.io.data_reader": [[40, 1, 1, "", "DataReader"]], "phenopacket_mapper.utils.io.data_reader.DataReader": [[40, 3, 1, "", "handle_file_extension"]], "phenopacket_mapper.utils.io.input": [[41, 4, 1, "", "load_data_using_data_model"], [41, 4, 1, "", "read_data_model"], [41, 4, 1, "", "read_phenopacket_from_json"], [41, 4, 1, "", "read_phenopackets"]], "phenopacket_mapper.utils.io.output": [[42, 4, 1, "", "write"]], "phenopacket_mapper.utils.io.read_json": [[43, 4, 1, "", "read_json"]], "phenopacket_mapper.utils.io.read_xml": [[44, 4, 1, "", "parse_xml"], [44, 4, 1, "", "read_xml"]], "phenopacket_mapper.utils.pandas_utils": [[45, 4, 1, "", "loc_default"]], "phenopacket_mapper.utils.parsing": [[47, 0, 0, "-", "get_codesystem_by_namespace_prefix"], [46, 4, 1, "", "get_codesystem_by_namespace_prefx"], [46, 4, 1, "", "parse_bool"], [48, 0, 0, "-", "parse_coding"], [49, 0, 0, "-", "parse_data_type"], [50, 0, 0, "-", "parse_date"], [46, 4, 1, "", "parse_float"], [46, 4, 1, "", "parse_int"], [51, 0, 0, "-", "parse_ordinal"], [52, 0, 0, "-", "parse_primitive_data_value"], [46, 4, 1, "", "parse_single_data_type"], [53, 0, 0, "-", "parse_value"], [54, 0, 0, "-", "parse_value_set"]], "phenopacket_mapper.utils.parsing.get_codesystem_by_namespace_prefix": [[47, 4, 1, "", "get_codesystem_by_namespace_prefx"]], "phenopacket_mapper.utils.parsing.parse_coding": [[48, 4, 1, "", "parse_coding"]], "phenopacket_mapper.utils.parsing.parse_data_type": [[49, 4, 1, "", "parse_data_type"], [49, 4, 1, "", "parse_single_data_type"]], "phenopacket_mapper.utils.parsing.parse_date": [[50, 4, 1, "", "parse_date"]], "phenopacket_mapper.utils.parsing.parse_ordinal": [[51, 4, 1, "", "parse_ordinal"]], "phenopacket_mapper.utils.parsing.parse_primitive_data_value": [[52, 4, 1, "", "parse_bool"], [52, 4, 1, "", "parse_float"], [52, 4, 1, "", "parse_int"], [52, 4, 1, "", "parse_primitive_data_value"]], "phenopacket_mapper.utils.parsing.parse_value": [[53, 4, 1, "", "parse_value"]], "phenopacket_mapper.utils.parsing.parse_value_set": [[54, 4, 1, "", "parse_value_set"]], "phenopacket_mapper.utils.str_to_valid_id": [[55, 4, 1, "", "str_to_valid_id"]], "phenopacket_mapper.validate": [[56, 4, 1, "", "read_validate"], [57, 0, 0, "-", "validate"]], "phenopacket_mapper.validate.validate": [[57, 1, 1, "", "Validator"], [57, 4, 1, "", "read_validate"], [57, 4, 1, "", "validate"]], "phenopacket_mapper.validate.validate.Validator": [[57, 3, 1, "", "validate"]]}, "objnames": {"0": ["py", "module", "Python module"], "1": ["py", "class", "Python class"], "2": ["py", "attribute", "Python attribute"], "3": ["py", "method", "Python method"], "4": ["py", "function", "Python function"], "5": ["py", "property", "Python property"]}, "objtypes": {"0": "py:module", "1": "py:class", "2": "py:attribute", "3": "py:method", "4": "py:function", "5": "py:property"}, "terms": {"": [36, 55, 59, 60], "0": [2, 5, 6, 12, 14, 15, 16, 17, 21, 22, 23, 26, 46, 48, 52], "01": [12, 21, 46, 50], "01357": 60, "02": [12, 21, 46, 50, 60], "022": 60, "0285433": 60, "02t16": [12, 21], "05": 60, "06": [12, 21], "1": [1, 12, 17, 21, 22, 39, 41, 46, 51, 52, 53, 59, 60, 61], "10": [59, 60], "1002": 60, "1038": 60, "1101": 60, "1371": 60, "15z": [12, 21], "18": 60, "1st": [12, 21, 46, 50], "2": [46, 53, 59, 60], "2021": [12, 21], "2022": 60, "202200016": 60, "2023": 60, "2024": [12, 21, 46, 50, 60], "24308104": 60, "29": 60, "2nd": [12, 21, 46, 50], "3": [46, 53, 59, 60], "4": [46, 53, 59, 60], "40": 60, "404684003": [12, 15, 46, 48], "5": [12, 17, 60], "52": [12, 21], "6": 60, "8": [39, 40, 44], "817": 60, "820": 60, "8601": [12, 21, 46, 50], "9": [12, 17, 21, 59], "A": [1, 2, 3, 5, 6, 12, 15, 16, 17, 22, 32, 34, 36, 37, 39, 41, 46, 54, 58, 59, 60], "At": 60, "By": [12, 22], "For": [59, 60], "If": [1, 12, 15, 17, 21, 23, 25, 32, 34, 35, 39, 41, 46, 47, 48, 50, 52, 59, 60], "In": [12, 18, 21, 46, 49, 50, 59, 60], "It": [1, 12, 15, 16, 17, 22, 46, 53, 60], "ONE": 60, "On": [46, 52, 59], "Or": [12, 17, 46, 52], "The": [1, 12, 15, 16, 17, 18, 21, 23, 25, 32, 34, 35, 36, 37, 39, 41, 42, 46, 47, 49, 50, 52, 53, 55, 57, 59, 60], "There": [12, 21, 46, 50, 59], "To": [1, 12, 17, 59, 60], "_": [12, 17], "_column": [1, 12, 17, 39, 41], "_resourc": [12, 22], "abbrevi": [12, 16], "abc": [2, 3], "abnorm": 60, "about": [2, 3, 5, 6, 60], "abov": [12, 17, 18, 46, 49, 59], "abput": [2, 3], "absent": 60, "abstract": [2, 3], "access": [1, 12, 17], "accord": 60, "act": [46, 53], "action": 60, "activ": 59, "ad": [36, 37], "add": [18, 36, 37, 46, 49, 59], "add_code_cel": [36, 37], "add_markdown_cel": [36, 37], "addit": [12, 15, 32, 35], "addition": [12, 15], "address": 60, "adher": [1, 12, 17, 23, 25, 60], "advanc": 60, "after": 59, "aid": 60, "aim": 60, "algorithm": 60, "all": [1, 12, 15, 17, 36, 39, 41, 46, 48, 55, 59], "allianc": 60, "allow": [1, 12, 18, 22, 23, 25, 46, 49, 59, 60], "allow_zero": [12, 21], "alphanumer": [12, 17, 36, 55], "alreadi": 59, "also": [12, 17, 22, 59], "altern": [12, 16], "alwai": [12, 21], "an": [1, 2, 3, 12, 16, 17, 21, 32, 35, 39, 44, 46, 50, 51, 52, 59, 60], "anaconda3": 59, "analys": 60, "analysi": 60, "analyz": 60, "ani": [1, 12, 17, 18, 22, 32, 33, 34, 35, 36, 45, 46, 49, 58, 59, 60], "api": [2, 3, 5, 6, 58], "api_base_url": [2, 5, 6], "api_request_super_class": 2, "apirequestsuperclass": [2, 3, 5, 6], "appli": 59, "applic": [59, 60], "appropri": [46, 53], "apt": 59, "ar": [1, 12, 17, 18, 21, 22, 36, 39, 41, 46, 49, 50, 56, 57, 59, 62], "arg": 57, "arg1": [12, 17], "arg2": [12, 17], "argument": [1, 12, 17, 32, 35], "arrai": 60, "ask": 59, "assign": [12, 22], "assum": [12, 21, 46, 50], "attach": [46, 51], "attempt": [12, 17, 21, 46, 50], "attribut": [1, 12, 17], "author": 60, "autom": [59, 60], "automat": 59, "avail": [59, 60, 62], "avoid": [46, 52], "b": 60, "bamshad": 60, "base": [1, 2, 3, 5, 6, 12, 13, 14, 15, 16, 17, 21, 22, 23, 25, 26, 36, 37, 39, 40, 57, 59], "bash": 59, "bash_profil": 59, "bashrc": 59, "basic": [59, 60], "baudi": 60, "baynam": 60, "bechraki": 60, "beckmann": 60, "beckwith": 60, "becom": 60, "befor": [32, 33, 59], "behavior": 60, "being": [12, 17], "belong": [12, 15, 17, 46, 48], "below": 60, "beltran": 60, "benefit": [12, 22, 59], "bespok": [58, 60], "better": [12, 16, 22], "between": [12, 21, 22, 46, 50, 60], "bih": [59, 62, 63, 64], "bin": 59, "binari": 59, "biolog": 60, "biopsi": 60, "biosampl": 60, "biotechnologi": 60, "birth": [1, 12, 17], "bit": 57, "block": 60, "book": 59, "bool": [1, 12, 17, 18, 21, 22, 39, 41, 46, 49, 52, 53, 56, 57], "bool_str": [46, 52], "boolean": [18, 46, 49, 52], "both": 60, "break": [1, 12, 17, 39, 41], "brew": 59, "bridg": 60, "build": [36, 37, 59, 60], "bundl": 60, "busk": 60, "c": [59, 60], "cacheiro": 60, "call": [1, 12, 15, 17, 32, 35, 46, 48, 59], "callabl": [12, 17, 32, 33, 35], "callahan": 60, "can": [1, 2, 3, 12, 15, 17, 18, 21, 22, 32, 35, 39, 41, 46, 48, 49, 51, 59, 60], "cannot": [12, 17, 46, 52], "captur": 60, "cardin": [1, 12, 17], "carmodi": 60, "case": [12, 17, 18, 46, 49, 60], "categor": 60, "caus": 60, "cd": 59, "cei": [59, 62, 63, 64], "cell": [12, 17, 36, 37, 60], "cento": 59, "centrifug": 60, "certain": 60, "challeng": 60, "chang": 59, "charact": [12, 17, 36, 55], "character": 60, "check": [1, 12, 17, 23, 25, 39, 41, 60], "check_fields_adheres_to_phenopacket_allowed_valu": [1, 23, 25], "chocolatei": 59, "chong": 60, "choos": 59, "chute": 60, "class": [1, 2, 3, 5, 6, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 25, 26, 36, 37, 39, 40, 41, 46, 49, 57, 60], "cli": 1, "click": 59, "clinic": 60, "clinician": 60, "clone": 59, "close": 59, "code": [1, 2, 3, 5, 6, 12, 16, 18, 22, 36, 37, 46, 48, 49, 53, 59, 60, 62], "code_system": [1, 2, 5, 6, 12, 15, 17, 22], "code_system_modul": [46, 48], "codeabl": [12, 22], "codeableconcept": [1, 12, 15, 22, 46, 53], "codesystem": [1, 2, 5, 6, 12, 15, 16, 17, 18, 22, 39, 41, 46, 47, 48, 49, 53, 54], "coding_str": [12, 15, 46, 48], "cold": 60, "coleman": 60, "collect": [12, 17], "column": [1, 12, 17, 36, 39, 41, 45], "column_nam": [1, 12, 17, 36, 39, 41, 45], "column_name_in_fil": [1, 12, 17, 39, 41], "com": [59, 62, 63, 64], "come": [12, 21, 46, 50, 59, 60], "command": 59, "commonli": [12, 16], "commun": 59, "compil": 60, "complet": 59, "complex": 60, "complianc": [1, 12, 15, 17, 18, 21, 22, 39, 41, 46, 48, 49, 50, 53, 54], "complic": 57, "comput": [12, 22, 60], "concept": [2, 3, 5, 6, 12, 15, 22, 60], "concept_id": [2, 3, 5, 6], "concern": 46, "conda": 59, "confirm": 59, "conform": 60, "confus": [46, 52], "consid": 60, "constructor": [1, 23, 25], "consult": [32, 33], "contain": [1, 12, 17, 32, 34, 36, 39, 41, 46, 51, 56, 57, 60, 62], "content": [36, 37], "context": 60, "contrast": 60, "convers": [12, 21, 46, 52], "convert": [12, 17, 36, 55], "coordin": 60, "core": 60, "corpu": 60, "correctli": 59, "correl": 60, "correspond": [32, 34], "could": [1, 12, 16, 17, 39, 41], "courtot": 60, "creat": [1, 12, 21, 23, 25, 26, 46, 50, 57, 60, 62], "create_ipynb_in_cod": 36, "creation": 60, "csv": [1, 12, 17, 39, 40, 41], "ct": [12, 15, 16, 18, 46, 48, 49], "cultur": 60, "current": [60, 62], "curv": 60, "d": 60, "dai": [12, 21, 46, 50], "dalgleish": 60, "dani": 60, "data": [1, 2, 5, 6, 12, 15, 16, 17, 18, 21, 22, 23, 25, 26, 32, 39, 41, 46, 49, 51, 53, 56, 58, 59, 60, 62], "data_field": [23, 26], "data_field_nam": [1, 12, 17, 39, 41], "data_fram": [12, 17], "data_model": [1, 12, 13, 23, 25, 26, 39, 41], "data_model_nam": [1, 12, 17, 39, 41], "data_read": 39, "data_standard": [1, 2, 5, 6, 23, 26, 46, 49], "data_typ": [18, 46, 49], "datafield": [1, 12, 17, 18, 22, 23, 26, 39, 41, 46, 49, 51], "datafieldvalu": [1, 12, 17, 23, 26], "datafram": [12, 17, 36, 45], "datamodel": [0, 1, 12, 13, 17, 23, 25, 26, 39, 41, 46, 51], "datamodel2phenopacketschema": 12, "datamodelinst": [1, 12, 17, 23, 25, 26, 39, 41], "datanod": [12, 17], "dataread": [39, 40], "datasect": [1, 12, 17], "dataset": [1, 12, 17, 23, 25, 39, 41], "date": [1, 12, 17, 18, 22, 46, 49, 50, 53, 59, 60], "date_of_birth": [1, 12, 17], "date_of_birth_column": [1, 12, 17], "date_str": [12, 21, 46, 50], "datetim": [12, 21], "day_str": [12, 21], "debian": 59, "deep": 60, "deeper": 60, "def": [12, 17], "default": [1, 12, 17, 18, 21, 22, 36, 45, 46, 49, 50], "default_first": [12, 21, 46, 50], "defin": [1, 12, 15, 16, 17, 21, 22, 46, 54, 60], "definit": [1, 12, 17, 21, 23, 25, 39, 41, 60], "depend": 59, "describ": [18, 46, 49, 60], "descript": [1, 12, 15, 17, 22, 39, 41, 46, 54], "design": 60, "desir": [12, 17, 59], "detail": [2, 3, 5, 6, 60], "determin": [12, 21, 46, 50], "develop": [60, 62, 63, 64], "deviat": 60, "df": [36, 45], "diagnosi": 60, "diagnost": 60, "dict": [1, 2, 4, 12, 17, 32, 33, 34, 39, 41, 43, 44], "dictionari": [1, 12, 17, 32, 33, 34, 39, 41, 44, 60], "differ": [12, 22, 46, 53, 59, 60], "digit": [12, 21], "dir_path": [39, 41], "directli": [12, 17], "directori": [39, 41, 42, 59], "discoveri": 60, "discuss": 59, "diseas": [2, 6, 18, 60], "displai": [12, 15, 46, 48], "distribut": 59, "dive": 60, "dmg": 59, "dna": 60, "dnf": 59, "do": [12, 17, 59, 60, 61], "doc": 60, "document": [32, 33, 60], "doe": [46, 52], "doi": 60, "don": 59, "done": [1, 12, 17], "download": 59, "dt": [12, 21], "dynam": [1, 12, 17], "e": [1, 12, 15, 16, 17, 18, 21, 22, 23, 26, 39, 41, 46, 48, 49, 51, 59, 60], "e0285433": 60, "each": [1, 12, 17, 21, 39, 41], "easi": 60, "easiest": 59, "edit": 59, "effici": 57, "effort": 60, "either": [1, 12, 17, 39, 41, 60], "element": [12, 22, 23, 26, 46, 54, 60], "elemento": 60, "els": [46, 53], "empti": [1, 12, 17, 22, 39, 41], "en": [2, 6, 59], "enabl": 60, "encod": [39, 40, 44], "encourag": 59, "end": 60, "enforc": [1, 12, 17, 39, 41], "ensur": [57, 59, 60], "enter": 59, "entiti": 60, "entri": [18, 46, 49], "enum": 60, "equival": [12, 17], "erdri_cd": 18, "erdri_cds_definition_in_cod": 63, "erdri_cds_from_fil": 64, "error": [1, 12, 17, 23, 25, 36, 45], "especi": [12, 21, 60], "essenwang": 60, "etc": [1, 12, 16, 17, 18, 22, 39, 41, 46, 49], "even": [12, 16], "ex": 59, "exampl": [2, 3, 12, 16, 21, 22, 23, 26, 60], "example_pseudonym": [23, 26], "excel": [1, 12, 17, 39, 41], "except": [32, 35], "exchang": 60, "exclud": 60, "exist": [12, 22], "expect": [12, 15, 46, 48], "experi": 60, "explain": 60, "export": 59, "express": [12, 21], "extend": [12, 22], "extra": [1, 12, 17, 39, 41], "extract": [1, 12, 17, 39, 41, 59, 60], "facilit": [12, 22, 23, 60], "fact": 57, "factori": [1, 12, 16, 17, 22], "fail": [12, 21, 46, 50], "fair": 60, "fals": [1, 2, 4, 12, 17, 22, 39, 41, 46, 52, 54, 56, 57], "familiar": 60, "fe": [39, 40], "februari": [12, 21, 46, 50], "fedora": 59, "few": 59, "field": [1, 12, 17, 22, 23, 25, 26, 38, 39, 41, 46, 51], "field1": [12, 17], "field2": [12, 17], "field_1": [12, 17], "field_1_column": [1, 12, 17, 39, 41], "field_2": [12, 17], "field_id": [1, 12, 17], "field_name_str": [46, 51], "file": [1, 12, 17, 18, 36, 37, 39, 40, 41, 42, 44, 46, 49, 51, 56, 57, 59, 62], "file_extens": [39, 40], "file_typ": [1, 12, 17, 39, 41], "filesjavajr": 59, "fill": [12, 16], "first": [12, 21, 46, 50, 59], "fix": 60, "flag": [12, 17], "flexibl": 60, "float": [12, 17, 22, 46, 52, 53], "float_str": [46, 52], "fmt": [12, 21], "folder": 59, "follow": [1, 12, 17, 46, 53, 59, 63, 64], "format": [1, 12, 15, 17, 21, 39, 41, 46, 48, 50, 58, 60], "formatted_str": [12, 21], "forwardref": [12, 17], "found": [1, 12, 15, 17, 46, 47, 48], "four": [12, 21], "frac_sec": [12, 21], "fraction": [12, 21, 60], "freeman": 60, "freimuth": 60, "from": [1, 2, 3, 5, 6, 12, 17, 18, 21, 22, 23, 25, 26, 39, 41, 46, 49, 50, 51, 52, 53, 54, 56, 57, 58, 59, 60, 61, 62], "from_datetim": [12, 21], "from_fil": [1, 12, 17], "from_iso_8601": [12, 21], "function": [2, 12, 17, 21, 32, 33, 36, 46, 50, 52, 55, 60], "further": [18, 46, 49, 60], "g": [1, 12, 15, 16, 17, 18, 39, 41, 46, 48, 49, 51, 59, 60], "ga4gh": [1, 58, 60], "gap": 60, "gargano": 60, "gener": [1, 12, 17, 59, 60], "genet": 60, "geneticist": 60, "genom": 60, "genotyp": 60, "get": [2, 3, 5, 6, 59, 61], "get_codesystem_by_namespace_prefx": [36, 46, 47], "get_field": [1, 12, 17], "get_field_id": [1, 12, 17], "get_field_nam": 36, "ggn2": 60, "gitforwindow": 59, "github": [59, 60, 62, 63, 64], "give": [1, 23, 25, 59], "given": [1, 12, 17, 18, 39, 41, 46, 49], "global": 60, "go": [12, 21, 59], "goe": [36, 45], "googl": [12, 21, 60], "gradient": 60, "graef": 60, "group": [12, 17], "groza": 60, "guid": [58, 61], "gz": 59, "h": 60, "ha": [1, 12, 17, 22], "haendel": 60, "hamosh": 60, "handl": [12, 17, 21, 39, 46, 50, 60], "handle_file_extens": [39, 40], "happen": [12, 17], "harbor": 60, "harri": 60, "have": [1, 12, 15, 17, 39, 41, 46, 51, 59, 60], "head": [12, 17], "health": 60, "healthcar": 60, "hegd": 60, "height": [12, 17], "help": 61, "here": [59, 60], "high": 60, "highli": [1, 12, 17, 39, 41], "hint": 60, "hit": 59, "homebrew": 59, "hour": [12, 21], "hour_str": [12, 21], "how": [12, 21, 46, 50], "howev": 60, "hp": [2, 5, 12, 16], "hpo": [2, 5, 12, 16], "hpo_api_request": 2, "hpo_code_system": [2, 5], "hpoapirequest": [2, 5], "html": 59, "http": [2, 5, 6, 59, 60, 62, 63, 64], "human": [2, 5, 12, 15, 16, 60], "hurdl": 60, "hybridis": 60, "hypothesi": 60, "i": [1, 2, 3, 12, 15, 16, 17, 18, 21, 22, 23, 25, 32, 34, 35, 39, 41, 46, 47, 48, 49, 50, 51, 52, 57, 59, 60, 61], "id": [1, 12, 17, 23, 26, 36, 39, 41, 55], "identifi": [12, 17], "ii": [1, 12, 17, 39, 41, 46, 51], "implement": [2, 3, 57], "import": [1, 12, 17, 23, 26, 60, 61], "inbuilt": [46, 52], "includ": [12, 16, 56, 60], "inclus": [18, 46, 49], "increas": 60, "independ": 59, "index": [36, 45, 58], "indic": [12, 18, 21, 46, 49], "individu": [23, 26, 60], "infer": [39, 44, 60], "inform": [32, 33, 59, 60, 63, 64], "input": [27, 39], "insight": 60, "inst": [23, 26], "instal": 58, "instanc": [12, 17, 23, 26, 57, 60], "instruct": 59, "int": [2, 5, 6, 12, 14, 17, 18, 21, 22, 36, 45, 46, 49, 52, 53], "int_str": [46, 52], "integ": [18, 46, 49], "integr": 60, "intend": [2, 12, 15, 46, 48, 60], "interest": 60, "intern": 57, "interoper": [12, 22, 60], "interpret": 60, "introduct": 58, "intuit": 60, "investig": 60, "iobas": [39, 40, 43, 44], "ipsum": 62, "ipynb": [63, 64], "iri": [12, 16], "iri_prefix": [12, 16], "iso": [12, 21, 46, 50], "iso_8601": [12, 21], "iso_8601_datestr": [12, 21], "issu": [18, 46, 49, 60], "item": [1, 12, 17], "its": [1, 12, 16, 17, 18, 46, 49, 60], "itself": 59, "j": 60, "jacobsen": 60, "januari": [12, 21, 46, 50], "java": [57, 60], "java_hom": 59, "javas": 59, "jax": [2, 5], "journal": 60, "jre": 59, "jre8": 59, "json": [2, 4, 39, 40, 41, 42], "jupyt": [36, 37], "just": [12, 15, 22, 46, 48, 59], "k": 60, "kaliyaperum": 60, "kassabi": 60, "keep": 60, "kei": [1, 12, 17, 23, 26, 39, 41], "keyword": [1, 12, 17, 32, 35], "klocperk": 60, "kuster": 60, "kwarg": [1, 12, 17, 23, 25, 26, 32, 33, 35, 57], "l": 60, "laboratori": 60, "ladewig": 60, "languag": [59, 60], "later": [1, 12, 16, 17, 39, 41], "latest": 59, "learn": 60, "least": 60, "leav": [1, 12, 17, 39, 41], "lenient": [1, 12, 15, 17, 18, 21, 22, 39, 41, 46, 48, 49, 50, 53, 54], "letter": [12, 17], "level": [1, 12, 17, 21, 22, 39, 41, 46, 50, 53, 54, 60], "librari": [58, 59, 60], "like": [1, 12, 17, 39, 41], "line": [1, 12, 17, 39, 41, 59], "link": 60, "linux": 59, "list": [1, 12, 15, 16, 17, 18, 22, 23, 25, 39, 40, 41, 42, 46, 47, 48, 49, 53, 54, 56, 57, 60], "liter": [1, 12, 14, 15, 17, 18, 21, 22, 39, 40, 41, 46, 48, 49, 50, 53, 54], "lloyd": 60, "load": [1, 12, 17, 39, 41, 60], "load_data": [1, 12, 17], "load_data_using_data_model": [1, 12, 17, 39, 41], "loc": [36, 45], "loc_default": [1, 36, 45], "local": [23, 60], "loinc": [12, 16], "look": [1, 12, 17, 39, 41, 63, 64], "lorem": 62, "lot": [12, 21, 46, 50], "lowercas": [12, 17], "m": [59, 60], "mac": 59, "machin": 60, "maco": 59, "made": [1, 12, 17, 60], "mai": [12, 15, 59, 60], "main": 7, "maintain": 59, "make": [2, 59], "manag": [59, 60], "mani": [12, 21, 46, 50, 59, 60], "manual": [12, 17], "map": [1, 12, 17, 32, 33, 34, 39, 41, 56, 58, 60], "map_field": 23, "map_singl": [23, 26], "mapper": [23, 27], "mapping_command": 7, "mapping_dict": [32, 34], "mappingproxi": [1, 12, 17, 39, 41], "marcello": 60, "markdown": [36, 37], "mass": 60, "match": [1, 12, 17, 46, 47, 60], "materi": 60, "mattina": 60, "maverick": 59, "max": [12, 14], "mcmurri": 60, "mean": [12, 16, 60], "meant": [46, 51], "measur": 60, "medic": [1, 12, 17, 60], "medicalact": 60, "medicin": 60, "medrxiv": 60, "messag": [1, 23, 25, 60], "meta": 60, "metadata": 60, "method": [1, 2, 3, 12, 17, 18, 32, 33, 35, 46, 49, 51, 53, 60], "might": [12, 17, 46, 51, 60], "min": [12, 14, 21], "minut": [12, 21], "minute_str": [12, 21], "miss": [1, 12, 17], "modal": 60, "model": [1, 12, 17, 18, 23, 26, 39, 41, 46, 49, 51, 60, 62], "modifi": [12, 17, 60], "modul": [2, 7, 12, 18, 23, 27, 32, 36, 39, 46, 56, 58], "molecul": 60, "molecular": 60, "moment": [63, 64], "mondo": [12, 16], "month": [12, 21, 46, 50], "month_str": [12, 21], "more": [12, 22, 32, 33, 59, 60, 63, 64], "morphologi": 60, "most": [59, 60], "move": 59, "multipl": [12, 18, 22, 46, 49, 60], "mungal": 60, "munoz": 60, "must": [1, 12, 17, 39, 41], "myenv": 59, "n": [12, 14, 17, 60], "name": [1, 2, 5, 6, 12, 15, 16, 17, 18, 22, 36, 37, 39, 41, 45, 46, 48, 49, 51, 54, 59], "namespac": [12, 15, 16, 46, 47, 48], "namespace_prefix": [12, 15, 16, 46, 48], "namespace_prefix_str": [46, 47], "nanosecond": [12, 21], "natur": 60, "navig": 59, "neatli": [46, 51], "necessari": [12, 16], "need": [59, 60], "net": [2, 6], "new": 59, "new_descript": [12, 22], "new_nam": [12, 22], "nomenclatur": [12, 16], "non": [36, 55, 60], "none": [1, 2, 4, 12, 16, 17, 21, 22, 39, 40, 46, 47, 50, 52, 54], "normal": 60, "note": 59, "notebook": [36, 37, 62, 63, 64], "notebookbuild": [1, 36, 37], "noth": [46, 53], "now": 59, "number": [1, 12, 17, 39, 41], "numer": [12, 22, 46, 52], "o": 60, "object": [1, 12, 13, 14, 15, 16, 17, 21, 22, 23, 25, 26, 36, 37, 39, 40, 41, 46, 47, 48, 50, 54, 57], "observ": 60, "occasion": 60, "occur": [36, 45], "offici": 59, "omim": [12, 16], "one": [2, 3, 12, 17, 18, 22, 46, 49, 57], "ones": 60, "onli": [12, 15, 17, 18, 22, 46, 48, 49, 57], "onset": 60, "onto": [12, 17, 60], "ontologi": [2, 5, 6, 12, 16, 60], "open": 59, "openjdk": 59, "openjr": 59, "oper": 59, "opt": 59, "optim": 60, "option": [1, 12, 17, 21, 39, 41, 59, 60], "oracl": 59, "order": [46, 53, 59], "ordin": [1, 12, 17, 39, 41, 46, 51, 60], "ordo": [12, 16], "org": [2, 5, 59, 60], "organ": 60, "orgroup": [1, 12, 17], "origin": [32, 34, 35], "orpha": [2, 6], "orpha_api_request": [2, 3], "orpha_code_system": [2, 6], "orphaapirequest": [2, 6], "orphanet": [2, 3, 5, 6], "other": [12, 15, 36, 55, 60], "otherwis": [1, 12, 17, 22, 23, 25, 56, 57], "out_dir": [39, 42], "output": [27, 39], "overwrit": [1, 12, 17, 39, 41], "own": 59, "p": [59, 60], "packag": [0, 59], "pad": [12, 21], "page": [58, 60], "pandas_util": 36, "param": [2, 4], "paramet": [1, 12, 15, 16, 17, 18, 21, 22, 23, 25, 26, 32, 34, 35, 36, 37, 39, 41, 42, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57], "pars": [1, 12, 15, 16, 17, 18, 21, 22, 36, 39, 41, 44, 60], "parse_bool": [36, 46, 52], "parse_cod": [12, 15, 36, 46, 53], "parse_d": [12, 21, 36, 46, 53], "parse_data_typ": [12, 18, 36, 46], "parse_float": [36, 46, 52], "parse_int": [36, 46, 52], "parse_ordin": [1, 12, 17, 36, 39, 41, 46], "parse_primitive_data_valu": [36, 46, 53], "parse_single_data_typ": [36, 46, 49], "parse_valu": [36, 46], "parse_value_set": [1, 12, 17, 22, 36, 39, 41, 46], "parse_xml": [39, 44], "parser": [12, 21, 46, 50], "part": [46, 51, 60], "pass": [1, 12, 17, 18, 23, 25, 32, 35, 46, 49], "path": [1, 12, 17, 36, 37, 39, 40, 41, 42, 43, 44, 56, 57, 59], "patient": 60, "pattern": 57, "pd": [36, 45], "perform": [36, 45], "permitt": [18, 46, 49], "phenopacket": [1, 12, 16, 17, 23, 25, 26, 32, 33, 39, 41, 42, 56, 57], "phenopacket_building_block": 23, "phenopacket_el": [23, 26], "phenopacket_mapp": [0, 59, 61, 62, 63, 64], "phenopacket_tool": 60, "phenopacketbuildingblock": [23, 26], "phenopacketmapp": [0, 1, 23, 25], "phenopackets_list": [39, 42], "phenopackets_venv": 59, "phenotyp": [2, 5, 12, 16, 60], "phenotypicfeatur": 60, "physician": 60, "physiologi": 60, "pipelin": 1, "pkg": 59, "place": [12, 17], "pleas": [32, 33, 35, 60, 63, 64], "plo": 60, "pone": 60, "popular": [12, 16, 59], "possibl": [12, 18, 21, 22, 46, 49, 50, 60], "post": 60, "power": 60, "practic": 60, "pre": 59, "precis": [1, 23, 25], "prefix": [2, 5, 6, 12, 15, 16, 18, 46, 47, 48, 49], "preprocess": [12, 17, 60, 61], "preprocess_dict": [32, 33], "preprocess_method": [12, 17, 32, 33], "preprocessed_valu": [12, 17], "present": [12, 17, 60], "press": 59, "primit": [18, 46, 49, 53], "principl": 60, "probabl": 59, "proband": 60, "problem": 60, "procedur": 60, "proceed": 59, "process": [1, 12, 17, 21, 46, 50, 60], "produc": 60, "profession": 60, "profil": 59, "prognosi": 60, "program": [59, 60], "programm": 60, "programmat": [36, 37], "project": [12, 59], "prompt": 59, "properti": [12, 17, 22, 59], "protein": 60, "protobuf": [12, 21, 60], "protobuf_timestamp": [12, 21], "provid": [2, 3, 12, 15, 22, 46, 48, 60], "pseudonym": [23, 26, 46, 51], "purpos": [18, 46, 49, 52, 57, 60], "py": [2, 3], "pypi": 59, "python": [1, 12, 17, 18, 36, 37, 39, 41, 46, 49, 52, 58, 60], "q": 60, "quantit": 60, "quickli": 60, "quickstart": 58, "quickstart_command": 7, "r": 60, "rais": [1, 12, 17, 32, 35], "rambla": 60, "rare": [2, 6, 18], "rarelink_datamodel": 18, "re": 59, "read": [1, 12, 17, 39, 41, 46, 51, 56, 57, 60, 62], "read_data_model": [39, 41], "read_json": 39, "read_phenopacket": [39, 41], "read_phenopacket_from_json": [39, 41], "read_valid": [56, 57], "read_xml": 39, "readabl": [12, 15, 60], "recogn": [12, 15, 46, 48], "recommend": [1, 12, 17, 39, 41, 60], "record": [12, 17, 60], "rees": 60, "refer": [58, 60], "rekerl": 60, "relat": [12, 17, 59, 60], "relev": 60, "reli": [32, 33, 46, 52], "remov": [1, 12, 17, 36, 39, 41, 55], "remove_dupl": [12, 22], "remove_line_break": [1, 12, 17, 39, 41], "replac": [36, 55, 59], "replic": 60, "report": 60, "repositori": 59, "repres": [12, 15, 18, 46, 48, 49, 53, 60], "represent": [12, 15, 22, 46, 53, 54, 60], "request": [2, 3, 5, 6], "requir": [1, 12, 17, 21, 32, 35, 39, 41, 60], "research": 59, "resolut": [12, 21], "resourc": [1, 12, 15, 16, 17, 18, 22, 39, 41, 46, 47, 48, 49, 53, 54], "respect": [32, 33, 46, 51, 52], "restart": 59, "result": [23, 26], "return": [1, 12, 15, 17, 18, 21, 22, 23, 25, 26, 32, 34, 35, 36, 39, 41, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57], "rhel": 59, "rna": 60, "robinson": 60, "row": [12, 17, 36, 45], "row_index": [36, 45], "row_no": [12, 17], "rpm": 59, "rule": [12, 17, 32, 34], "run": 59, "s41587": 60, "safe": [36, 45], "same": 60, "save": [36, 37], "schema": [1, 12, 17, 23, 25, 26, 58, 60], "schofield": 60, "scienc": 59, "scm": 59, "screen": 59, "script": 59, "sct": [18, 46, 49], "search": [46, 47, 58], "sec": [12, 21], "second": [12, 21], "second_str": [12, 21], "section": [12, 17, 60], "see": [1, 23, 25, 59], "seelow": 60, "seen": [2, 3], "seitz": 60, "select": [18, 59], "separ": [12, 21, 46, 50, 51, 59], "seq": 60, "sequenc": 60, "set": [2, 12, 15, 16, 17, 18, 21, 22, 46, 49, 50, 54, 59, 60], "set_vers": [12, 16], "sever": [59, 60], "sh": 59, "shell": 59, "short": 60, "should": [1, 2, 3, 12, 17, 39, 41, 59, 60], "simpl": 60, "simpli": 59, "sinc": [59, 60], "singl": [12, 17, 60], "singleton": 57, "smith": 60, "snome": [12, 15, 16, 18, 46, 48, 49], "snomed_ct": [12, 15, 46, 48], "so": [12, 21, 46, 50, 59], "softwar": 60, "solv": 60, "some": [36, 45, 60], "someth": [12, 17, 36, 45], "sometim": [12, 17, 21, 46, 50], "sota": 60, "sourc": [1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 25, 26, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 59], "space": [2, 5, 6, 12, 15, 16, 18, 36, 46, 48, 49, 55], "specif": [1, 2, 3, 12, 17, 18, 21, 22, 39, 41, 46, 49, 60], "specifi": [12, 15, 21, 23, 26, 36, 45, 46, 48], "spectrometri": 60, "spread": 60, "spring": 60, "standard": [12, 60], "standardis": 60, "start": [12, 17, 59, 61], "state": [12, 17], "static": [1, 12, 15, 17, 21, 22], "steep": 60, "steinhau": 60, "step": [59, 61], "str": [1, 2, 4, 5, 6, 12, 15, 16, 17, 18, 21, 22, 23, 26, 36, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55], "str_to_valid_id": [1, 12, 17, 36], "strict": [1, 12, 15, 17, 18, 21, 22, 39, 41, 46, 48, 49, 50, 53, 54], "string": [1, 12, 15, 17, 18, 21, 22, 36, 39, 41, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55], "structur": 60, "studi": 60, "subject": 60, "submodul": 1, "subpackag": 0, "substrat": 60, "success": [1, 23, 25], "sudo": 59, "suffix": [12, 21], "suitabl": 60, "super": [2, 3], "sure": 59, "synonym": [12, 16], "syntact": 60, "system": [2, 3, 12, 15, 18, 22, 46, 48, 49, 59], "t": [12, 21, 59, 60], "tabl": [12, 17, 60], "tabular": [1, 18, 46, 49, 58, 60], "take": [32, 34, 35, 63, 64], "taken": 60, "tar": 59, "technic": 60, "technologi": 59, "term": [2, 5, 18, 46, 49], "termin": 59, "terminologi": [12, 16], "test": [1, 12, 17, 39, 41], "text": [12, 15, 36, 37, 46, 48], "thei": [12, 22, 32, 35], "them": [12, 21, 46, 50, 51, 56, 57, 60], "thi": [1, 2, 3, 12, 16, 17, 18, 21, 22, 23, 36, 39, 41, 46, 49, 50, 51, 53, 55, 56, 57, 59, 60, 61], "those": 60, "through": [46, 47, 59], "throughout": 36, "throw": [12, 15, 18, 46, 48, 49], "time": 59, "timestamp": [12, 21], "timezon": [12, 21], "tissu": 60, "tool": [56, 57, 59, 60], "torr": 60, "trait": 60, "treatment": 60, "tree": [62, 63, 64], "tri": [46, 53], "true": [1, 12, 17, 21, 22, 39, 41, 46, 52, 54, 56, 57], "truefalsevalueset": [12, 22], "try": 59, "tupl": [1, 12, 17, 46, 51], "turn": 59, "two": [12, 21, 60, 62], "type": [1, 12, 16, 17, 18, 22, 39, 41, 44, 46, 49, 52, 53, 60], "type_str": [18, 46, 49], "typic": [12, 16, 18, 46, 49], "ubuntu": 59, "unclear": [12, 21, 46, 50], "under": 59, "underli": 60, "underscor": [12, 17, 36, 55], "understand": 60, "union": [12, 17, 39, 41], "uniqu": [1, 12, 17], "unit": [12, 21, 46, 50, 60], "unix": 59, "unknow": [12, 21, 46, 50], "unknown": [1, 12, 17, 22, 39, 41], "unrecogn": [18, 46, 49], "up": [1, 12, 17, 21, 59, 60], "updat": 59, "url": [2, 4, 12, 16], "us": [1, 2, 3, 12, 15, 17, 21, 22, 23, 25, 32, 33, 34, 35, 36, 39, 41, 46, 48, 50, 53, 54, 56, 57, 60], "usag": [12, 16], "usecas": [12, 22], "user": [18, 46, 49, 58, 59, 60], "utc": [12, 21], "utf": [39, 40, 44], "util": [1, 12, 17, 21], "v2": [1, 59, 60], "valid": [1, 12, 17, 22, 27, 36, 39, 41, 55, 59, 60], "validate_command": 7, "valu": [1, 12, 16, 17, 22, 23, 25, 32, 33, 34, 35, 36, 39, 41, 45, 46, 52, 53, 54, 59, 60], "value1": [12, 17], "value2": [12, 17], "value_set": [1, 12, 17, 39, 41], "value_set_descript": [12, 22, 46, 54], "value_set_nam": [12, 22, 46, 54], "value_set_str": [12, 22, 46, 54], "value_str": [46, 52, 53], "valueerror": [12, 15, 18, 46, 48, 49], "valueset": [1, 12, 17, 22, 39, 41, 46, 54], "variabl": [1, 12, 15, 16, 17, 21, 22, 59], "variat": [12, 21, 46, 50], "variou": 2, "venv": 59, "veri": [59, 60], "verifi": 59, "version": [2, 5, 6, 12, 15, 16, 46, 48, 59, 60], "via": 59, "viabl": [12, 22], "visit": 59, "wa": 60, "wagner": 60, "wai": [59, 60], "want": 59, "warn": [1, 12, 15, 17, 18, 39, 41, 46, 48, 49, 60], "we": [12, 22, 59, 60], "websit": [59, 60], "well": 60, "when": [1, 12, 17, 18, 39, 41, 46, 49], "where": [2, 3, 12, 21, 36, 37, 46, 51, 59], "whether": [1, 12, 15, 17, 21, 39, 41, 46, 48, 50], "which": [12, 17, 21, 23, 26, 46, 50, 51, 59, 60], "while": [12, 21, 60], "who": 60, "width": [12, 17], "win": 59, "window": 59, "within": [12, 17, 60], "word": 60, "work": [12, 17, 46, 53, 59], "would": 60, "wrapper": [46, 53], "write": [32, 35, 36, 37, 39, 42], "write_to_fil": [36, 37], "written": 59, "wrong": [36, 45], "www": [2, 6, 59], "x": 60, "x86_64": 59, "xcode": 59, "xlsx": [39, 40], "xml": [39, 40, 44], "y": [59, 60], "year": [12, 21], "year_str": [12, 21], "yet": 59, "you": [59, 60, 61], "your": 59, "yournam": 59, "z": [12, 17, 21], "zero": [12, 21]}, "titles": ["API reference", "phenopacket_mapper package", "phenopacket_mapper.api_requests package", "phenopacket_mapper.api_requests.api_request_super_class module", "phenopacket_mapper.api_requests.get module", "phenopacket_mapper.api_requests.hpo_api_request module", "phenopacket_mapper.api_requests.orpha_api_request module", "phenopacket_mapper.cli package", "phenopacket_mapper.cli.main module", "phenopacket_mapper.cli.mapping_command module", "phenopacket_mapper.cli.quickstart_command module", "phenopacket_mapper.cli.validate_command module", "phenopacket_mapper.data_standards package", "phenopacket_mapper.data_standards.DataModel2PhenopacketSchema module", "phenopacket_mapper.data_standards.cardinality module", "phenopacket_mapper.data_standards.code module", "phenopacket_mapper.data_standards.code_system module", "phenopacket_mapper.data_standards.data_model module", "phenopacket_mapper.data_standards.data_models package", "phenopacket_mapper.data_standards.data_models.erdri_cds module", "phenopacket_mapper.data_standards.data_models.rarelink_datamodel module", "phenopacket_mapper.data_standards.date module", "phenopacket_mapper.data_standards.value_set module", "phenopacket_mapper.mapping package", "phenopacket_mapper.mapping.map_field module", "phenopacket_mapper.mapping.mapper module", "phenopacket_mapper.mapping.phenopacket_building_block module", "phenopacket_mapper.pipeline package", "phenopacket_mapper.pipeline.input module", "phenopacket_mapper.pipeline.mapper module", "phenopacket_mapper.pipeline.output module", "phenopacket_mapper.pipeline.validate module", "phenopacket_mapper.preprocessing package", "phenopacket_mapper.preprocessing.preprocess module", "phenopacket_mapper.preprocessing.preprocess_dict module", "phenopacket_mapper.preprocessing.preprocess_method module", "phenopacket_mapper.utils package", "phenopacket_mapper.utils.create_ipynb_in_code module", "phenopacket_mapper.utils.get_field_name module", "phenopacket_mapper.utils.io package", "phenopacket_mapper.utils.io.data_reader module", "phenopacket_mapper.utils.io.input module", "phenopacket_mapper.utils.io.output module", "phenopacket_mapper.utils.io.read_json module", "phenopacket_mapper.utils.io.read_xml module", "phenopacket_mapper.utils.pandas_utils module", "phenopacket_mapper.utils.parsing package", "phenopacket_mapper.utils.parsing.get_codesystem_by_namespace_prefix module", "phenopacket_mapper.utils.parsing.parse_coding module", "phenopacket_mapper.utils.parsing.parse_data_type module", "phenopacket_mapper.utils.parsing.parse_date module", "phenopacket_mapper.utils.parsing.parse_ordinal module", "phenopacket_mapper.utils.parsing.parse_primitive_data_value module", "phenopacket_mapper.utils.parsing.parse_value module", "phenopacket_mapper.utils.parsing.parse_value_set module", "phenopacket_mapper.utils.str_to_valid_id module", "phenopacket_mapper.validate package", "phenopacket_mapper.validate.validate module", "Welcome to Phenopacket Mapper\u2019s documentation!", "Installation", "Introduction", "Quickstart", "User Guides", "Create a Data Model in Code", "Read a Data Model from a File"], "titleterms": {"": 58, "about": 58, "anaconda": 59, "api": 0, "api_request": [2, 3, 4, 5, 6], "api_request_super_class": 3, "ar": 60, "cardin": 14, "cli": [7, 8, 9, 10, 11], "code": [15, 63], "code_system": 16, "content": [58, 62], "creat": [59, 63], "create_ipynb_in_cod": 37, "data": [63, 64], "data_model": [17, 18, 19, 20], "data_read": 40, "data_standard": [12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22], "datamodel2phenopacketschema": 13, "date": 21, "document": 58, "environ": 59, "erdri_cd": 19, "featur": 60, "file": 64, "from": 64, "get": 4, "get_codesystem_by_namespace_prefix": 47, "get_field_nam": 38, "git": 59, "guid": 62, "hpo_api_request": 5, "indic": 58, "input": [28, 41], "instal": 59, "introduct": 60, "io": [39, 40, 41, 42, 43, 44], "java": 59, "local": 59, "main": 8, "map": [23, 24, 25, 26], "map_field": 24, "mapper": [25, 29, 58, 59], "mapping_command": 9, "model": [63, 64], "modul": [3, 4, 5, 6, 8, 9, 10, 11, 13, 14, 15, 16, 17, 19, 20, 21, 22, 24, 25, 26, 28, 29, 30, 31, 33, 34, 35, 37, 38, 40, 41, 42, 43, 44, 45, 47, 48, 49, 50, 51, 52, 53, 54, 55, 57], "motiv": 60, "orpha_api_request": 6, "output": [30, 42], "packag": [1, 2, 7, 12, 18, 23, 27, 32, 36, 39, 46, 56], "pandas_util": 45, "pars": [46, 47, 48, 49, 50, 51, 52, 53, 54], "parse_cod": 48, "parse_d": 50, "parse_data_typ": 49, "parse_ordin": 51, "parse_primitive_data_valu": 52, "parse_valu": 53, "parse_value_set": 54, "phenopacket": [58, 59, 60], "phenopacket_building_block": 26, "phenopacket_mapp": [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57], "pip": 59, "pipelin": [27, 28, 29, 30, 31], "preprocess": [32, 33, 34, 35], "preprocess_dict": 34, "preprocess_method": 35, "public": 60, "python": 59, "quickstart": 61, "quickstart_command": 10, "rarelink_datamodel": 20, "read": 64, "read_json": 43, "read_xml": 44, "refer": 0, "resourc": 60, "standard": 59, "str_to_valid_id": 55, "submodul": [2, 7, 12, 18, 23, 27, 32, 36, 39, 46, 56], "subpackag": [1, 12, 36], "tabl": 58, "tldr": 60, "us": 59, "user": 62, "util": [36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55], "valid": [31, 56, 57], "validate_command": 11, "value_set": 22, "virtual": 59, "welcom": 58, "what": 60, "why": 60, "wip": 59}}) \ No newline at end of file +Search.setIndex({"alltitles": {"API reference": [[0, null]], "About": [[58, "about"]], "Anaconda": [[59, "anaconda"], [59, "id2"]], "Contents:": [[58, null], [62, null]], "Create a Data Model in Code": [[63, null]], "Creating a virtual environment": [[59, "creating-a-virtual-environment"]], "Features": [[60, "features"]], "Indices and tables": [[58, "indices-and-tables"]], "Installation": [[59, null]], "Installing Git": [[59, "installing-git"]], "Installing Java": [[59, "installing-java"]], "Installing Python": [[59, "installing-python"]], "Installing the Phenopacket Mapper": [[59, "installing-the-phenopacket-mapper"]], "Introduction": [[60, null]], "Motivation": [[60, "motivation"]], "Phenopackets": [[60, "phenopackets"]], "Publications": [[60, "publications"]], "Quickstart": [[61, null]], "Read a Data Model from a File": [[64, null]], "Resources": [[60, "resources"]], "Standard Python": [[59, "standard-python"], [59, "id1"]], "Submodules": [[2, "submodules"], [7, "submodules"], [12, "submodules"], [18, "submodules"], [23, "submodules"], [27, "submodules"], [32, "submodules"], [36, "submodules"], [39, "submodules"], [46, "submodules"], [56, "submodules"]], "Subpackages": [[1, "subpackages"], [12, "subpackages"], [36, "subpackages"]], "TLDR": [[60, "tldr"]], "User Guides": [[62, null]], "Using pip": [[59, "using-pip"]], "Welcome to Phenopacket Mapper\u2019s documentation!": [[58, null]], "What are Phenopackets?": [[60, "what-are-phenopackets"]], "Why Phenopackets?": [[60, "why-phenopackets"]], "[WIP] Local installation": [[59, "wip-local-installation"]], "phenopacket_mapper package": [[1, null]], "phenopacket_mapper.api_requests package": [[2, null]], "phenopacket_mapper.api_requests.api_request_super_class module": [[3, null]], "phenopacket_mapper.api_requests.get module": [[4, null]], "phenopacket_mapper.api_requests.hpo_api_request module": [[5, null]], "phenopacket_mapper.api_requests.orpha_api_request module": [[6, null]], "phenopacket_mapper.cli package": [[7, null]], "phenopacket_mapper.cli.main module": [[8, null]], "phenopacket_mapper.cli.mapping_command module": [[9, null]], "phenopacket_mapper.cli.quickstart_command module": [[10, null]], "phenopacket_mapper.cli.validate_command module": [[11, null]], "phenopacket_mapper.data_standards package": [[12, null]], "phenopacket_mapper.data_standards.DataModel2PhenopacketSchema module": [[13, null]], "phenopacket_mapper.data_standards.cardinality module": [[14, null]], "phenopacket_mapper.data_standards.code module": [[15, null]], "phenopacket_mapper.data_standards.code_system module": [[16, null]], "phenopacket_mapper.data_standards.data_model module": [[17, null]], "phenopacket_mapper.data_standards.data_models package": [[18, null]], "phenopacket_mapper.data_standards.data_models.erdri_cds module": [[19, null]], "phenopacket_mapper.data_standards.data_models.rarelink_datamodel module": [[20, null]], "phenopacket_mapper.data_standards.date module": [[21, null]], "phenopacket_mapper.data_standards.value_set module": [[22, null]], "phenopacket_mapper.mapping package": [[23, null]], "phenopacket_mapper.mapping.map_field module": [[24, null]], "phenopacket_mapper.mapping.mapper module": [[25, null]], "phenopacket_mapper.mapping.phenopacket_building_block module": [[26, null]], "phenopacket_mapper.pipeline package": [[27, null]], "phenopacket_mapper.pipeline.input module": [[28, null]], "phenopacket_mapper.pipeline.mapper module": [[29, null]], "phenopacket_mapper.pipeline.output module": [[30, null]], "phenopacket_mapper.pipeline.validate module": [[31, null]], "phenopacket_mapper.preprocessing package": [[32, null]], "phenopacket_mapper.preprocessing.preprocess module": [[33, null]], "phenopacket_mapper.preprocessing.preprocess_dict module": [[34, null]], "phenopacket_mapper.preprocessing.preprocess_method module": [[35, null]], "phenopacket_mapper.utils package": [[36, null]], "phenopacket_mapper.utils.create_ipynb_in_code module": [[37, null]], "phenopacket_mapper.utils.get_field_name module": [[38, null]], "phenopacket_mapper.utils.io package": [[39, null]], "phenopacket_mapper.utils.io.data_reader module": [[40, null]], "phenopacket_mapper.utils.io.input module": [[41, null]], "phenopacket_mapper.utils.io.output module": [[42, null]], "phenopacket_mapper.utils.io.read_json module": [[43, null]], "phenopacket_mapper.utils.io.read_xml module": [[44, null]], "phenopacket_mapper.utils.pandas_utils module": [[45, null]], "phenopacket_mapper.utils.parsing package": [[46, null]], "phenopacket_mapper.utils.parsing.get_codesystem_by_namespace_prefix module": [[47, null]], "phenopacket_mapper.utils.parsing.parse_coding module": [[48, null]], "phenopacket_mapper.utils.parsing.parse_data_type module": [[49, null]], "phenopacket_mapper.utils.parsing.parse_date module": [[50, null]], "phenopacket_mapper.utils.parsing.parse_ordinal module": [[51, null]], "phenopacket_mapper.utils.parsing.parse_primitive_data_value module": [[52, null]], "phenopacket_mapper.utils.parsing.parse_value module": [[53, null]], "phenopacket_mapper.utils.parsing.parse_value_set module": [[54, null]], "phenopacket_mapper.utils.str_to_valid_id module": [[55, null]], "phenopacket_mapper.validate package": [[56, null]], "phenopacket_mapper.validate.validate module": [[57, null]]}, "docnames": ["apidocs/modules", "apidocs/phenopacket_mapper", "apidocs/phenopacket_mapper.api_requests", "apidocs/phenopacket_mapper.api_requests.api_request_super_class", "apidocs/phenopacket_mapper.api_requests.get", "apidocs/phenopacket_mapper.api_requests.hpo_api_request", "apidocs/phenopacket_mapper.api_requests.orpha_api_request", "apidocs/phenopacket_mapper.cli", "apidocs/phenopacket_mapper.cli.main", "apidocs/phenopacket_mapper.cli.mapping_command", "apidocs/phenopacket_mapper.cli.quickstart_command", "apidocs/phenopacket_mapper.cli.validate_command", "apidocs/phenopacket_mapper.data_standards", "apidocs/phenopacket_mapper.data_standards.DataModel2PhenopacketSchema", "apidocs/phenopacket_mapper.data_standards.cardinality", "apidocs/phenopacket_mapper.data_standards.code", "apidocs/phenopacket_mapper.data_standards.code_system", "apidocs/phenopacket_mapper.data_standards.data_model", "apidocs/phenopacket_mapper.data_standards.data_models", "apidocs/phenopacket_mapper.data_standards.data_models.erdri_cds", "apidocs/phenopacket_mapper.data_standards.data_models.rarelink_datamodel", "apidocs/phenopacket_mapper.data_standards.date", "apidocs/phenopacket_mapper.data_standards.value_set", "apidocs/phenopacket_mapper.mapping", "apidocs/phenopacket_mapper.mapping.map_field", "apidocs/phenopacket_mapper.mapping.mapper", "apidocs/phenopacket_mapper.mapping.phenopacket_building_block", "apidocs/phenopacket_mapper.pipeline", "apidocs/phenopacket_mapper.pipeline.input", "apidocs/phenopacket_mapper.pipeline.mapper", "apidocs/phenopacket_mapper.pipeline.output", "apidocs/phenopacket_mapper.pipeline.validate", "apidocs/phenopacket_mapper.preprocessing", "apidocs/phenopacket_mapper.preprocessing.preprocess", "apidocs/phenopacket_mapper.preprocessing.preprocess_dict", "apidocs/phenopacket_mapper.preprocessing.preprocess_method", "apidocs/phenopacket_mapper.utils", "apidocs/phenopacket_mapper.utils.create_ipynb_in_code", "apidocs/phenopacket_mapper.utils.get_field_name", "apidocs/phenopacket_mapper.utils.io", "apidocs/phenopacket_mapper.utils.io.data_reader", "apidocs/phenopacket_mapper.utils.io.input", "apidocs/phenopacket_mapper.utils.io.output", "apidocs/phenopacket_mapper.utils.io.read_json", "apidocs/phenopacket_mapper.utils.io.read_xml", "apidocs/phenopacket_mapper.utils.pandas_utils", "apidocs/phenopacket_mapper.utils.parsing", "apidocs/phenopacket_mapper.utils.parsing.get_codesystem_by_namespace_prefix", "apidocs/phenopacket_mapper.utils.parsing.parse_coding", "apidocs/phenopacket_mapper.utils.parsing.parse_data_type", "apidocs/phenopacket_mapper.utils.parsing.parse_date", "apidocs/phenopacket_mapper.utils.parsing.parse_ordinal", "apidocs/phenopacket_mapper.utils.parsing.parse_primitive_data_value", "apidocs/phenopacket_mapper.utils.parsing.parse_value", "apidocs/phenopacket_mapper.utils.parsing.parse_value_set", "apidocs/phenopacket_mapper.utils.str_to_valid_id", "apidocs/phenopacket_mapper.validate", "apidocs/phenopacket_mapper.validate.validate", "index", "installation", "introduction", "quickstart", "user_guides", "user_guides/create_data_model_in_code", "user_guides/read_data_model_from_file"], "envversion": {"sphinx": 64, "sphinx.domains.c": 3, "sphinx.domains.changeset": 1, "sphinx.domains.citation": 1, "sphinx.domains.cpp": 9, "sphinx.domains.index": 1, "sphinx.domains.javascript": 3, "sphinx.domains.math": 2, "sphinx.domains.python": 4, "sphinx.domains.rst": 2, "sphinx.domains.std": 2, "sphinx.ext.intersphinx": 1, "sphinx.ext.viewcode": 1}, "filenames": ["apidocs/modules.rst", "apidocs/phenopacket_mapper.rst", "apidocs/phenopacket_mapper.api_requests.rst", "apidocs/phenopacket_mapper.api_requests.api_request_super_class.rst", "apidocs/phenopacket_mapper.api_requests.get.rst", "apidocs/phenopacket_mapper.api_requests.hpo_api_request.rst", "apidocs/phenopacket_mapper.api_requests.orpha_api_request.rst", "apidocs/phenopacket_mapper.cli.rst", "apidocs/phenopacket_mapper.cli.main.rst", "apidocs/phenopacket_mapper.cli.mapping_command.rst", "apidocs/phenopacket_mapper.cli.quickstart_command.rst", "apidocs/phenopacket_mapper.cli.validate_command.rst", "apidocs/phenopacket_mapper.data_standards.rst", "apidocs/phenopacket_mapper.data_standards.DataModel2PhenopacketSchema.rst", "apidocs/phenopacket_mapper.data_standards.cardinality.rst", "apidocs/phenopacket_mapper.data_standards.code.rst", "apidocs/phenopacket_mapper.data_standards.code_system.rst", "apidocs/phenopacket_mapper.data_standards.data_model.rst", "apidocs/phenopacket_mapper.data_standards.data_models.rst", "apidocs/phenopacket_mapper.data_standards.data_models.erdri_cds.rst", "apidocs/phenopacket_mapper.data_standards.data_models.rarelink_datamodel.rst", "apidocs/phenopacket_mapper.data_standards.date.rst", "apidocs/phenopacket_mapper.data_standards.value_set.rst", "apidocs/phenopacket_mapper.mapping.rst", "apidocs/phenopacket_mapper.mapping.map_field.rst", "apidocs/phenopacket_mapper.mapping.mapper.rst", "apidocs/phenopacket_mapper.mapping.phenopacket_building_block.rst", "apidocs/phenopacket_mapper.pipeline.rst", "apidocs/phenopacket_mapper.pipeline.input.rst", "apidocs/phenopacket_mapper.pipeline.mapper.rst", "apidocs/phenopacket_mapper.pipeline.output.rst", "apidocs/phenopacket_mapper.pipeline.validate.rst", "apidocs/phenopacket_mapper.preprocessing.rst", "apidocs/phenopacket_mapper.preprocessing.preprocess.rst", "apidocs/phenopacket_mapper.preprocessing.preprocess_dict.rst", "apidocs/phenopacket_mapper.preprocessing.preprocess_method.rst", "apidocs/phenopacket_mapper.utils.rst", "apidocs/phenopacket_mapper.utils.create_ipynb_in_code.rst", "apidocs/phenopacket_mapper.utils.get_field_name.rst", "apidocs/phenopacket_mapper.utils.io.rst", "apidocs/phenopacket_mapper.utils.io.data_reader.rst", "apidocs/phenopacket_mapper.utils.io.input.rst", "apidocs/phenopacket_mapper.utils.io.output.rst", "apidocs/phenopacket_mapper.utils.io.read_json.rst", "apidocs/phenopacket_mapper.utils.io.read_xml.rst", "apidocs/phenopacket_mapper.utils.pandas_utils.rst", "apidocs/phenopacket_mapper.utils.parsing.rst", "apidocs/phenopacket_mapper.utils.parsing.get_codesystem_by_namespace_prefix.rst", "apidocs/phenopacket_mapper.utils.parsing.parse_coding.rst", "apidocs/phenopacket_mapper.utils.parsing.parse_data_type.rst", "apidocs/phenopacket_mapper.utils.parsing.parse_date.rst", "apidocs/phenopacket_mapper.utils.parsing.parse_ordinal.rst", "apidocs/phenopacket_mapper.utils.parsing.parse_primitive_data_value.rst", "apidocs/phenopacket_mapper.utils.parsing.parse_value.rst", "apidocs/phenopacket_mapper.utils.parsing.parse_value_set.rst", "apidocs/phenopacket_mapper.utils.str_to_valid_id.rst", "apidocs/phenopacket_mapper.validate.rst", "apidocs/phenopacket_mapper.validate.validate.rst", "index.rst", "installation.rst", "introduction.rst", "quickstart.rst", "user_guides.rst", "user_guides/create_data_model_in_code.rst", "user_guides/read_data_model_from_file.rst"], "indexentries": {"add_code_cell() (phenopacket_mapper.utils.create_ipynb_in_code.notebookbuilder method)": [[37, "phenopacket_mapper.utils.create_ipynb_in_code.NotebookBuilder.add_code_cell", false]], "add_code_cell() (phenopacket_mapper.utils.notebookbuilder method)": [[36, "phenopacket_mapper.utils.NotebookBuilder.add_code_cell", false]], "add_markdown_cell() (phenopacket_mapper.utils.create_ipynb_in_code.notebookbuilder method)": [[37, "phenopacket_mapper.utils.create_ipynb_in_code.NotebookBuilder.add_markdown_cell", false]], "add_markdown_cell() (phenopacket_mapper.utils.notebookbuilder method)": [[36, "phenopacket_mapper.utils.NotebookBuilder.add_markdown_cell", false]], "api_base_url (phenopacket_mapper.api_requests.hpo_api_request.hpoapirequest attribute)": [[5, "phenopacket_mapper.api_requests.hpo_api_request.HPOAPIRequest.api_base_url", false]], "api_base_url (phenopacket_mapper.api_requests.hpoapirequest attribute)": [[2, "phenopacket_mapper.api_requests.HPOAPIRequest.api_base_url", false]], "api_base_url (phenopacket_mapper.api_requests.orpha_api_request.orphaapirequest attribute)": [[6, "phenopacket_mapper.api_requests.orpha_api_request.OrphaAPIRequest.api_base_url", false]], "api_base_url (phenopacket_mapper.api_requests.orphaapirequest attribute)": [[2, "phenopacket_mapper.api_requests.OrphaAPIRequest.api_base_url", false]], "apirequestsuperclass (class in phenopacket_mapper.api_requests)": [[2, "phenopacket_mapper.api_requests.APIRequestSuperClass", false]], "apirequestsuperclass (class in phenopacket_mapper.api_requests.api_request_super_class)": [[3, "phenopacket_mapper.api_requests.api_request_super_class.APIRequestSuperClass", false]], "cardinality (class in phenopacket_mapper.data_standards)": [[12, "phenopacket_mapper.data_standards.Cardinality", false]], "cardinality (class in phenopacket_mapper.data_standards.cardinality)": [[14, "phenopacket_mapper.data_standards.cardinality.Cardinality", false]], "cardinality (phenopacket_mapper.data_standards.data_model.datafield attribute)": [[17, "phenopacket_mapper.data_standards.data_model.DataField.cardinality", false]], "cardinality (phenopacket_mapper.data_standards.data_model.datasection attribute)": [[17, "phenopacket_mapper.data_standards.data_model.DataSection.cardinality", false]], "cardinality (phenopacket_mapper.data_standards.data_model.orgroup attribute)": [[17, "phenopacket_mapper.data_standards.data_model.OrGroup.cardinality", false]], "cardinality (phenopacket_mapper.data_standards.datafield attribute)": [[12, "phenopacket_mapper.data_standards.DataField.cardinality", false]], "cardinality (phenopacket_mapper.data_standards.datasection attribute)": [[12, "phenopacket_mapper.data_standards.DataSection.cardinality", false]], "cardinality (phenopacket_mapper.data_standards.orgroup attribute)": [[12, "phenopacket_mapper.data_standards.OrGroup.cardinality", false]], "check_fields_adheres_to_phenopacket_allowed_values() (phenopacket_mapper.mapping.mapper.phenopacketmapper method)": [[25, "phenopacket_mapper.mapping.mapper.PhenopacketMapper.check_fields_adheres_to_phenopacket_allowed_values", false]], "check_fields_adheres_to_phenopacket_allowed_values() (phenopacket_mapper.mapping.phenopacketmapper method)": [[23, "phenopacket_mapper.mapping.PhenopacketMapper.check_fields_adheres_to_phenopacket_allowed_values", false]], "check_fields_adheres_to_phenopacket_allowed_values() (phenopacket_mapper.phenopacketmapper method)": [[1, "phenopacket_mapper.PhenopacketMapper.check_fields_adheres_to_phenopacket_allowed_values", false]], "code (phenopacket_mapper.data_standards.code.coding attribute)": [[15, "phenopacket_mapper.data_standards.code.Coding.code", false]], "code (phenopacket_mapper.data_standards.coding attribute)": [[12, "phenopacket_mapper.data_standards.Coding.code", false]], "codeableconcept (class in phenopacket_mapper.data_standards)": [[12, "phenopacket_mapper.data_standards.CodeableConcept", false]], "codeableconcept (class in phenopacket_mapper.data_standards.code)": [[15, "phenopacket_mapper.data_standards.code.CodeableConcept", false]], "codesystem (class in phenopacket_mapper.data_standards)": [[12, "phenopacket_mapper.data_standards.CodeSystem", false]], "codesystem (class in phenopacket_mapper.data_standards.code_system)": [[16, "phenopacket_mapper.data_standards.code_system.CodeSystem", false]], "coding (class in phenopacket_mapper.data_standards)": [[12, "phenopacket_mapper.data_standards.Coding", false]], "coding (class in phenopacket_mapper.data_standards.code)": [[15, "phenopacket_mapper.data_standards.code.Coding", false]], "coding (phenopacket_mapper.data_standards.code.codeableconcept attribute)": [[15, "phenopacket_mapper.data_standards.code.CodeableConcept.coding", false]], "coding (phenopacket_mapper.data_standards.codeableconcept attribute)": [[12, "phenopacket_mapper.data_standards.CodeableConcept.coding", false]], "compliance (phenopacket_mapper.data_standards.data_model.datamodelinstance attribute)": [[17, "phenopacket_mapper.data_standards.data_model.DataModelInstance.compliance", false]], "compliance (phenopacket_mapper.data_standards.datamodelinstance attribute)": [[12, "phenopacket_mapper.data_standards.DataModelInstance.compliance", false]], "data (phenopacket_mapper.data_standards.data_model.dataset attribute)": [[17, "phenopacket_mapper.data_standards.data_model.DataSet.data", false]], "data (phenopacket_mapper.data_standards.dataset attribute)": [[12, "phenopacket_mapper.data_standards.DataSet.data", false]], "data_frame (phenopacket_mapper.data_standards.data_model.dataset property)": [[17, "phenopacket_mapper.data_standards.data_model.DataSet.data_frame", false]], "data_frame (phenopacket_mapper.data_standards.dataset property)": [[12, "phenopacket_mapper.data_standards.DataSet.data_frame", false]], "data_model (phenopacket_mapper.data_standards.data_model.datamodelinstance attribute)": [[17, "phenopacket_mapper.data_standards.data_model.DataModelInstance.data_model", false]], "data_model (phenopacket_mapper.data_standards.data_model.dataset attribute)": [[17, "phenopacket_mapper.data_standards.data_model.DataSet.data_model", false]], "data_model (phenopacket_mapper.data_standards.datamodelinstance attribute)": [[12, "phenopacket_mapper.data_standards.DataModelInstance.data_model", false]], "data_model (phenopacket_mapper.data_standards.dataset attribute)": [[12, "phenopacket_mapper.data_standards.DataSet.data_model", false]], "data_model_name (phenopacket_mapper.data_standards.data_model.datamodel attribute)": [[17, "phenopacket_mapper.data_standards.data_model.DataModel.data_model_name", false]], "data_model_name (phenopacket_mapper.data_standards.datamodel attribute)": [[12, "phenopacket_mapper.data_standards.DataModel.data_model_name", false]], "data_model_name (phenopacket_mapper.datamodel attribute)": [[1, "phenopacket_mapper.DataModel.data_model_name", false]], "datafield (class in phenopacket_mapper.data_standards)": [[12, "phenopacket_mapper.data_standards.DataField", false]], "datafield (class in phenopacket_mapper.data_standards.data_model)": [[17, "phenopacket_mapper.data_standards.data_model.DataField", false]], "datafieldvalue (class in phenopacket_mapper.data_standards)": [[12, "phenopacket_mapper.data_standards.DataFieldValue", false]], "datafieldvalue (class in phenopacket_mapper.data_standards.data_model)": [[17, "phenopacket_mapper.data_standards.data_model.DataFieldValue", false]], "datamodel (class in phenopacket_mapper)": [[1, "phenopacket_mapper.DataModel", false]], "datamodel (class in phenopacket_mapper.data_standards)": [[12, "phenopacket_mapper.data_standards.DataModel", false]], "datamodel (class in phenopacket_mapper.data_standards.data_model)": [[17, "phenopacket_mapper.data_standards.data_model.DataModel", false]], "datamodel2phenopacketschema (class in phenopacket_mapper.data_standards.datamodel2phenopacketschema)": [[13, "phenopacket_mapper.data_standards.DataModel2PhenopacketSchema.DataModel2PhenopacketSchema", false]], "datamodelinstance (class in phenopacket_mapper.data_standards)": [[12, "phenopacket_mapper.data_standards.DataModelInstance", false]], "datamodelinstance (class in phenopacket_mapper.data_standards.data_model)": [[17, "phenopacket_mapper.data_standards.data_model.DataModelInstance", false]], "datareader (class in phenopacket_mapper.utils.io)": [[39, "phenopacket_mapper.utils.io.DataReader", false]], "datareader (class in phenopacket_mapper.utils.io.data_reader)": [[40, "phenopacket_mapper.utils.io.data_reader.DataReader", false]], "datasection (class in phenopacket_mapper.data_standards)": [[12, "phenopacket_mapper.data_standards.DataSection", false]], "datasection (class in phenopacket_mapper.data_standards.data_model)": [[17, "phenopacket_mapper.data_standards.data_model.DataSection", false]], "dataset (class in phenopacket_mapper.data_standards)": [[12, "phenopacket_mapper.data_standards.DataSet", false]], "dataset (class in phenopacket_mapper.data_standards.data_model)": [[17, "phenopacket_mapper.data_standards.data_model.DataSet", false]], "date (class in phenopacket_mapper.data_standards)": [[12, "phenopacket_mapper.data_standards.Date", false]], "date (class in phenopacket_mapper.data_standards.date)": [[21, "phenopacket_mapper.data_standards.date.Date", false]], "day (phenopacket_mapper.data_standards.date attribute)": [[12, "phenopacket_mapper.data_standards.Date.day", false]], "day (phenopacket_mapper.data_standards.date.date attribute)": [[21, "phenopacket_mapper.data_standards.date.Date.day", false]], "day_str (phenopacket_mapper.data_standards.date attribute)": [[12, "phenopacket_mapper.data_standards.Date.day_str", false]], "day_str (phenopacket_mapper.data_standards.date.date attribute)": [[21, "phenopacket_mapper.data_standards.date.Date.day_str", false]], "description (phenopacket_mapper.data_standards.data_model.datafield attribute)": [[17, "phenopacket_mapper.data_standards.data_model.DataField.description", false]], "description (phenopacket_mapper.data_standards.data_model.orgroup attribute)": [[17, "phenopacket_mapper.data_standards.data_model.OrGroup.description", false]], "description (phenopacket_mapper.data_standards.datafield attribute)": [[12, "phenopacket_mapper.data_standards.DataField.description", false]], "description (phenopacket_mapper.data_standards.orgroup attribute)": [[12, "phenopacket_mapper.data_standards.OrGroup.description", false]], "description (phenopacket_mapper.data_standards.value_set.valueset attribute)": [[22, "phenopacket_mapper.data_standards.value_set.ValueSet.description", false]], "description (phenopacket_mapper.data_standards.valueset attribute)": [[12, "phenopacket_mapper.data_standards.ValueSet.description", false]], "display (phenopacket_mapper.data_standards.code.coding attribute)": [[15, "phenopacket_mapper.data_standards.code.Coding.display", false]], "display (phenopacket_mapper.data_standards.coding attribute)": [[12, "phenopacket_mapper.data_standards.Coding.display", false]], "elements (phenopacket_mapper.data_standards.value_set.valueset attribute)": [[22, "phenopacket_mapper.data_standards.value_set.ValueSet.elements", false]], "elements (phenopacket_mapper.data_standards.valueset attribute)": [[12, "phenopacket_mapper.data_standards.ValueSet.elements", false]], "extend() (phenopacket_mapper.data_standards.value_set.valueset method)": [[22, "phenopacket_mapper.data_standards.value_set.ValueSet.extend", false]], "extend() (phenopacket_mapper.data_standards.valueset method)": [[12, "phenopacket_mapper.data_standards.ValueSet.extend", false]], "field (phenopacket_mapper.data_standards.data_model.datafieldvalue attribute)": [[17, "phenopacket_mapper.data_standards.data_model.DataFieldValue.field", false]], "field (phenopacket_mapper.data_standards.datafieldvalue attribute)": [[12, "phenopacket_mapper.data_standards.DataFieldValue.field", false]], "fields (phenopacket_mapper.data_standards.data_model.datamodel attribute)": [[17, "phenopacket_mapper.data_standards.data_model.DataModel.fields", false]], "fields (phenopacket_mapper.data_standards.data_model.datasection attribute)": [[17, "phenopacket_mapper.data_standards.data_model.DataSection.fields", false]], "fields (phenopacket_mapper.data_standards.data_model.orgroup attribute)": [[17, "phenopacket_mapper.data_standards.data_model.OrGroup.fields", false]], "fields (phenopacket_mapper.data_standards.datamodel attribute)": [[12, "phenopacket_mapper.data_standards.DataModel.fields", false]], "fields (phenopacket_mapper.data_standards.datasection attribute)": [[12, "phenopacket_mapper.data_standards.DataSection.fields", false]], "fields (phenopacket_mapper.data_standards.orgroup attribute)": [[12, "phenopacket_mapper.data_standards.OrGroup.fields", false]], "fields (phenopacket_mapper.datamodel attribute)": [[1, "phenopacket_mapper.DataModel.fields", false]], "formatted_string() (phenopacket_mapper.data_standards.date method)": [[12, "phenopacket_mapper.data_standards.Date.formatted_string", false]], "formatted_string() (phenopacket_mapper.data_standards.date.date method)": [[21, "phenopacket_mapper.data_standards.date.Date.formatted_string", false]], "from_datetime() (phenopacket_mapper.data_standards.date static method)": [[12, "phenopacket_mapper.data_standards.Date.from_datetime", false]], "from_datetime() (phenopacket_mapper.data_standards.date.date static method)": [[21, "phenopacket_mapper.data_standards.date.Date.from_datetime", false]], "from_file() (phenopacket_mapper.data_standards.data_model.datamodel static method)": [[17, "phenopacket_mapper.data_standards.data_model.DataModel.from_file", false]], "from_file() (phenopacket_mapper.data_standards.datamodel static method)": [[12, "phenopacket_mapper.data_standards.DataModel.from_file", false]], "from_file() (phenopacket_mapper.datamodel static method)": [[1, "phenopacket_mapper.DataModel.from_file", false]], "from_iso_8601() (phenopacket_mapper.data_standards.date static method)": [[12, "phenopacket_mapper.data_standards.Date.from_iso_8601", false]], "from_iso_8601() (phenopacket_mapper.data_standards.date.date static method)": [[21, "phenopacket_mapper.data_standards.date.Date.from_iso_8601", false]], "get() (in module phenopacket_mapper.api_requests)": [[2, "phenopacket_mapper.api_requests.get", false]], "get() (in module phenopacket_mapper.api_requests.get)": [[4, "phenopacket_mapper.api_requests.get.get", false]], "get() (phenopacket_mapper.api_requests.api_request_super_class.apirequestsuperclass method)": [[3, "phenopacket_mapper.api_requests.api_request_super_class.APIRequestSuperClass.get", false]], "get() (phenopacket_mapper.api_requests.apirequestsuperclass method)": [[2, "phenopacket_mapper.api_requests.APIRequestSuperClass.get", false]], "get() (phenopacket_mapper.api_requests.hpo_api_request.hpoapirequest method)": [[5, "phenopacket_mapper.api_requests.hpo_api_request.HPOAPIRequest.get", false]], "get() (phenopacket_mapper.api_requests.hpoapirequest method)": [[2, "phenopacket_mapper.api_requests.HPOAPIRequest.get", false]], "get() (phenopacket_mapper.api_requests.orpha_api_request.orphaapirequest method)": [[6, "phenopacket_mapper.api_requests.orpha_api_request.OrphaAPIRequest.get", false]], "get() (phenopacket_mapper.api_requests.orphaapirequest method)": [[2, "phenopacket_mapper.api_requests.OrphaAPIRequest.get", false]], "get_codesystem_by_namespace_prefx() (in module phenopacket_mapper.utils.parsing)": [[46, "phenopacket_mapper.utils.parsing.get_codesystem_by_namespace_prefx", false]], "get_codesystem_by_namespace_prefx() (in module phenopacket_mapper.utils.parsing.get_codesystem_by_namespace_prefix)": [[47, "phenopacket_mapper.utils.parsing.get_codesystem_by_namespace_prefix.get_codesystem_by_namespace_prefx", false]], "get_field() (phenopacket_mapper.data_standards.data_model.datamodel method)": [[17, "phenopacket_mapper.data_standards.data_model.DataModel.get_field", false]], "get_field() (phenopacket_mapper.data_standards.datamodel method)": [[12, "phenopacket_mapper.data_standards.DataModel.get_field", false]], "get_field() (phenopacket_mapper.datamodel method)": [[1, "phenopacket_mapper.DataModel.get_field", false]], "get_field_ids() (phenopacket_mapper.data_standards.data_model.datamodel method)": [[17, "phenopacket_mapper.data_standards.data_model.DataModel.get_field_ids", false]], "get_field_ids() (phenopacket_mapper.data_standards.datamodel method)": [[12, "phenopacket_mapper.data_standards.DataModel.get_field_ids", false]], "get_field_ids() (phenopacket_mapper.datamodel method)": [[1, "phenopacket_mapper.DataModel.get_field_ids", false]], "get_field_name() (in module phenopacket_mapper.utils.get_field_name)": [[38, "phenopacket_mapper.utils.get_field_name.get_field_name", false]], "handle_file_extension() (phenopacket_mapper.utils.io.data_reader.datareader method)": [[40, "phenopacket_mapper.utils.io.data_reader.DataReader.handle_file_extension", false]], "handle_file_extension() (phenopacket_mapper.utils.io.datareader method)": [[39, "phenopacket_mapper.utils.io.DataReader.handle_file_extension", false]], "head() (phenopacket_mapper.data_standards.data_model.dataset method)": [[17, "phenopacket_mapper.data_standards.data_model.DataSet.head", false]], "head() (phenopacket_mapper.data_standards.dataset method)": [[12, "phenopacket_mapper.data_standards.DataSet.head", false]], "height (phenopacket_mapper.data_standards.data_model.dataset property)": [[17, "phenopacket_mapper.data_standards.data_model.DataSet.height", false]], "height (phenopacket_mapper.data_standards.dataset property)": [[12, "phenopacket_mapper.data_standards.DataSet.height", false]], "hour (phenopacket_mapper.data_standards.date attribute)": [[12, "phenopacket_mapper.data_standards.Date.hour", false]], "hour (phenopacket_mapper.data_standards.date.date attribute)": [[21, "phenopacket_mapper.data_standards.date.Date.hour", false]], "hour_str (phenopacket_mapper.data_standards.date attribute)": [[12, "phenopacket_mapper.data_standards.Date.hour_str", false]], "hour_str (phenopacket_mapper.data_standards.date.date attribute)": [[21, "phenopacket_mapper.data_standards.date.Date.hour_str", false]], "hpoapirequest (class in phenopacket_mapper.api_requests)": [[2, "phenopacket_mapper.api_requests.HPOAPIRequest", false]], "hpoapirequest (class in phenopacket_mapper.api_requests.hpo_api_request)": [[5, "phenopacket_mapper.api_requests.hpo_api_request.HPOAPIRequest", false]], "id (phenopacket_mapper.data_standards.data_model.datafield attribute)": [[17, "phenopacket_mapper.data_standards.data_model.DataField.id", false]], "id (phenopacket_mapper.data_standards.data_model.datasection attribute)": [[17, "phenopacket_mapper.data_standards.data_model.DataSection.id", false]], "id (phenopacket_mapper.data_standards.data_model.orgroup attribute)": [[17, "phenopacket_mapper.data_standards.data_model.OrGroup.id", false]], "id (phenopacket_mapper.data_standards.datafield attribute)": [[12, "phenopacket_mapper.data_standards.DataField.id", false]], "id (phenopacket_mapper.data_standards.datasection attribute)": [[12, "phenopacket_mapper.data_standards.DataSection.id", false]], "id (phenopacket_mapper.data_standards.orgroup attribute)": [[12, "phenopacket_mapper.data_standards.OrGroup.id", false]], "iri_prefix (phenopacket_mapper.data_standards.code_system.codesystem attribute)": [[16, "phenopacket_mapper.data_standards.code_system.CodeSystem.iri_prefix", false]], "iri_prefix (phenopacket_mapper.data_standards.codesystem attribute)": [[12, "phenopacket_mapper.data_standards.CodeSystem.iri_prefix", false]], "iso_8601_datestring() (phenopacket_mapper.data_standards.date method)": [[12, "phenopacket_mapper.data_standards.Date.iso_8601_datestring", false]], "iso_8601_datestring() (phenopacket_mapper.data_standards.date.date method)": [[21, "phenopacket_mapper.data_standards.date.Date.iso_8601_datestring", false]], "load_data() (phenopacket_mapper.data_standards.data_model.datamodel method)": [[17, "phenopacket_mapper.data_standards.data_model.DataModel.load_data", false]], "load_data() (phenopacket_mapper.data_standards.datamodel method)": [[12, "phenopacket_mapper.data_standards.DataModel.load_data", false]], "load_data() (phenopacket_mapper.datamodel method)": [[1, "phenopacket_mapper.DataModel.load_data", false]], "load_data_using_data_model() (in module phenopacket_mapper.utils.io)": [[39, "phenopacket_mapper.utils.io.load_data_using_data_model", false]], "load_data_using_data_model() (in module phenopacket_mapper.utils.io.input)": [[41, "phenopacket_mapper.utils.io.input.load_data_using_data_model", false]], "load_data_using_data_model() (phenopacket_mapper.data_standards.data_model.datamodel static method)": [[17, "phenopacket_mapper.data_standards.data_model.DataModel.load_data_using_data_model", false]], "load_data_using_data_model() (phenopacket_mapper.data_standards.datamodel static method)": [[12, "phenopacket_mapper.data_standards.DataModel.load_data_using_data_model", false]], "load_data_using_data_model() (phenopacket_mapper.datamodel static method)": [[1, "phenopacket_mapper.DataModel.load_data_using_data_model", false]], "loc_default() (in module phenopacket_mapper.utils)": [[36, "phenopacket_mapper.utils.loc_default", false]], "loc_default() (in module phenopacket_mapper.utils.pandas_utils)": [[45, "phenopacket_mapper.utils.pandas_utils.loc_default", false]], "map() (phenopacket_mapper.mapping.mapper.phenopacketmapper method)": [[25, "phenopacket_mapper.mapping.mapper.PhenopacketMapper.map", false]], "map() (phenopacket_mapper.mapping.phenopacket_building_block.phenopacketbuildingblock method)": [[26, "phenopacket_mapper.mapping.phenopacket_building_block.PhenopacketBuildingBlock.map", false]], "map() (phenopacket_mapper.mapping.phenopacketbuildingblock method)": [[23, "phenopacket_mapper.mapping.PhenopacketBuildingBlock.map", false]], "map() (phenopacket_mapper.mapping.phenopacketmapper method)": [[23, "phenopacket_mapper.mapping.PhenopacketMapper.map", false]], "map() (phenopacket_mapper.phenopacketmapper method)": [[1, "phenopacket_mapper.PhenopacketMapper.map", false]], "map_single() (in module phenopacket_mapper.mapping)": [[23, "phenopacket_mapper.mapping.map_single", false]], "map_single() (in module phenopacket_mapper.mapping.phenopacket_building_block)": [[26, "phenopacket_mapper.mapping.phenopacket_building_block.map_single", false]], "max (phenopacket_mapper.data_standards.cardinality attribute)": [[12, "phenopacket_mapper.data_standards.Cardinality.max", false]], "max (phenopacket_mapper.data_standards.cardinality.cardinality attribute)": [[14, "phenopacket_mapper.data_standards.cardinality.Cardinality.max", false]], "min (phenopacket_mapper.data_standards.cardinality attribute)": [[12, "phenopacket_mapper.data_standards.Cardinality.min", false]], "min (phenopacket_mapper.data_standards.cardinality.cardinality attribute)": [[14, "phenopacket_mapper.data_standards.cardinality.Cardinality.min", false]], "minute (phenopacket_mapper.data_standards.date attribute)": [[12, "phenopacket_mapper.data_standards.Date.minute", false]], "minute (phenopacket_mapper.data_standards.date.date attribute)": [[21, "phenopacket_mapper.data_standards.date.Date.minute", false]], "minute_str (phenopacket_mapper.data_standards.date attribute)": [[12, "phenopacket_mapper.data_standards.Date.minute_str", false]], "minute_str (phenopacket_mapper.data_standards.date.date attribute)": [[21, "phenopacket_mapper.data_standards.date.Date.minute_str", false]], "module": [[1, "module-phenopacket_mapper", false], [2, "module-phenopacket_mapper.api_requests", false], [3, "module-phenopacket_mapper.api_requests.api_request_super_class", false], [4, "module-phenopacket_mapper.api_requests.get", false], [5, "module-phenopacket_mapper.api_requests.hpo_api_request", false], [6, "module-phenopacket_mapper.api_requests.orpha_api_request", false], [7, "module-phenopacket_mapper.cli", false], [12, "module-phenopacket_mapper.data_standards", false], [13, "module-phenopacket_mapper.data_standards.DataModel2PhenopacketSchema", false], [14, "module-phenopacket_mapper.data_standards.cardinality", false], [15, "module-phenopacket_mapper.data_standards.code", false], [16, "module-phenopacket_mapper.data_standards.code_system", false], [17, "module-phenopacket_mapper.data_standards.data_model", false], [18, "module-phenopacket_mapper.data_standards.data_models", false], [19, "module-phenopacket_mapper.data_standards.data_models.erdri_cds", false], [21, "module-phenopacket_mapper.data_standards.date", false], [22, "module-phenopacket_mapper.data_standards.value_set", false], [23, "module-phenopacket_mapper.mapping", false], [24, "module-phenopacket_mapper.mapping.map_field", false], [25, "module-phenopacket_mapper.mapping.mapper", false], [26, "module-phenopacket_mapper.mapping.phenopacket_building_block", false], [27, "module-phenopacket_mapper.pipeline", false], [32, "module-phenopacket_mapper.preprocessing", false], [33, "module-phenopacket_mapper.preprocessing.preprocess", false], [34, "module-phenopacket_mapper.preprocessing.preprocess_dict", false], [35, "module-phenopacket_mapper.preprocessing.preprocess_method", false], [36, "module-phenopacket_mapper.utils", false], [37, "module-phenopacket_mapper.utils.create_ipynb_in_code", false], [38, "module-phenopacket_mapper.utils.get_field_name", false], [39, "module-phenopacket_mapper.utils.io", false], [40, "module-phenopacket_mapper.utils.io.data_reader", false], [41, "module-phenopacket_mapper.utils.io.input", false], [42, "module-phenopacket_mapper.utils.io.output", false], [43, "module-phenopacket_mapper.utils.io.read_json", false], [44, "module-phenopacket_mapper.utils.io.read_xml", false], [45, "module-phenopacket_mapper.utils.pandas_utils", false], [46, "module-phenopacket_mapper.utils.parsing", false], [47, "module-phenopacket_mapper.utils.parsing.get_codesystem_by_namespace_prefix", false], [48, "module-phenopacket_mapper.utils.parsing.parse_coding", false], [49, "module-phenopacket_mapper.utils.parsing.parse_data_type", false], [50, "module-phenopacket_mapper.utils.parsing.parse_date", false], [51, "module-phenopacket_mapper.utils.parsing.parse_ordinal", false], [52, "module-phenopacket_mapper.utils.parsing.parse_primitive_data_value", false], [53, "module-phenopacket_mapper.utils.parsing.parse_value", false], [54, "module-phenopacket_mapper.utils.parsing.parse_value_set", false], [55, "module-phenopacket_mapper.utils.str_to_valid_id", false], [56, "module-phenopacket_mapper.validate", false], [57, "module-phenopacket_mapper.validate.validate", false]], "month (phenopacket_mapper.data_standards.date attribute)": [[12, "phenopacket_mapper.data_standards.Date.month", false]], "month (phenopacket_mapper.data_standards.date.date attribute)": [[21, "phenopacket_mapper.data_standards.date.Date.month", false]], "month_str (phenopacket_mapper.data_standards.date attribute)": [[12, "phenopacket_mapper.data_standards.Date.month_str", false]], "month_str (phenopacket_mapper.data_standards.date.date attribute)": [[21, "phenopacket_mapper.data_standards.date.Date.month_str", false]], "name (phenopacket_mapper.data_standards.code_system.codesystem attribute)": [[16, "phenopacket_mapper.data_standards.code_system.CodeSystem.name", false]], "name (phenopacket_mapper.data_standards.codesystem attribute)": [[12, "phenopacket_mapper.data_standards.CodeSystem.name", false]], "name (phenopacket_mapper.data_standards.data_model.datafield attribute)": [[17, "phenopacket_mapper.data_standards.data_model.DataField.name", false]], "name (phenopacket_mapper.data_standards.data_model.datasection attribute)": [[17, "phenopacket_mapper.data_standards.data_model.DataSection.name", false]], "name (phenopacket_mapper.data_standards.data_model.orgroup attribute)": [[17, "phenopacket_mapper.data_standards.data_model.OrGroup.name", false]], "name (phenopacket_mapper.data_standards.datafield attribute)": [[12, "phenopacket_mapper.data_standards.DataField.name", false]], "name (phenopacket_mapper.data_standards.datasection attribute)": [[12, "phenopacket_mapper.data_standards.DataSection.name", false]], "name (phenopacket_mapper.data_standards.orgroup attribute)": [[12, "phenopacket_mapper.data_standards.OrGroup.name", false]], "name (phenopacket_mapper.data_standards.value_set.valueset attribute)": [[22, "phenopacket_mapper.data_standards.value_set.ValueSet.name", false]], "name (phenopacket_mapper.data_standards.valueset attribute)": [[12, "phenopacket_mapper.data_standards.ValueSet.name", false]], "namespace_prefix (phenopacket_mapper.data_standards.code_system.codesystem attribute)": [[16, "phenopacket_mapper.data_standards.code_system.CodeSystem.namespace_prefix", false]], "namespace_prefix (phenopacket_mapper.data_standards.codesystem attribute)": [[12, "phenopacket_mapper.data_standards.CodeSystem.namespace_prefix", false]], "notebookbuilder (class in phenopacket_mapper.utils)": [[36, "phenopacket_mapper.utils.NotebookBuilder", false]], "notebookbuilder (class in phenopacket_mapper.utils.create_ipynb_in_code)": [[37, "phenopacket_mapper.utils.create_ipynb_in_code.NotebookBuilder", false]], "orgroup (class in phenopacket_mapper.data_standards)": [[12, "phenopacket_mapper.data_standards.OrGroup", false]], "orgroup (class in phenopacket_mapper.data_standards.data_model)": [[17, "phenopacket_mapper.data_standards.data_model.OrGroup", false]], "orphaapirequest (class in phenopacket_mapper.api_requests)": [[2, "phenopacket_mapper.api_requests.OrphaAPIRequest", false]], "orphaapirequest (class in phenopacket_mapper.api_requests.orpha_api_request)": [[6, "phenopacket_mapper.api_requests.orpha_api_request.OrphaAPIRequest", false]], "parse_bool() (in module phenopacket_mapper.utils.parsing)": [[46, "phenopacket_mapper.utils.parsing.parse_bool", false]], "parse_bool() (in module phenopacket_mapper.utils.parsing.parse_primitive_data_value)": [[52, "phenopacket_mapper.utils.parsing.parse_primitive_data_value.parse_bool", false]], "parse_coding() (in module phenopacket_mapper.utils.parsing)": [[46, "phenopacket_mapper.utils.parsing.parse_coding", false]], "parse_coding() (in module phenopacket_mapper.utils.parsing.parse_coding)": [[48, "phenopacket_mapper.utils.parsing.parse_coding.parse_coding", false]], "parse_coding() (phenopacket_mapper.data_standards.code.coding static method)": [[15, "phenopacket_mapper.data_standards.code.Coding.parse_coding", false]], "parse_coding() (phenopacket_mapper.data_standards.coding static method)": [[12, "phenopacket_mapper.data_standards.Coding.parse_coding", false]], "parse_data_type() (in module phenopacket_mapper.data_standards.data_models)": [[18, "phenopacket_mapper.data_standards.data_models.parse_data_type", false]], "parse_data_type() (in module phenopacket_mapper.utils.parsing)": [[46, "phenopacket_mapper.utils.parsing.parse_data_type", false]], "parse_data_type() (in module phenopacket_mapper.utils.parsing.parse_data_type)": [[49, "phenopacket_mapper.utils.parsing.parse_data_type.parse_data_type", false]], "parse_date() (in module phenopacket_mapper.utils.parsing)": [[46, "phenopacket_mapper.utils.parsing.parse_date", false]], "parse_date() (in module phenopacket_mapper.utils.parsing.parse_date)": [[50, "phenopacket_mapper.utils.parsing.parse_date.parse_date", false]], "parse_date() (phenopacket_mapper.data_standards.date static method)": [[12, "phenopacket_mapper.data_standards.Date.parse_date", false]], "parse_date() (phenopacket_mapper.data_standards.date.date static method)": [[21, "phenopacket_mapper.data_standards.date.Date.parse_date", false]], "parse_float() (in module phenopacket_mapper.utils.parsing)": [[46, "phenopacket_mapper.utils.parsing.parse_float", false]], "parse_float() (in module phenopacket_mapper.utils.parsing.parse_primitive_data_value)": [[52, "phenopacket_mapper.utils.parsing.parse_primitive_data_value.parse_float", false]], "parse_int() (in module phenopacket_mapper.utils.parsing)": [[46, "phenopacket_mapper.utils.parsing.parse_int", false]], "parse_int() (in module phenopacket_mapper.utils.parsing.parse_primitive_data_value)": [[52, "phenopacket_mapper.utils.parsing.parse_primitive_data_value.parse_int", false]], "parse_ordinal() (in module phenopacket_mapper.utils.parsing)": [[46, "phenopacket_mapper.utils.parsing.parse_ordinal", false]], "parse_ordinal() (in module phenopacket_mapper.utils.parsing.parse_ordinal)": [[51, "phenopacket_mapper.utils.parsing.parse_ordinal.parse_ordinal", false]], "parse_primitive_data_value() (in module phenopacket_mapper.utils.parsing)": [[46, "phenopacket_mapper.utils.parsing.parse_primitive_data_value", false]], "parse_primitive_data_value() (in module phenopacket_mapper.utils.parsing.parse_primitive_data_value)": [[52, "phenopacket_mapper.utils.parsing.parse_primitive_data_value.parse_primitive_data_value", false]], "parse_single_data_type() (in module phenopacket_mapper.utils.parsing)": [[46, "phenopacket_mapper.utils.parsing.parse_single_data_type", false]], "parse_single_data_type() (in module phenopacket_mapper.utils.parsing.parse_data_type)": [[49, "phenopacket_mapper.utils.parsing.parse_data_type.parse_single_data_type", false]], "parse_value() (in module phenopacket_mapper.utils.parsing)": [[46, "phenopacket_mapper.utils.parsing.parse_value", false]], "parse_value() (in module phenopacket_mapper.utils.parsing.parse_value)": [[53, "phenopacket_mapper.utils.parsing.parse_value.parse_value", false]], "parse_value_set() (in module phenopacket_mapper.utils.parsing)": [[46, "phenopacket_mapper.utils.parsing.parse_value_set", false]], "parse_value_set() (in module phenopacket_mapper.utils.parsing.parse_value_set)": [[54, "phenopacket_mapper.utils.parsing.parse_value_set.parse_value_set", false]], "parse_value_set() (phenopacket_mapper.data_standards.value_set.valueset static method)": [[22, "phenopacket_mapper.data_standards.value_set.ValueSet.parse_value_set", false]], "parse_value_set() (phenopacket_mapper.data_standards.valueset static method)": [[12, "phenopacket_mapper.data_standards.ValueSet.parse_value_set", false]], "parse_xml() (in module phenopacket_mapper.utils.io)": [[39, "phenopacket_mapper.utils.io.parse_xml", false]], "parse_xml() (in module phenopacket_mapper.utils.io.read_xml)": [[44, "phenopacket_mapper.utils.io.read_xml.parse_xml", false]], "phenopacket_mapper": [[1, "module-phenopacket_mapper", false]], "phenopacket_mapper.api_requests": [[2, "module-phenopacket_mapper.api_requests", false]], "phenopacket_mapper.api_requests.api_request_super_class": [[3, "module-phenopacket_mapper.api_requests.api_request_super_class", false]], "phenopacket_mapper.api_requests.get": [[4, "module-phenopacket_mapper.api_requests.get", false]], "phenopacket_mapper.api_requests.hpo_api_request": [[5, "module-phenopacket_mapper.api_requests.hpo_api_request", false]], "phenopacket_mapper.api_requests.orpha_api_request": [[6, "module-phenopacket_mapper.api_requests.orpha_api_request", false]], "phenopacket_mapper.cli": [[7, "module-phenopacket_mapper.cli", false]], "phenopacket_mapper.data_standards": [[12, "module-phenopacket_mapper.data_standards", false]], "phenopacket_mapper.data_standards.cardinality": [[14, "module-phenopacket_mapper.data_standards.cardinality", false]], "phenopacket_mapper.data_standards.code": [[15, "module-phenopacket_mapper.data_standards.code", false]], "phenopacket_mapper.data_standards.code_system": [[16, "module-phenopacket_mapper.data_standards.code_system", false]], "phenopacket_mapper.data_standards.data_model": [[17, "module-phenopacket_mapper.data_standards.data_model", false]], "phenopacket_mapper.data_standards.data_models": [[18, "module-phenopacket_mapper.data_standards.data_models", false]], "phenopacket_mapper.data_standards.data_models.erdri_cds": [[19, "module-phenopacket_mapper.data_standards.data_models.erdri_cds", false]], "phenopacket_mapper.data_standards.datamodel2phenopacketschema": [[13, "module-phenopacket_mapper.data_standards.DataModel2PhenopacketSchema", false]], "phenopacket_mapper.data_standards.date": [[21, "module-phenopacket_mapper.data_standards.date", false]], "phenopacket_mapper.data_standards.value_set": [[22, "module-phenopacket_mapper.data_standards.value_set", false]], "phenopacket_mapper.mapping": [[23, "module-phenopacket_mapper.mapping", false]], "phenopacket_mapper.mapping.map_field": [[24, "module-phenopacket_mapper.mapping.map_field", false]], "phenopacket_mapper.mapping.mapper": [[25, "module-phenopacket_mapper.mapping.mapper", false]], "phenopacket_mapper.mapping.phenopacket_building_block": [[26, "module-phenopacket_mapper.mapping.phenopacket_building_block", false]], "phenopacket_mapper.pipeline": [[27, "module-phenopacket_mapper.pipeline", false]], "phenopacket_mapper.preprocessing": [[32, "module-phenopacket_mapper.preprocessing", false]], "phenopacket_mapper.preprocessing.preprocess": [[33, "module-phenopacket_mapper.preprocessing.preprocess", false]], "phenopacket_mapper.preprocessing.preprocess_dict": [[34, "module-phenopacket_mapper.preprocessing.preprocess_dict", false]], "phenopacket_mapper.preprocessing.preprocess_method": [[35, "module-phenopacket_mapper.preprocessing.preprocess_method", false]], "phenopacket_mapper.utils": [[36, "module-phenopacket_mapper.utils", false]], "phenopacket_mapper.utils.create_ipynb_in_code": [[37, "module-phenopacket_mapper.utils.create_ipynb_in_code", false]], "phenopacket_mapper.utils.get_field_name": [[38, "module-phenopacket_mapper.utils.get_field_name", false]], "phenopacket_mapper.utils.io": [[39, "module-phenopacket_mapper.utils.io", false]], "phenopacket_mapper.utils.io.data_reader": [[40, "module-phenopacket_mapper.utils.io.data_reader", false]], "phenopacket_mapper.utils.io.input": [[41, "module-phenopacket_mapper.utils.io.input", false]], "phenopacket_mapper.utils.io.output": [[42, "module-phenopacket_mapper.utils.io.output", false]], "phenopacket_mapper.utils.io.read_json": [[43, "module-phenopacket_mapper.utils.io.read_json", false]], "phenopacket_mapper.utils.io.read_xml": [[44, "module-phenopacket_mapper.utils.io.read_xml", false]], "phenopacket_mapper.utils.pandas_utils": [[45, "module-phenopacket_mapper.utils.pandas_utils", false]], "phenopacket_mapper.utils.parsing": [[46, "module-phenopacket_mapper.utils.parsing", false]], "phenopacket_mapper.utils.parsing.get_codesystem_by_namespace_prefix": [[47, "module-phenopacket_mapper.utils.parsing.get_codesystem_by_namespace_prefix", false]], "phenopacket_mapper.utils.parsing.parse_coding": [[48, "module-phenopacket_mapper.utils.parsing.parse_coding", false]], "phenopacket_mapper.utils.parsing.parse_data_type": [[49, "module-phenopacket_mapper.utils.parsing.parse_data_type", false]], "phenopacket_mapper.utils.parsing.parse_date": [[50, "module-phenopacket_mapper.utils.parsing.parse_date", false]], "phenopacket_mapper.utils.parsing.parse_ordinal": [[51, "module-phenopacket_mapper.utils.parsing.parse_ordinal", false]], "phenopacket_mapper.utils.parsing.parse_primitive_data_value": [[52, "module-phenopacket_mapper.utils.parsing.parse_primitive_data_value", false]], "phenopacket_mapper.utils.parsing.parse_value": [[53, "module-phenopacket_mapper.utils.parsing.parse_value", false]], "phenopacket_mapper.utils.parsing.parse_value_set": [[54, "module-phenopacket_mapper.utils.parsing.parse_value_set", false]], "phenopacket_mapper.utils.str_to_valid_id": [[55, "module-phenopacket_mapper.utils.str_to_valid_id", false]], "phenopacket_mapper.validate": [[56, "module-phenopacket_mapper.validate", false]], "phenopacket_mapper.validate.validate": [[57, "module-phenopacket_mapper.validate.validate", false]], "phenopacketbuildingblock (class in phenopacket_mapper.mapping)": [[23, "phenopacket_mapper.mapping.PhenopacketBuildingBlock", false]], "phenopacketbuildingblock (class in phenopacket_mapper.mapping.phenopacket_building_block)": [[26, "phenopacket_mapper.mapping.phenopacket_building_block.PhenopacketBuildingBlock", false]], "phenopacketmapper (class in phenopacket_mapper)": [[1, "phenopacket_mapper.PhenopacketMapper", false]], "phenopacketmapper (class in phenopacket_mapper.mapping)": [[23, "phenopacket_mapper.mapping.PhenopacketMapper", false]], "phenopacketmapper (class in phenopacket_mapper.mapping.mapper)": [[25, "phenopacket_mapper.mapping.mapper.PhenopacketMapper", false]], "preprocess() (in module phenopacket_mapper.preprocessing)": [[32, "phenopacket_mapper.preprocessing.preprocess", false]], "preprocess() (in module phenopacket_mapper.preprocessing.preprocess)": [[33, "phenopacket_mapper.preprocessing.preprocess.preprocess", false]], "preprocess() (phenopacket_mapper.data_standards.data_model.dataset method)": [[17, "phenopacket_mapper.data_standards.data_model.DataSet.preprocess", false]], "preprocess() (phenopacket_mapper.data_standards.dataset method)": [[12, "phenopacket_mapper.data_standards.DataSet.preprocess", false]], "preprocess_dict() (in module phenopacket_mapper.preprocessing)": [[32, "phenopacket_mapper.preprocessing.preprocess_dict", false]], "preprocess_dict() (in module phenopacket_mapper.preprocessing.preprocess_dict)": [[34, "phenopacket_mapper.preprocessing.preprocess_dict.preprocess_dict", false]], "preprocess_method() (in module phenopacket_mapper.preprocessing)": [[32, "phenopacket_mapper.preprocessing.preprocess_method", false]], "preprocess_method() (in module phenopacket_mapper.preprocessing.preprocess_method)": [[35, "phenopacket_mapper.preprocessing.preprocess_method.preprocess_method", false]], "protobuf_timestamp() (phenopacket_mapper.data_standards.date method)": [[12, "phenopacket_mapper.data_standards.Date.protobuf_timestamp", false]], "protobuf_timestamp() (phenopacket_mapper.data_standards.date.date method)": [[21, "phenopacket_mapper.data_standards.date.Date.protobuf_timestamp", false]], "read_data_model() (in module phenopacket_mapper.utils.io)": [[39, "phenopacket_mapper.utils.io.read_data_model", false]], "read_data_model() (in module phenopacket_mapper.utils.io.input)": [[41, "phenopacket_mapper.utils.io.input.read_data_model", false]], "read_json() (in module phenopacket_mapper.utils.io)": [[39, "phenopacket_mapper.utils.io.read_json", false]], "read_json() (in module phenopacket_mapper.utils.io.read_json)": [[43, "phenopacket_mapper.utils.io.read_json.read_json", false]], "read_phenopacket_from_json() (in module phenopacket_mapper.utils.io)": [[39, "phenopacket_mapper.utils.io.read_phenopacket_from_json", false]], "read_phenopacket_from_json() (in module phenopacket_mapper.utils.io.input)": [[41, "phenopacket_mapper.utils.io.input.read_phenopacket_from_json", false]], "read_phenopackets() (in module phenopacket_mapper.utils.io)": [[39, "phenopacket_mapper.utils.io.read_phenopackets", false]], "read_phenopackets() (in module phenopacket_mapper.utils.io.input)": [[41, "phenopacket_mapper.utils.io.input.read_phenopackets", false]], "read_validate() (in module phenopacket_mapper.validate)": [[56, "phenopacket_mapper.validate.read_validate", false]], "read_validate() (in module phenopacket_mapper.validate.validate)": [[57, "phenopacket_mapper.validate.validate.read_validate", false]], "read_xml() (in module phenopacket_mapper.utils.io)": [[39, "phenopacket_mapper.utils.io.read_xml", false]], "read_xml() (in module phenopacket_mapper.utils.io.read_xml)": [[44, "phenopacket_mapper.utils.io.read_xml.read_xml", false]], "remove_at_symbols() (in module phenopacket_mapper.utils.io.read_xml)": [[44, "phenopacket_mapper.utils.io.read_xml.remove_at_symbols", false]], "remove_duplicates() (phenopacket_mapper.data_standards.value_set.valueset method)": [[22, "phenopacket_mapper.data_standards.value_set.ValueSet.remove_duplicates", false]], "remove_duplicates() (phenopacket_mapper.data_standards.valueset method)": [[12, "phenopacket_mapper.data_standards.ValueSet.remove_duplicates", false]], "required (phenopacket_mapper.data_standards.data_model.datafield attribute)": [[17, "phenopacket_mapper.data_standards.data_model.DataField.required", false]], "required (phenopacket_mapper.data_standards.data_model.datasection attribute)": [[17, "phenopacket_mapper.data_standards.data_model.DataSection.required", false]], "required (phenopacket_mapper.data_standards.data_model.orgroup attribute)": [[17, "phenopacket_mapper.data_standards.data_model.OrGroup.required", false]], "required (phenopacket_mapper.data_standards.datafield attribute)": [[12, "phenopacket_mapper.data_standards.DataField.required", false]], "required (phenopacket_mapper.data_standards.datasection attribute)": [[12, "phenopacket_mapper.data_standards.DataSection.required", false]], "required (phenopacket_mapper.data_standards.orgroup attribute)": [[12, "phenopacket_mapper.data_standards.OrGroup.required", false]], "resources (phenopacket_mapper.data_standards.data_model.datamodel attribute)": [[17, "phenopacket_mapper.data_standards.data_model.DataModel.resources", false]], "resources (phenopacket_mapper.data_standards.datamodel attribute)": [[12, "phenopacket_mapper.data_standards.DataModel.resources", false]], "resources (phenopacket_mapper.data_standards.value_set.valueset property)": [[22, "phenopacket_mapper.data_standards.value_set.ValueSet.resources", false]], "resources (phenopacket_mapper.data_standards.valueset property)": [[12, "phenopacket_mapper.data_standards.ValueSet.resources", false]], "resources (phenopacket_mapper.datamodel attribute)": [[1, "phenopacket_mapper.DataModel.resources", false]], "row_no (phenopacket_mapper.data_standards.data_model.datafieldvalue attribute)": [[17, "phenopacket_mapper.data_standards.data_model.DataFieldValue.row_no", false]], "row_no (phenopacket_mapper.data_standards.data_model.datamodelinstance attribute)": [[17, "phenopacket_mapper.data_standards.data_model.DataModelInstance.row_no", false]], "row_no (phenopacket_mapper.data_standards.datafieldvalue attribute)": [[12, "phenopacket_mapper.data_standards.DataFieldValue.row_no", false]], "row_no (phenopacket_mapper.data_standards.datamodelinstance attribute)": [[12, "phenopacket_mapper.data_standards.DataModelInstance.row_no", false]], "second (phenopacket_mapper.data_standards.date attribute)": [[12, "phenopacket_mapper.data_standards.Date.second", false]], "second (phenopacket_mapper.data_standards.date.date attribute)": [[21, "phenopacket_mapper.data_standards.date.Date.second", false]], "second_str (phenopacket_mapper.data_standards.date attribute)": [[12, "phenopacket_mapper.data_standards.Date.second_str", false]], "second_str (phenopacket_mapper.data_standards.date.date attribute)": [[21, "phenopacket_mapper.data_standards.date.Date.second_str", false]], "set_version() (phenopacket_mapper.data_standards.code_system.codesystem method)": [[16, "phenopacket_mapper.data_standards.code_system.CodeSystem.set_version", false]], "set_version() (phenopacket_mapper.data_standards.codesystem method)": [[12, "phenopacket_mapper.data_standards.CodeSystem.set_version", false]], "specification (phenopacket_mapper.data_standards.data_model.datafield attribute)": [[17, "phenopacket_mapper.data_standards.data_model.DataField.specification", false]], "specification (phenopacket_mapper.data_standards.datafield attribute)": [[12, "phenopacket_mapper.data_standards.DataField.specification", false]], "str_to_valid_id() (in module phenopacket_mapper.utils)": [[36, "phenopacket_mapper.utils.str_to_valid_id", false]], "str_to_valid_id() (in module phenopacket_mapper.utils.str_to_valid_id)": [[55, "phenopacket_mapper.utils.str_to_valid_id.str_to_valid_id", false]], "synonyms (phenopacket_mapper.data_standards.code_system.codesystem attribute)": [[16, "phenopacket_mapper.data_standards.code_system.CodeSystem.synonyms", false]], "synonyms (phenopacket_mapper.data_standards.codesystem attribute)": [[12, "phenopacket_mapper.data_standards.CodeSystem.synonyms", false]], "system (phenopacket_mapper.data_standards.code.coding attribute)": [[15, "phenopacket_mapper.data_standards.code.Coding.system", false]], "system (phenopacket_mapper.data_standards.coding attribute)": [[12, "phenopacket_mapper.data_standards.Coding.system", false]], "text (phenopacket_mapper.data_standards.code.codeableconcept attribute)": [[15, "phenopacket_mapper.data_standards.code.CodeableConcept.text", false]], "text (phenopacket_mapper.data_standards.code.coding attribute)": [[15, "phenopacket_mapper.data_standards.code.Coding.text", false]], "text (phenopacket_mapper.data_standards.codeableconcept attribute)": [[12, "phenopacket_mapper.data_standards.CodeableConcept.text", false]], "text (phenopacket_mapper.data_standards.coding attribute)": [[12, "phenopacket_mapper.data_standards.Coding.text", false]], "url (phenopacket_mapper.data_standards.code_system.codesystem attribute)": [[16, "phenopacket_mapper.data_standards.code_system.CodeSystem.url", false]], "url (phenopacket_mapper.data_standards.codesystem attribute)": [[12, "phenopacket_mapper.data_standards.CodeSystem.url", false]], "validate() (in module phenopacket_mapper.validate)": [[56, "phenopacket_mapper.validate.validate", false]], "validate() (in module phenopacket_mapper.validate.validate)": [[57, "phenopacket_mapper.validate.validate.validate", false]], "validate() (phenopacket_mapper.data_standards.data_model.datafieldvalue method)": [[17, "phenopacket_mapper.data_standards.data_model.DataFieldValue.validate", false]], "validate() (phenopacket_mapper.data_standards.data_model.datamodelinstance method)": [[17, "phenopacket_mapper.data_standards.data_model.DataModelInstance.validate", false]], "validate() (phenopacket_mapper.data_standards.datafieldvalue method)": [[12, "phenopacket_mapper.data_standards.DataFieldValue.validate", false]], "validate() (phenopacket_mapper.data_standards.datamodelinstance method)": [[12, "phenopacket_mapper.data_standards.DataModelInstance.validate", false]], "validate() (phenopacket_mapper.validate.validate.validator method)": [[57, "phenopacket_mapper.validate.validate.Validator.validate", false]], "validator (class in phenopacket_mapper.validate.validate)": [[57, "phenopacket_mapper.validate.validate.Validator", false]], "value (phenopacket_mapper.data_standards.data_model.datafieldvalue attribute)": [[17, "phenopacket_mapper.data_standards.data_model.DataFieldValue.value", false]], "value (phenopacket_mapper.data_standards.datafieldvalue attribute)": [[12, "phenopacket_mapper.data_standards.DataFieldValue.value", false]], "values (phenopacket_mapper.data_standards.data_model.datamodelinstance attribute)": [[17, "phenopacket_mapper.data_standards.data_model.DataModelInstance.values", false]], "values (phenopacket_mapper.data_standards.datamodelinstance attribute)": [[12, "phenopacket_mapper.data_standards.DataModelInstance.values", false]], "valueset (class in phenopacket_mapper.data_standards)": [[12, "phenopacket_mapper.data_standards.ValueSet", false]], "valueset (class in phenopacket_mapper.data_standards.value_set)": [[22, "phenopacket_mapper.data_standards.value_set.ValueSet", false]], "version (phenopacket_mapper.data_standards.code_system.codesystem attribute)": [[16, "phenopacket_mapper.data_standards.code_system.CodeSystem.version", false]], "version (phenopacket_mapper.data_standards.codesystem attribute)": [[12, "phenopacket_mapper.data_standards.CodeSystem.version", false]], "width (phenopacket_mapper.data_standards.data_model.dataset property)": [[17, "phenopacket_mapper.data_standards.data_model.DataSet.width", false]], "width (phenopacket_mapper.data_standards.dataset property)": [[12, "phenopacket_mapper.data_standards.DataSet.width", false]], "write() (in module phenopacket_mapper.utils.io)": [[39, "phenopacket_mapper.utils.io.write", false]], "write() (in module phenopacket_mapper.utils.io.output)": [[42, "phenopacket_mapper.utils.io.output.write", false]], "write_to_file() (phenopacket_mapper.utils.create_ipynb_in_code.notebookbuilder method)": [[37, "phenopacket_mapper.utils.create_ipynb_in_code.NotebookBuilder.write_to_file", false]], "write_to_file() (phenopacket_mapper.utils.notebookbuilder method)": [[36, "phenopacket_mapper.utils.NotebookBuilder.write_to_file", false]], "year (phenopacket_mapper.data_standards.date attribute)": [[12, "phenopacket_mapper.data_standards.Date.year", false]], "year (phenopacket_mapper.data_standards.date.date attribute)": [[21, "phenopacket_mapper.data_standards.date.Date.year", false]], "year_str (phenopacket_mapper.data_standards.date attribute)": [[12, "phenopacket_mapper.data_standards.Date.year_str", false]], "year_str (phenopacket_mapper.data_standards.date.date attribute)": [[21, "phenopacket_mapper.data_standards.date.Date.year_str", false]]}, "objects": {"": [[1, 0, 0, "-", "phenopacket_mapper"]], "phenopacket_mapper": [[1, 1, 1, "", "DataModel"], [1, 1, 1, "", "PhenopacketMapper"], [2, 0, 0, "-", "api_requests"], [7, 0, 0, "-", "cli"], [12, 0, 0, "-", "data_standards"], [23, 0, 0, "-", "mapping"], [27, 0, 0, "-", "pipeline"], [32, 0, 0, "-", "preprocessing"], [36, 0, 0, "-", "utils"], [56, 0, 0, "-", "validate"]], "phenopacket_mapper.DataModel": [[1, 2, 1, "", "data_model_name"], [1, 2, 1, "", "fields"], [1, 3, 1, "", "from_file"], [1, 3, 1, "", "get_field"], [1, 3, 1, "", "get_field_ids"], [1, 3, 1, "", "load_data"], [1, 3, 1, "", "load_data_using_data_model"], [1, 2, 1, "", "resources"]], "phenopacket_mapper.PhenopacketMapper": [[1, 3, 1, "", "check_fields_adheres_to_phenopacket_allowed_values"], [1, 3, 1, "", "map"]], "phenopacket_mapper.api_requests": [[2, 1, 1, "", "APIRequestSuperClass"], [2, 1, 1, "", "HPOAPIRequest"], [2, 1, 1, "", "OrphaAPIRequest"], [3, 0, 0, "-", "api_request_super_class"], [4, 0, 0, "-", "get"], [5, 0, 0, "-", "hpo_api_request"], [6, 0, 0, "-", "orpha_api_request"]], "phenopacket_mapper.api_requests.APIRequestSuperClass": [[2, 3, 1, "", "get"]], "phenopacket_mapper.api_requests.HPOAPIRequest": [[2, 2, 1, "", "api_base_url"], [2, 3, 1, "", "get"]], "phenopacket_mapper.api_requests.OrphaAPIRequest": [[2, 2, 1, "", "api_base_url"], [2, 3, 1, "", "get"]], "phenopacket_mapper.api_requests.api_request_super_class": [[3, 1, 1, "", "APIRequestSuperClass"]], "phenopacket_mapper.api_requests.api_request_super_class.APIRequestSuperClass": [[3, 3, 1, "", "get"]], "phenopacket_mapper.api_requests.get": [[4, 4, 1, "", "get"]], "phenopacket_mapper.api_requests.hpo_api_request": [[5, 1, 1, "", "HPOAPIRequest"]], "phenopacket_mapper.api_requests.hpo_api_request.HPOAPIRequest": [[5, 2, 1, "", "api_base_url"], [5, 3, 1, "", "get"]], "phenopacket_mapper.api_requests.orpha_api_request": [[6, 1, 1, "", "OrphaAPIRequest"]], "phenopacket_mapper.api_requests.orpha_api_request.OrphaAPIRequest": [[6, 2, 1, "", "api_base_url"], [6, 3, 1, "", "get"]], "phenopacket_mapper.data_standards": [[12, 1, 1, "", "Cardinality"], [12, 1, 1, "", "CodeSystem"], [12, 1, 1, "", "CodeableConcept"], [12, 1, 1, "", "Coding"], [12, 1, 1, "", "DataField"], [12, 1, 1, "", "DataFieldValue"], [12, 1, 1, "", "DataModel"], [13, 0, 0, "-", "DataModel2PhenopacketSchema"], [12, 1, 1, "", "DataModelInstance"], [12, 1, 1, "", "DataSection"], [12, 1, 1, "", "DataSet"], [12, 1, 1, "", "Date"], [12, 1, 1, "", "OrGroup"], [12, 1, 1, "", "ValueSet"], [14, 0, 0, "-", "cardinality"], [15, 0, 0, "-", "code"], [16, 0, 0, "-", "code_system"], [17, 0, 0, "-", "data_model"], [18, 0, 0, "-", "data_models"], [21, 0, 0, "-", "date"], [22, 0, 0, "-", "value_set"]], "phenopacket_mapper.data_standards.Cardinality": [[12, 2, 1, "", "max"], [12, 2, 1, "", "min"]], "phenopacket_mapper.data_standards.CodeSystem": [[12, 2, 1, "", "iri_prefix"], [12, 2, 1, "", "name"], [12, 2, 1, "", "namespace_prefix"], [12, 3, 1, "", "set_version"], [12, 2, 1, "", "synonyms"], [12, 2, 1, "", "url"], [12, 2, 1, "", "version"]], "phenopacket_mapper.data_standards.CodeableConcept": [[12, 2, 1, "", "coding"], [12, 2, 1, "", "text"]], "phenopacket_mapper.data_standards.Coding": [[12, 2, 1, "", "code"], [12, 2, 1, "", "display"], [12, 3, 1, "", "parse_coding"], [12, 2, 1, "", "system"], [12, 2, 1, "", "text"]], "phenopacket_mapper.data_standards.DataField": [[12, 2, 1, "", "cardinality"], [12, 2, 1, "", "description"], [12, 2, 1, "", "id"], [12, 2, 1, "", "name"], [12, 2, 1, "", "required"], [12, 2, 1, "", "specification"]], "phenopacket_mapper.data_standards.DataFieldValue": [[12, 2, 1, "", "field"], [12, 2, 1, "", "row_no"], [12, 3, 1, "", "validate"], [12, 2, 1, "", "value"]], "phenopacket_mapper.data_standards.DataModel": [[12, 2, 1, "", "data_model_name"], [12, 2, 1, "", "fields"], [12, 3, 1, "", "from_file"], [12, 3, 1, "", "get_field"], [12, 3, 1, "", "get_field_ids"], [12, 3, 1, "", "load_data"], [12, 3, 1, "", "load_data_using_data_model"], [12, 2, 1, "", "resources"]], "phenopacket_mapper.data_standards.DataModel2PhenopacketSchema": [[13, 1, 1, "", "DataModel2PhenopacketSchema"]], "phenopacket_mapper.data_standards.DataModelInstance": [[12, 2, 1, "", "compliance"], [12, 2, 1, "", "data_model"], [12, 2, 1, "", "row_no"], [12, 3, 1, "", "validate"], [12, 2, 1, "", "values"]], "phenopacket_mapper.data_standards.DataSection": [[12, 2, 1, "", "cardinality"], [12, 2, 1, "", "fields"], [12, 2, 1, "", "id"], [12, 2, 1, "", "name"], [12, 2, 1, "", "required"]], "phenopacket_mapper.data_standards.DataSet": [[12, 2, 1, "", "data"], [12, 5, 1, "", "data_frame"], [12, 2, 1, "", "data_model"], [12, 3, 1, "", "head"], [12, 5, 1, "", "height"], [12, 3, 1, "", "preprocess"], [12, 5, 1, "", "width"]], "phenopacket_mapper.data_standards.Date": [[12, 2, 1, "", "day"], [12, 2, 1, "", "day_str"], [12, 3, 1, "", "formatted_string"], [12, 3, 1, "", "from_datetime"], [12, 3, 1, "", "from_iso_8601"], [12, 2, 1, "", "hour"], [12, 2, 1, "", "hour_str"], [12, 3, 1, "", "iso_8601_datestring"], [12, 2, 1, "", "minute"], [12, 2, 1, "", "minute_str"], [12, 2, 1, "", "month"], [12, 2, 1, "", "month_str"], [12, 3, 1, "", "parse_date"], [12, 3, 1, "", "protobuf_timestamp"], [12, 2, 1, "", "second"], [12, 2, 1, "", "second_str"], [12, 2, 1, "", "year"], [12, 2, 1, "", "year_str"]], "phenopacket_mapper.data_standards.OrGroup": [[12, 2, 1, "", "cardinality"], [12, 2, 1, "", "description"], [12, 2, 1, "", "fields"], [12, 2, 1, "", "id"], [12, 2, 1, "", "name"], [12, 2, 1, "", "required"]], "phenopacket_mapper.data_standards.ValueSet": [[12, 2, 1, "", "description"], [12, 2, 1, "", "elements"], [12, 3, 1, "", "extend"], [12, 2, 1, "", "name"], [12, 3, 1, "", "parse_value_set"], [12, 3, 1, "", "remove_duplicates"], [12, 5, 1, "", "resources"]], "phenopacket_mapper.data_standards.cardinality": [[14, 1, 1, "", "Cardinality"]], "phenopacket_mapper.data_standards.cardinality.Cardinality": [[14, 2, 1, "", "max"], [14, 2, 1, "", "min"]], "phenopacket_mapper.data_standards.code": [[15, 1, 1, "", "CodeableConcept"], [15, 1, 1, "", "Coding"]], "phenopacket_mapper.data_standards.code.CodeableConcept": [[15, 2, 1, "", "coding"], [15, 2, 1, "", "text"]], "phenopacket_mapper.data_standards.code.Coding": [[15, 2, 1, "", "code"], [15, 2, 1, "", "display"], [15, 3, 1, "", "parse_coding"], [15, 2, 1, "", "system"], [15, 2, 1, "", "text"]], "phenopacket_mapper.data_standards.code_system": [[16, 1, 1, "", "CodeSystem"]], "phenopacket_mapper.data_standards.code_system.CodeSystem": [[16, 2, 1, "", "iri_prefix"], [16, 2, 1, "", "name"], [16, 2, 1, "", "namespace_prefix"], [16, 3, 1, "", "set_version"], [16, 2, 1, "", "synonyms"], [16, 2, 1, "", "url"], [16, 2, 1, "", "version"]], "phenopacket_mapper.data_standards.data_model": [[17, 1, 1, "", "DataField"], [17, 1, 1, "", "DataFieldValue"], [17, 1, 1, "", "DataModel"], [17, 1, 1, "", "DataModelInstance"], [17, 1, 1, "", "DataSection"], [17, 1, 1, "", "DataSet"], [17, 1, 1, "", "OrGroup"]], "phenopacket_mapper.data_standards.data_model.DataField": [[17, 2, 1, "", "cardinality"], [17, 2, 1, "", "description"], [17, 2, 1, "", "id"], [17, 2, 1, "", "name"], [17, 2, 1, "", "required"], [17, 2, 1, "", "specification"]], "phenopacket_mapper.data_standards.data_model.DataFieldValue": [[17, 2, 1, "", "field"], [17, 2, 1, "", "row_no"], [17, 3, 1, "", "validate"], [17, 2, 1, "", "value"]], "phenopacket_mapper.data_standards.data_model.DataModel": [[17, 2, 1, "", "data_model_name"], [17, 2, 1, "", "fields"], [17, 3, 1, "", "from_file"], [17, 3, 1, "", "get_field"], [17, 3, 1, "", "get_field_ids"], [17, 3, 1, "", "load_data"], [17, 3, 1, "", "load_data_using_data_model"], [17, 2, 1, "", "resources"]], "phenopacket_mapper.data_standards.data_model.DataModelInstance": [[17, 2, 1, "", "compliance"], [17, 2, 1, "", "data_model"], [17, 2, 1, "", "row_no"], [17, 3, 1, "", "validate"], [17, 2, 1, "", "values"]], "phenopacket_mapper.data_standards.data_model.DataSection": [[17, 2, 1, "", "cardinality"], [17, 2, 1, "", "fields"], [17, 2, 1, "", "id"], [17, 2, 1, "", "name"], [17, 2, 1, "", "required"]], "phenopacket_mapper.data_standards.data_model.DataSet": [[17, 2, 1, "", "data"], [17, 5, 1, "", "data_frame"], [17, 2, 1, "", "data_model"], [17, 3, 1, "", "head"], [17, 5, 1, "", "height"], [17, 3, 1, "", "preprocess"], [17, 5, 1, "", "width"]], "phenopacket_mapper.data_standards.data_model.OrGroup": [[17, 2, 1, "", "cardinality"], [17, 2, 1, "", "description"], [17, 2, 1, "", "fields"], [17, 2, 1, "", "id"], [17, 2, 1, "", "name"], [17, 2, 1, "", "required"]], "phenopacket_mapper.data_standards.data_models": [[19, 0, 0, "-", "erdri_cds"], [18, 4, 1, "", "parse_data_type"]], "phenopacket_mapper.data_standards.date": [[21, 1, 1, "", "Date"]], "phenopacket_mapper.data_standards.date.Date": [[21, 2, 1, "", "day"], [21, 2, 1, "", "day_str"], [21, 3, 1, "", "formatted_string"], [21, 3, 1, "", "from_datetime"], [21, 3, 1, "", "from_iso_8601"], [21, 2, 1, "", "hour"], [21, 2, 1, "", "hour_str"], [21, 3, 1, "", "iso_8601_datestring"], [21, 2, 1, "", "minute"], [21, 2, 1, "", "minute_str"], [21, 2, 1, "", "month"], [21, 2, 1, "", "month_str"], [21, 3, 1, "", "parse_date"], [21, 3, 1, "", "protobuf_timestamp"], [21, 2, 1, "", "second"], [21, 2, 1, "", "second_str"], [21, 2, 1, "", "year"], [21, 2, 1, "", "year_str"]], "phenopacket_mapper.data_standards.value_set": [[22, 1, 1, "", "ValueSet"]], "phenopacket_mapper.data_standards.value_set.ValueSet": [[22, 2, 1, "", "description"], [22, 2, 1, "", "elements"], [22, 3, 1, "", "extend"], [22, 2, 1, "", "name"], [22, 3, 1, "", "parse_value_set"], [22, 3, 1, "", "remove_duplicates"], [22, 5, 1, "", "resources"]], "phenopacket_mapper.mapping": [[23, 1, 1, "", "PhenopacketBuildingBlock"], [23, 1, 1, "", "PhenopacketMapper"], [24, 0, 0, "-", "map_field"], [23, 4, 1, "", "map_single"], [25, 0, 0, "-", "mapper"], [26, 0, 0, "-", "phenopacket_building_block"]], "phenopacket_mapper.mapping.PhenopacketBuildingBlock": [[23, 3, 1, "", "map"]], "phenopacket_mapper.mapping.PhenopacketMapper": [[23, 3, 1, "", "check_fields_adheres_to_phenopacket_allowed_values"], [23, 3, 1, "", "map"]], "phenopacket_mapper.mapping.mapper": [[25, 1, 1, "", "PhenopacketMapper"]], "phenopacket_mapper.mapping.mapper.PhenopacketMapper": [[25, 3, 1, "", "check_fields_adheres_to_phenopacket_allowed_values"], [25, 3, 1, "", "map"]], "phenopacket_mapper.mapping.phenopacket_building_block": [[26, 1, 1, "", "PhenopacketBuildingBlock"], [26, 4, 1, "", "map_single"]], "phenopacket_mapper.mapping.phenopacket_building_block.PhenopacketBuildingBlock": [[26, 3, 1, "", "map"]], "phenopacket_mapper.preprocessing": [[33, 0, 0, "-", "preprocess"], [34, 0, 0, "-", "preprocess_dict"], [35, 0, 0, "-", "preprocess_method"]], "phenopacket_mapper.preprocessing.preprocess": [[33, 4, 1, "", "preprocess"]], "phenopacket_mapper.preprocessing.preprocess_dict": [[34, 4, 1, "", "preprocess_dict"]], "phenopacket_mapper.preprocessing.preprocess_method": [[35, 4, 1, "", "preprocess_method"]], "phenopacket_mapper.utils": [[36, 1, 1, "", "NotebookBuilder"], [37, 0, 0, "-", "create_ipynb_in_code"], [38, 0, 0, "-", "get_field_name"], [39, 0, 0, "-", "io"], [36, 4, 1, "", "loc_default"], [45, 0, 0, "-", "pandas_utils"], [46, 0, 0, "-", "parsing"], [55, 0, 0, "-", "str_to_valid_id"]], "phenopacket_mapper.utils.NotebookBuilder": [[36, 3, 1, "", "add_code_cell"], [36, 3, 1, "", "add_markdown_cell"], [36, 3, 1, "", "write_to_file"]], "phenopacket_mapper.utils.create_ipynb_in_code": [[37, 1, 1, "", "NotebookBuilder"]], "phenopacket_mapper.utils.create_ipynb_in_code.NotebookBuilder": [[37, 3, 1, "", "add_code_cell"], [37, 3, 1, "", "add_markdown_cell"], [37, 3, 1, "", "write_to_file"]], "phenopacket_mapper.utils.get_field_name": [[38, 4, 1, "", "get_field_name"]], "phenopacket_mapper.utils.io": [[39, 1, 1, "", "DataReader"], [40, 0, 0, "-", "data_reader"], [41, 0, 0, "-", "input"], [39, 4, 1, "", "load_data_using_data_model"], [42, 0, 0, "-", "output"], [39, 4, 1, "", "parse_xml"], [39, 4, 1, "", "read_data_model"], [43, 0, 0, "-", "read_json"], [39, 4, 1, "", "read_phenopacket_from_json"], [39, 4, 1, "", "read_phenopackets"], [44, 0, 0, "-", "read_xml"], [39, 4, 1, "", "write"]], "phenopacket_mapper.utils.io.DataReader": [[39, 3, 1, "", "handle_file_extension"]], "phenopacket_mapper.utils.io.data_reader": [[40, 1, 1, "", "DataReader"]], "phenopacket_mapper.utils.io.data_reader.DataReader": [[40, 3, 1, "", "handle_file_extension"]], "phenopacket_mapper.utils.io.input": [[41, 4, 1, "", "load_data_using_data_model"], [41, 4, 1, "", "read_data_model"], [41, 4, 1, "", "read_phenopacket_from_json"], [41, 4, 1, "", "read_phenopackets"]], "phenopacket_mapper.utils.io.output": [[42, 4, 1, "", "write"]], "phenopacket_mapper.utils.io.read_json": [[43, 4, 1, "", "read_json"]], "phenopacket_mapper.utils.io.read_xml": [[44, 4, 1, "", "parse_xml"], [44, 4, 1, "", "read_xml"], [44, 4, 1, "", "remove_at_symbols"]], "phenopacket_mapper.utils.pandas_utils": [[45, 4, 1, "", "loc_default"]], "phenopacket_mapper.utils.parsing": [[47, 0, 0, "-", "get_codesystem_by_namespace_prefix"], [46, 4, 1, "", "get_codesystem_by_namespace_prefx"], [46, 4, 1, "", "parse_bool"], [48, 0, 0, "-", "parse_coding"], [49, 0, 0, "-", "parse_data_type"], [50, 0, 0, "-", "parse_date"], [46, 4, 1, "", "parse_float"], [46, 4, 1, "", "parse_int"], [51, 0, 0, "-", "parse_ordinal"], [52, 0, 0, "-", "parse_primitive_data_value"], [46, 4, 1, "", "parse_single_data_type"], [53, 0, 0, "-", "parse_value"], [54, 0, 0, "-", "parse_value_set"]], "phenopacket_mapper.utils.parsing.get_codesystem_by_namespace_prefix": [[47, 4, 1, "", "get_codesystem_by_namespace_prefx"]], "phenopacket_mapper.utils.parsing.parse_coding": [[48, 4, 1, "", "parse_coding"]], "phenopacket_mapper.utils.parsing.parse_data_type": [[49, 4, 1, "", "parse_data_type"], [49, 4, 1, "", "parse_single_data_type"]], "phenopacket_mapper.utils.parsing.parse_date": [[50, 4, 1, "", "parse_date"]], "phenopacket_mapper.utils.parsing.parse_ordinal": [[51, 4, 1, "", "parse_ordinal"]], "phenopacket_mapper.utils.parsing.parse_primitive_data_value": [[52, 4, 1, "", "parse_bool"], [52, 4, 1, "", "parse_float"], [52, 4, 1, "", "parse_int"], [52, 4, 1, "", "parse_primitive_data_value"]], "phenopacket_mapper.utils.parsing.parse_value": [[53, 4, 1, "", "parse_value"]], "phenopacket_mapper.utils.parsing.parse_value_set": [[54, 4, 1, "", "parse_value_set"]], "phenopacket_mapper.utils.str_to_valid_id": [[55, 4, 1, "", "str_to_valid_id"]], "phenopacket_mapper.validate": [[56, 4, 1, "", "read_validate"], [57, 0, 0, "-", "validate"]], "phenopacket_mapper.validate.validate": [[57, 1, 1, "", "Validator"], [57, 4, 1, "", "read_validate"], [57, 4, 1, "", "validate"]], "phenopacket_mapper.validate.validate.Validator": [[57, 3, 1, "", "validate"]]}, "objnames": {"0": ["py", "module", "Python module"], "1": ["py", "class", "Python class"], "2": ["py", "attribute", "Python attribute"], "3": ["py", "method", "Python method"], "4": ["py", "function", "Python function"], "5": ["py", "property", "Python property"]}, "objtypes": {"0": "py:module", "1": "py:class", "2": "py:attribute", "3": "py:method", "4": "py:function", "5": "py:property"}, "terms": {"": [36, 55, 59, 60], "0": [2, 5, 6, 12, 14, 15, 16, 17, 21, 22, 23, 26, 46, 48, 52], "01": [12, 21, 46, 50], "01357": 60, "02": [12, 21, 46, 50, 60], "022": 60, "0285433": 60, "02t16": [12, 21], "05": 60, "06": [12, 21], "1": [1, 12, 17, 21, 22, 39, 41, 46, 51, 52, 53, 59, 60, 61], "10": [59, 60], "1002": 60, "1038": 60, "1101": 60, "1371": 60, "15z": [12, 21], "18": 60, "1st": [12, 21, 46, 50], "2": [46, 53, 59, 60], "2021": [12, 21], "2022": 60, "202200016": 60, "2023": 60, "2024": [12, 21, 46, 50, 60], "24308104": 60, "29": 60, "2nd": [12, 21, 46, 50], "3": [46, 53, 59, 60], "4": [46, 53, 59, 60], "40": 60, "404684003": [12, 15, 46, 48], "5": [12, 17, 60], "52": [12, 21], "6": 60, "8": [39, 40, 44], "817": 60, "820": 60, "8601": [12, 21, 46, 50], "9": [12, 17, 21, 59], "A": [1, 2, 3, 5, 6, 12, 15, 16, 17, 22, 32, 34, 36, 37, 39, 41, 46, 54, 58, 59, 60], "At": 60, "By": [12, 22], "For": [59, 60], "If": [1, 12, 15, 17, 21, 23, 25, 32, 34, 35, 39, 41, 46, 47, 48, 50, 52, 59, 60], "In": [12, 18, 21, 46, 49, 50, 59, 60], "It": [1, 12, 15, 16, 17, 22, 46, 53, 60], "ONE": 60, "On": [46, 52, 59], "Or": [12, 17, 46, 52], "The": [1, 12, 15, 16, 17, 18, 21, 23, 25, 32, 34, 35, 36, 37, 39, 41, 42, 46, 47, 49, 50, 52, 53, 55, 57, 59, 60], "There": [12, 21, 46, 50, 59], "To": [1, 12, 17, 59, 60], "_": [12, 17], "_column": [1, 12, 17, 39, 41], "_resourc": [12, 22], "abbrevi": [12, 16], "abc": [2, 3], "abnorm": 60, "about": [2, 3, 5, 6, 60], "abov": [12, 17, 18, 46, 49, 59], "abput": [2, 3], "absent": 60, "abstract": [2, 3], "access": [1, 12, 17], "accord": 60, "act": [46, 53], "action": 60, "activ": 59, "ad": [36, 37], "add": [18, 36, 37, 46, 49, 59], "add_code_cel": [36, 37], "add_markdown_cel": [36, 37], "addit": [12, 15, 32, 35], "addition": [12, 15], "address": 60, "adher": [1, 12, 17, 23, 25, 60], "advanc": 60, "after": 59, "aid": 60, "aim": 60, "algorithm": 60, "all": [1, 12, 15, 17, 36, 39, 41, 46, 48, 55, 59], "allianc": 60, "allow": [1, 12, 18, 22, 23, 25, 46, 49, 59, 60], "allow_zero": [12, 21], "alphanumer": [12, 17, 36, 55], "alreadi": 59, "also": [12, 17, 22, 59], "altern": [12, 16], "alwai": [12, 21], "an": [1, 2, 3, 12, 16, 17, 21, 32, 35, 39, 44, 46, 50, 51, 52, 59, 60], "anaconda3": 59, "analys": 60, "analysi": 60, "analyz": 60, "ani": [1, 12, 17, 18, 22, 32, 33, 34, 35, 36, 45, 46, 49, 58, 59, 60], "api": [2, 3, 5, 6, 58], "api_base_url": [2, 5, 6], "api_request_super_class": 2, "apirequestsuperclass": [2, 3, 5, 6], "appli": 59, "applic": [59, 60], "appropri": [46, 53], "apt": 59, "ar": [1, 12, 17, 18, 21, 22, 36, 39, 41, 46, 49, 50, 56, 57, 59, 62], "arg": 57, "arg1": [12, 17], "arg2": [12, 17], "argument": [1, 12, 17, 32, 35], "arrai": 60, "ask": 59, "assign": [12, 22], "assum": [12, 21, 46, 50], "attach": [46, 51], "attempt": [12, 17, 21, 46, 50], "attribut": [1, 12, 17], "author": 60, "autom": [59, 60], "automat": 59, "avail": [59, 60, 62], "avoid": [46, 52], "b": 60, "bamshad": 60, "base": [1, 2, 3, 5, 6, 12, 13, 14, 15, 16, 17, 21, 22, 23, 25, 26, 36, 37, 39, 40, 57, 59], "bash": 59, "bash_profil": 59, "bashrc": 59, "basic": [59, 60], "baudi": 60, "baynam": 60, "bechraki": 60, "beckmann": 60, "beckwith": 60, "becom": 60, "befor": [32, 33, 59], "behavior": 60, "being": [12, 17], "belong": [12, 15, 17, 46, 48], "below": 60, "beltran": 60, "benefit": [12, 22, 59], "bespok": [58, 60], "better": [12, 16, 22], "between": [12, 21, 22, 46, 50, 60], "bih": [59, 62, 63, 64], "bin": 59, "binari": 59, "biolog": 60, "biopsi": 60, "biosampl": 60, "biotechnologi": 60, "birth": [1, 12, 17], "bit": 57, "block": 60, "book": 59, "bool": [1, 12, 17, 18, 21, 22, 39, 41, 46, 49, 52, 53, 56, 57], "bool_str": [46, 52], "boolean": [18, 46, 49, 52], "both": 60, "break": [1, 12, 17, 39, 41], "brew": 59, "bridg": 60, "build": [36, 37, 59, 60], "bundl": 60, "busk": 60, "c": [59, 60], "cacheiro": 60, "call": [1, 12, 15, 17, 32, 35, 46, 48, 59], "callabl": [12, 17, 32, 33, 35], "callahan": 60, "can": [1, 2, 3, 12, 15, 17, 18, 21, 22, 32, 35, 39, 41, 46, 48, 49, 51, 59, 60], "cannot": [12, 17, 46, 52], "captur": 60, "cardin": [1, 12, 17], "carmodi": 60, "case": [12, 17, 18, 46, 49, 60], "categor": 60, "caus": 60, "cd": 59, "cei": [59, 62, 63, 64], "cell": [12, 17, 36, 37, 60], "cento": 59, "centrifug": 60, "certain": 60, "challeng": 60, "chang": 59, "charact": [12, 17, 36, 55], "character": 60, "check": [1, 12, 17, 23, 25, 39, 41, 60], "check_fields_adheres_to_phenopacket_allowed_valu": [1, 23, 25], "chocolatei": 59, "chong": 60, "choos": 59, "chute": 60, "class": [1, 2, 3, 5, 6, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 25, 26, 36, 37, 39, 40, 41, 46, 49, 57, 60], "cli": 1, "click": 59, "clinic": 60, "clinician": 60, "clone": 59, "close": 59, "code": [1, 2, 3, 5, 6, 12, 16, 18, 22, 36, 37, 46, 48, 49, 53, 59, 60, 62], "code_system": [1, 2, 5, 6, 12, 15, 17, 22], "code_system_modul": [46, 48], "codeabl": [12, 22], "codeableconcept": [1, 12, 15, 22, 46, 53], "codesystem": [1, 2, 5, 6, 12, 15, 16, 17, 18, 22, 39, 41, 46, 47, 48, 49, 53, 54], "coding_str": [12, 15, 46, 48], "cold": 60, "coleman": 60, "collect": [12, 17], "column": [1, 12, 17, 36, 39, 41, 45], "column_nam": [1, 12, 17, 36, 39, 41, 45], "column_name_in_fil": [1, 12, 17, 39, 41], "com": [59, 62, 63, 64], "come": [12, 21, 46, 50, 59, 60], "command": 59, "commonli": [12, 16], "commun": 59, "compil": 60, "complet": 59, "complex": 60, "complianc": [1, 12, 15, 17, 18, 21, 22, 39, 41, 46, 48, 49, 50, 53, 54], "complic": 57, "comput": [12, 22, 60], "concept": [2, 3, 5, 6, 12, 15, 22, 60], "concept_id": [2, 3, 5, 6], "concern": 46, "conda": 59, "confirm": 59, "conform": 60, "confus": [46, 52], "consid": 60, "constructor": [1, 23, 25], "consult": [32, 33], "contain": [1, 12, 17, 32, 34, 36, 39, 41, 46, 51, 56, 57, 60, 62], "content": [36, 37], "context": 60, "contrast": 60, "convers": [12, 21, 46, 52], "convert": [12, 17, 36, 55], "coordin": 60, "core": 60, "corpu": 60, "correctli": 59, "correl": 60, "correspond": [32, 34], "could": [1, 12, 16, 17, 39, 41], "courtot": 60, "creat": [1, 12, 21, 23, 25, 26, 46, 50, 57, 60, 62], "create_ipynb_in_cod": 36, "creation": 60, "csv": [1, 12, 17, 39, 40, 41], "ct": [12, 15, 16, 18, 46, 48, 49], "cultur": 60, "current": [60, 62], "curv": 60, "d": 60, "dai": [12, 21, 46, 50], "dalgleish": 60, "dani": 60, "data": [1, 2, 5, 6, 12, 15, 16, 17, 18, 21, 22, 23, 25, 26, 32, 39, 41, 46, 49, 51, 53, 56, 58, 59, 60, 62], "data_field": [23, 26], "data_field_nam": [1, 12, 17, 39, 41], "data_fram": [12, 17], "data_model": [1, 12, 13, 23, 25, 26, 39, 41], "data_model_nam": [1, 12, 17, 39, 41], "data_read": 39, "data_standard": [1, 2, 5, 6, 23, 26, 46, 49], "data_typ": [18, 46, 49], "datafield": [1, 12, 17, 18, 22, 23, 26, 39, 41, 46, 49, 51], "datafieldvalu": [1, 12, 17, 23, 26], "datafram": [12, 17, 36, 45], "datamodel": [0, 1, 12, 13, 17, 23, 25, 26, 39, 41, 46, 51], "datamodel2phenopacketschema": 12, "datamodelinst": [1, 12, 17, 23, 25, 26, 39, 41], "datanod": [12, 17], "dataread": [39, 40], "datasect": [1, 12, 17], "dataset": [1, 12, 17, 23, 25, 39, 41], "date": [1, 12, 17, 18, 22, 46, 49, 50, 53, 59, 60], "date_of_birth": [1, 12, 17], "date_of_birth_column": [1, 12, 17], "date_str": [12, 21, 46, 50], "datetim": [12, 21], "day_str": [12, 21], "debian": 59, "deep": 60, "deeper": 60, "def": [12, 17], "default": [1, 12, 17, 18, 21, 22, 36, 45, 46, 49, 50], "default_first": [12, 21, 46, 50], "defin": [1, 12, 15, 16, 17, 21, 22, 46, 54, 60], "definit": [1, 12, 17, 21, 23, 25, 39, 41, 60], "depend": 59, "describ": [18, 46, 49, 60], "descript": [1, 12, 15, 17, 22, 39, 41, 46, 54], "design": 60, "desir": [12, 17, 59], "detail": [2, 3, 5, 6, 60], "determin": [12, 21, 46, 50], "develop": [60, 62, 63, 64], "deviat": 60, "df": [36, 45], "diagnosi": 60, "diagnost": 60, "dict": [1, 2, 4, 12, 17, 32, 33, 34, 39, 41, 43, 44], "dict_": 44, "dictionari": [1, 12, 17, 32, 33, 34, 39, 41, 44, 60], "differ": [12, 22, 46, 53, 59, 60], "digit": [12, 21], "dir_path": [39, 41], "directli": [12, 17], "directori": [39, 41, 42, 59], "discoveri": 60, "discuss": 59, "diseas": [2, 6, 18, 60], "displai": [12, 15, 46, 48], "distribut": 59, "dive": 60, "dmg": 59, "dna": 60, "dnf": 59, "do": [12, 17, 59, 60, 61], "doc": 60, "document": [32, 33, 60], "doe": [46, 52], "doi": 60, "don": 59, "done": [1, 12, 17], "download": 59, "dt": [12, 21], "dynam": [1, 12, 17], "e": [1, 12, 15, 16, 17, 18, 21, 22, 23, 26, 39, 41, 46, 48, 49, 51, 59, 60], "e0285433": 60, "each": [1, 12, 17, 21, 39, 41], "easi": 60, "easiest": 59, "edit": 59, "effici": 57, "effort": 60, "either": [1, 12, 17, 39, 41, 60], "element": [12, 22, 23, 26, 46, 54, 60], "elemento": 60, "els": [46, 53], "empti": [1, 12, 17, 22, 39, 41], "en": [2, 6, 59], "enabl": 60, "encod": [39, 40, 44], "encourag": 59, "end": 60, "enforc": [1, 12, 17, 39, 41], "ensur": [57, 59, 60], "enter": 59, "entiti": 60, "entri": [18, 46, 49], "enum": 60, "equival": [12, 17], "erdri_cd": 18, "erdri_cds_definition_in_cod": 63, "erdri_cds_from_fil": 64, "error": [1, 12, 17, 23, 25, 36, 45], "especi": [12, 21, 60], "essenwang": 60, "etc": [1, 12, 16, 17, 18, 22, 39, 41, 46, 49], "even": [12, 16], "ex": 59, "exampl": [2, 3, 12, 16, 21, 22, 23, 26, 60], "example_pseudonym": [23, 26], "excel": [1, 12, 17, 39, 41], "except": [32, 35], "exchang": 60, "exclud": 60, "exist": [12, 22], "expect": [12, 15, 46, 48], "experi": 60, "explain": 60, "export": 59, "express": [12, 21], "extend": [12, 22], "extra": [1, 12, 17, 39, 41], "extract": [1, 12, 17, 39, 41, 59, 60], "facilit": [12, 22, 23, 60], "fact": 57, "factori": [1, 12, 16, 17, 22], "fail": [12, 21, 46, 50], "fair": 60, "fals": [1, 2, 4, 12, 17, 22, 39, 41, 46, 52, 54, 56, 57], "familiar": 60, "fe": [39, 40], "februari": [12, 21, 46, 50], "fedora": 59, "few": 59, "field": [1, 12, 17, 22, 23, 25, 26, 38, 39, 41, 46, 51], "field1": [12, 17], "field2": [12, 17], "field_1": [12, 17], "field_1_column": [1, 12, 17, 39, 41], "field_2": [12, 17], "field_id": [1, 12, 17], "field_name_str": [46, 51], "file": [1, 12, 17, 18, 36, 37, 39, 40, 41, 42, 44, 46, 49, 51, 56, 57, 59, 62], "file_extens": [39, 40], "file_typ": [1, 12, 17, 39, 41], "filesjavajr": 59, "fill": [12, 16], "first": [12, 21, 46, 50, 59], "fix": 60, "flag": [12, 17], "flexibl": 60, "float": [12, 17, 22, 46, 52, 53], "float_str": [46, 52], "fmt": [12, 21], "folder": 59, "follow": [1, 12, 17, 46, 53, 59, 63, 64], "format": [1, 12, 15, 17, 21, 39, 41, 46, 48, 50, 58, 60], "formatted_str": [12, 21], "forwardref": [12, 17], "found": [1, 12, 15, 17, 46, 47, 48], "four": [12, 21], "frac_sec": [12, 21], "fraction": [12, 21, 60], "freeman": 60, "freimuth": 60, "from": [1, 2, 3, 5, 6, 12, 17, 18, 21, 22, 23, 25, 26, 39, 41, 46, 49, 50, 51, 52, 53, 54, 56, 57, 58, 59, 60, 61, 62], "from_datetim": [12, 21], "from_fil": [1, 12, 17], "from_iso_8601": [12, 21], "function": [2, 12, 17, 21, 32, 33, 36, 46, 50, 52, 55, 60], "further": [18, 46, 49, 60], "g": [1, 12, 15, 16, 17, 18, 39, 41, 46, 48, 49, 51, 59, 60], "ga4gh": [1, 58, 60], "gap": 60, "gargano": 60, "gener": [1, 12, 17, 59, 60], "genet": 60, "geneticist": 60, "genom": 60, "genotyp": 60, "get": [2, 3, 5, 6, 59, 61], "get_codesystem_by_namespace_prefx": [36, 46, 47], "get_field": [1, 12, 17], "get_field_id": [1, 12, 17], "get_field_nam": 36, "ggn2": 60, "gitforwindow": 59, "github": [59, 60, 62, 63, 64], "give": [1, 23, 25, 59], "given": [1, 12, 17, 18, 39, 41, 46, 49], "global": 60, "go": [12, 21, 59], "goe": [36, 45], "googl": [12, 21, 60], "gradient": 60, "graef": 60, "group": [12, 17], "groza": 60, "guid": [58, 61], "gz": 59, "h": 60, "ha": [1, 12, 17, 22], "haendel": 60, "hamosh": 60, "handl": [12, 17, 21, 39, 46, 50, 60], "handle_file_extens": [39, 40], "happen": [12, 17], "harbor": 60, "harri": 60, "have": [1, 12, 15, 17, 39, 41, 46, 51, 59, 60], "head": [12, 17], "health": 60, "healthcar": 60, "hegd": 60, "height": [12, 17], "help": 61, "here": [59, 60], "high": 60, "highli": [1, 12, 17, 39, 41], "hint": 60, "hit": 59, "homebrew": 59, "hour": [12, 21], "hour_str": [12, 21], "how": [12, 21, 46, 50], "howev": 60, "hp": [2, 5, 12, 16], "hpo": [2, 5, 12, 16], "hpo_api_request": 2, "hpo_code_system": [2, 5], "hpoapirequest": [2, 5], "html": 59, "http": [2, 5, 6, 59, 60, 62, 63, 64], "human": [2, 5, 12, 15, 16, 60], "hurdl": 60, "hybridis": 60, "hypothesi": 60, "i": [1, 2, 3, 12, 15, 16, 17, 18, 21, 22, 23, 25, 32, 34, 35, 39, 41, 46, 47, 48, 49, 50, 51, 52, 57, 59, 60, 61], "id": [1, 12, 17, 23, 26, 36, 39, 41, 55], "identifi": [12, 17], "ii": [1, 12, 17, 39, 41, 46, 51], "implement": [2, 3, 57], "import": [1, 12, 17, 23, 26, 60, 61], "inbuilt": [46, 52], "includ": [12, 16, 56, 60], "inclus": [18, 46, 49], "increas": 60, "independ": 59, "index": [36, 45, 58], "indic": [12, 18, 21, 46, 49], "individu": [23, 26, 60], "infer": [39, 44, 60], "inform": [32, 33, 59, 60, 63, 64], "input": [27, 39], "insight": 60, "inst": [23, 26], "instal": 58, "instanc": [12, 17, 23, 26, 57, 60], "instruct": 59, "int": [2, 5, 6, 12, 14, 17, 18, 21, 22, 36, 45, 46, 49, 52, 53], "int_str": [46, 52], "integ": [18, 46, 49], "integr": 60, "intend": [2, 12, 15, 46, 48, 60], "interest": 60, "intern": 57, "interoper": [12, 22, 60], "interpret": 60, "introduct": 58, "intuit": 60, "investig": 60, "iobas": [39, 40, 43, 44], "ipsum": 62, "ipynb": [63, 64], "iri": [12, 16], "iri_prefix": [12, 16], "iso": [12, 21, 46, 50], "iso_8601": [12, 21], "iso_8601_datestr": [12, 21], "issu": [18, 46, 49, 60], "item": [1, 12, 17], "its": [1, 12, 16, 17, 18, 46, 49, 60], "itself": 59, "j": 60, "jacobsen": 60, "januari": [12, 21, 46, 50], "java": [57, 60], "java_hom": 59, "javas": 59, "jax": [2, 5], "journal": 60, "jre": 59, "jre8": 59, "json": [2, 4, 39, 40, 41, 42], "jupyt": [36, 37], "just": [12, 15, 22, 46, 48, 59], "k": 60, "kaliyaperum": 60, "kassabi": 60, "keep": 60, "kei": [1, 12, 17, 23, 26, 39, 41], "keyword": [1, 12, 17, 32, 35], "klocperk": 60, "kuster": 60, "kwarg": [1, 12, 17, 23, 25, 26, 32, 33, 35, 57], "l": 60, "laboratori": 60, "ladewig": 60, "languag": [59, 60], "later": [1, 12, 16, 17, 39, 41], "latest": 59, "learn": 60, "least": 60, "leav": [1, 12, 17, 39, 41], "lenient": [1, 12, 15, 17, 18, 21, 22, 39, 41, 46, 48, 49, 50, 53, 54], "letter": [12, 17], "level": [1, 12, 17, 21, 22, 39, 41, 46, 50, 53, 54, 60], "librari": [58, 59, 60], "like": [1, 12, 17, 39, 41], "line": [1, 12, 17, 39, 41, 59], "link": 60, "linux": 59, "list": [1, 12, 15, 16, 17, 18, 22, 23, 25, 39, 40, 41, 42, 46, 47, 48, 49, 53, 54, 56, 57, 60], "liter": [1, 12, 14, 15, 17, 18, 21, 22, 39, 40, 41, 46, 48, 49, 50, 53, 54], "lloyd": 60, "load": [1, 12, 17, 39, 41, 60], "load_data": [1, 12, 17], "load_data_using_data_model": [1, 12, 17, 39, 41], "loc": [36, 45], "loc_default": [1, 36, 45], "local": [23, 60], "loinc": [12, 16], "look": [1, 12, 17, 39, 41, 63, 64], "lorem": 62, "lot": [12, 21, 46, 50], "lowercas": [12, 17], "m": [59, 60], "mac": 59, "machin": 60, "maco": 59, "made": [1, 12, 17, 60], "mai": [12, 15, 59, 60], "main": 7, "maintain": 59, "make": [2, 59], "manag": [59, 60], "mani": [12, 21, 46, 50, 59, 60], "manual": [12, 17], "map": [1, 12, 17, 32, 33, 34, 39, 41, 56, 58, 60], "map_field": 23, "map_singl": [23, 26], "mapper": [23, 27], "mapping_command": 7, "mapping_dict": [32, 34], "mappingproxi": [1, 12, 17, 39, 41], "marcello": 60, "markdown": [36, 37], "mass": 60, "match": [1, 12, 17, 46, 47, 60], "materi": 60, "mattina": 60, "maverick": 59, "max": [12, 14], "mcmurri": 60, "mean": [12, 16, 60], "meant": [46, 51], "measur": 60, "medic": [1, 12, 17, 60], "medicalact": 60, "medicin": 60, "medrxiv": 60, "messag": [1, 23, 25, 60], "meta": 60, "metadata": 60, "method": [1, 2, 3, 12, 17, 18, 32, 33, 35, 46, 49, 51, 53, 60], "might": [12, 17, 46, 51, 60], "min": [12, 14, 21], "minut": [12, 21], "minute_str": [12, 21], "miss": [1, 12, 17], "modal": 60, "model": [1, 12, 17, 18, 23, 26, 39, 41, 46, 49, 51, 60, 62], "modifi": [12, 17, 60], "modul": [2, 7, 12, 18, 23, 27, 32, 36, 39, 46, 56, 58], "molecul": 60, "molecular": 60, "moment": [63, 64], "mondo": [12, 16], "month": [12, 21, 46, 50], "month_str": [12, 21], "more": [12, 22, 32, 33, 59, 60, 63, 64], "morphologi": 60, "most": [59, 60], "move": 59, "multipl": [12, 18, 22, 46, 49, 60], "mungal": 60, "munoz": 60, "must": [1, 12, 17, 39, 41], "myenv": 59, "n": [12, 14, 17, 60], "name": [1, 2, 5, 6, 12, 15, 16, 17, 18, 22, 36, 37, 39, 41, 45, 46, 48, 49, 51, 54, 59], "namespac": [12, 15, 16, 46, 47, 48], "namespace_prefix": [12, 15, 16, 46, 48], "namespace_prefix_str": [46, 47], "nanosecond": [12, 21], "natur": 60, "navig": 59, "neatli": [46, 51], "necessari": [12, 16], "need": [59, 60], "net": [2, 6], "new": 59, "new_descript": [12, 22], "new_nam": [12, 22], "nomenclatur": [12, 16], "non": [36, 55, 60], "none": [1, 2, 4, 12, 16, 17, 21, 22, 39, 40, 46, 47, 50, 52, 54], "normal": 60, "note": 59, "notebook": [36, 37, 62, 63, 64], "notebookbuild": [1, 36, 37], "noth": [46, 53], "now": 59, "number": [1, 12, 17, 39, 41], "numer": [12, 22, 46, 52], "o": 60, "object": [1, 12, 13, 14, 15, 16, 17, 21, 22, 23, 25, 26, 36, 37, 39, 40, 41, 46, 47, 48, 50, 54, 57], "observ": 60, "occasion": 60, "occur": [36, 45], "offici": 59, "omim": [12, 16], "one": [2, 3, 12, 17, 18, 22, 46, 49, 57], "ones": 60, "onli": [12, 15, 17, 18, 22, 46, 48, 49, 57], "onset": 60, "onto": [12, 17, 60], "ontologi": [2, 5, 6, 12, 16, 60], "open": 59, "openjdk": 59, "openjr": 59, "oper": 59, "opt": 59, "optim": 60, "option": [1, 12, 17, 21, 39, 41, 59, 60], "oracl": 59, "order": [46, 53, 59], "ordin": [1, 12, 17, 39, 41, 46, 51, 60], "ordo": [12, 16], "org": [2, 5, 59, 60], "organ": 60, "orgroup": [1, 12, 17], "origin": [32, 34, 35], "orpha": [2, 6], "orpha_api_request": [2, 3], "orpha_code_system": [2, 6], "orphaapirequest": [2, 6], "orphanet": [2, 3, 5, 6], "other": [12, 15, 36, 55, 60], "otherwis": [1, 12, 17, 22, 23, 25, 56, 57], "out_dir": [39, 42], "output": [27, 39], "overwrit": [1, 12, 17, 39, 41], "own": 59, "p": [59, 60], "packag": [0, 59], "pad": [12, 21], "page": [58, 60], "pandas_util": 36, "param": [2, 4], "paramet": [1, 12, 15, 16, 17, 18, 21, 22, 23, 25, 26, 32, 34, 35, 36, 37, 39, 41, 42, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57], "pars": [1, 12, 15, 16, 17, 18, 21, 22, 36, 39, 41, 44, 60], "parse_bool": [36, 46, 52], "parse_cod": [12, 15, 36, 46, 53], "parse_d": [12, 21, 36, 46, 53], "parse_data_typ": [12, 18, 36, 46], "parse_float": [36, 46, 52], "parse_int": [36, 46, 52], "parse_ordin": [1, 12, 17, 36, 39, 41, 46], "parse_primitive_data_valu": [36, 46, 53], "parse_single_data_typ": [36, 46, 49], "parse_valu": [36, 46], "parse_value_set": [1, 12, 17, 22, 36, 39, 41, 46], "parse_xml": [39, 44], "parser": [12, 21, 46, 50], "part": [46, 51, 60], "pass": [1, 12, 17, 18, 23, 25, 32, 35, 46, 49], "path": [1, 12, 17, 36, 37, 39, 40, 41, 42, 43, 44, 56, 57, 59], "patient": 60, "pattern": 57, "pd": [36, 45], "perform": [36, 45], "permitt": [18, 46, 49], "phenopacket": [1, 12, 16, 17, 23, 25, 26, 32, 33, 39, 41, 42, 56, 57], "phenopacket_building_block": 23, "phenopacket_el": [23, 26], "phenopacket_mapp": [0, 59, 61, 62, 63, 64], "phenopacket_tool": 60, "phenopacketbuildingblock": [23, 26], "phenopacketmapp": [0, 1, 23, 25], "phenopackets_list": [39, 42], "phenopackets_venv": 59, "phenotyp": [2, 5, 12, 16, 60], "phenotypicfeatur": 60, "physician": 60, "physiologi": 60, "pipelin": 1, "pkg": 59, "place": [12, 17], "pleas": [32, 33, 35, 60, 63, 64], "plo": 60, "pone": 60, "popular": [12, 16, 59], "possibl": [12, 18, 21, 22, 46, 49, 50, 60], "post": 60, "power": 60, "practic": 60, "pre": 59, "precis": [1, 23, 25], "prefix": [2, 5, 6, 12, 15, 16, 18, 46, 47, 48, 49], "preprocess": [12, 17, 60, 61], "preprocess_dict": [32, 33], "preprocess_method": [12, 17, 32, 33], "preprocessed_valu": [12, 17], "present": [12, 17, 60], "press": 59, "primit": [18, 46, 49, 53], "principl": 60, "probabl": 59, "proband": 60, "problem": 60, "procedur": 60, "proceed": 59, "process": [1, 12, 17, 21, 46, 50, 60], "produc": 60, "profession": 60, "profil": 59, "prognosi": 60, "program": [59, 60], "programm": 60, "programmat": [36, 37], "project": [12, 59], "prompt": 59, "properti": [12, 17, 22, 59], "protein": 60, "protobuf": [12, 21, 60], "protobuf_timestamp": [12, 21], "provid": [2, 3, 12, 15, 22, 46, 48, 60], "pseudonym": [23, 26, 46, 51], "purpos": [18, 46, 49, 52, 57, 60], "py": [2, 3], "pypi": 59, "python": [1, 12, 17, 18, 36, 37, 39, 41, 46, 49, 52, 58, 60], "q": 60, "quantit": 60, "quickli": 60, "quickstart": 58, "quickstart_command": 7, "r": 60, "rais": [1, 12, 17, 32, 35], "rambla": 60, "rare": [2, 6, 18], "rarelink_datamodel": 18, "re": 59, "read": [1, 12, 17, 39, 41, 46, 51, 56, 57, 60, 62], "read_data_model": [39, 41], "read_json": 39, "read_phenopacket": [39, 41], "read_phenopacket_from_json": [39, 41], "read_valid": [56, 57], "read_xml": 39, "readabl": [12, 15, 60], "recogn": [12, 15, 46, 48], "recommend": [1, 12, 17, 39, 41, 60], "record": [12, 17, 60], "rees": 60, "refer": [58, 60], "rekerl": 60, "relat": [12, 17, 59, 60], "relev": 60, "reli": [32, 33, 46, 52], "remov": [1, 12, 17, 36, 39, 41, 55], "remove_at_symbol": [39, 44], "remove_dupl": [12, 22], "remove_line_break": [1, 12, 17, 39, 41], "replac": [36, 55, 59], "replic": 60, "report": 60, "repositori": 59, "repres": [12, 15, 18, 46, 48, 49, 53, 60], "represent": [12, 15, 22, 46, 53, 54, 60], "request": [2, 3, 5, 6], "requir": [1, 12, 17, 21, 32, 35, 39, 41, 60], "research": 59, "resolut": [12, 21], "resourc": [1, 12, 15, 16, 17, 18, 22, 39, 41, 46, 47, 48, 49, 53, 54], "respect": [32, 33, 46, 51, 52], "restart": 59, "result": [23, 26], "return": [1, 12, 15, 17, 18, 21, 22, 23, 25, 26, 32, 34, 35, 36, 39, 41, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57], "rhel": 59, "rna": 60, "robinson": 60, "row": [12, 17, 36, 45], "row_index": [36, 45], "row_no": [12, 17], "rpm": 59, "rule": [12, 17, 32, 34], "run": 59, "s41587": 60, "safe": [36, 45], "same": 60, "save": [36, 37], "schema": [1, 12, 17, 23, 25, 26, 58, 60], "schofield": 60, "scienc": 59, "scm": 59, "screen": 59, "script": 59, "sct": [18, 46, 49], "search": [46, 47, 58], "sec": [12, 21], "second": [12, 21], "second_str": [12, 21], "section": [12, 17, 60], "see": [1, 23, 25, 59], "seelow": 60, "seen": [2, 3], "seitz": 60, "select": [18, 59], "separ": [12, 21, 46, 50, 51, 59], "seq": 60, "sequenc": 60, "set": [2, 12, 15, 16, 17, 18, 21, 22, 46, 49, 50, 54, 59, 60], "set_vers": [12, 16], "sever": [59, 60], "sh": 59, "shell": 59, "short": 60, "should": [1, 2, 3, 12, 17, 39, 41, 59, 60], "simpl": 60, "simpli": 59, "sinc": [59, 60], "singl": [12, 17, 60], "singleton": 57, "smith": 60, "snome": [12, 15, 16, 18, 46, 48, 49], "snomed_ct": [12, 15, 46, 48], "so": [12, 21, 46, 50, 59], "softwar": 60, "solv": 60, "some": [36, 45, 60], "someth": [12, 17, 36, 45], "sometim": [12, 17, 21, 46, 50], "sota": 60, "sourc": [1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 25, 26, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 59], "space": [2, 5, 6, 12, 15, 16, 18, 36, 46, 48, 49, 55], "specif": [1, 2, 3, 12, 17, 18, 21, 22, 39, 41, 46, 49, 60], "specifi": [12, 15, 21, 23, 26, 36, 45, 46, 48], "spectrometri": 60, "spread": 60, "spring": 60, "standard": [12, 60], "standardis": 60, "start": [12, 17, 59, 61], "state": [12, 17], "static": [1, 12, 15, 17, 21, 22], "steep": 60, "steinhau": 60, "step": [59, 61], "str": [1, 2, 4, 5, 6, 12, 15, 16, 17, 18, 21, 22, 23, 26, 36, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55], "str_to_valid_id": [1, 12, 17, 36], "strict": [1, 12, 15, 17, 18, 21, 22, 39, 41, 46, 48, 49, 50, 53, 54], "string": [1, 12, 15, 17, 18, 21, 22, 36, 39, 41, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55], "structur": 60, "studi": 60, "subject": 60, "submodul": 1, "subpackag": 0, "substrat": 60, "success": [1, 23, 25], "sudo": 59, "suffix": [12, 21], "suitabl": 60, "super": [2, 3], "sure": 59, "synonym": [12, 16], "syntact": 60, "system": [2, 3, 12, 15, 18, 22, 46, 48, 49, 59], "t": [12, 21, 59, 60], "tabl": [12, 17, 60], "tabular": [1, 18, 46, 49, 58, 60], "take": [32, 34, 35, 63, 64], "taken": 60, "tar": 59, "technic": 60, "technologi": 59, "term": [2, 5, 18, 46, 49], "termin": 59, "terminologi": [12, 16], "test": [1, 12, 17, 39, 41], "text": [12, 15, 36, 37, 46, 48], "thei": [12, 22, 32, 35], "them": [12, 21, 46, 50, 51, 56, 57, 60], "thi": [1, 2, 3, 12, 16, 17, 18, 21, 22, 23, 36, 39, 41, 46, 49, 50, 51, 53, 55, 56, 57, 59, 60, 61], "those": 60, "through": [46, 47, 59], "throughout": 36, "throw": [12, 15, 18, 46, 48, 49], "time": 59, "timestamp": [12, 21], "timezon": [12, 21], "tissu": 60, "tool": [56, 57, 59, 60], "torr": 60, "trait": 60, "treatment": 60, "tree": [62, 63, 64], "tri": [46, 53], "true": [1, 12, 17, 21, 22, 39, 41, 46, 52, 54, 56, 57], "truefalsevalueset": [12, 22], "try": 59, "tupl": [1, 12, 17, 46, 51], "turn": 59, "two": [12, 21, 60, 62], "type": [1, 12, 16, 17, 18, 22, 39, 41, 44, 46, 49, 52, 53, 60], "type_str": [18, 46, 49], "typic": [12, 16, 18, 46, 49], "ubuntu": 59, "unclear": [12, 21, 46, 50], "under": 59, "underli": 60, "underscor": [12, 17, 36, 55], "understand": 60, "union": [12, 17, 39, 41], "uniqu": [1, 12, 17], "unit": [12, 21, 46, 50, 60], "unix": 59, "unknow": [12, 21, 46, 50], "unknown": [1, 12, 17, 22, 39, 41], "unrecogn": [18, 46, 49], "up": [1, 12, 17, 21, 59, 60], "updat": 59, "url": [2, 4, 12, 16], "us": [1, 2, 3, 12, 15, 17, 21, 22, 23, 25, 32, 33, 34, 35, 36, 39, 41, 46, 48, 50, 53, 54, 56, 57, 60], "usag": [12, 16], "usecas": [12, 22], "user": [18, 46, 49, 58, 59, 60], "utc": [12, 21], "utf": [39, 40, 44], "util": [1, 12, 17, 21], "v2": [1, 59, 60], "valid": [1, 12, 17, 22, 27, 36, 39, 41, 55, 59, 60], "validate_command": 7, "valu": [1, 12, 16, 17, 22, 23, 25, 32, 33, 34, 35, 36, 39, 41, 45, 46, 52, 53, 54, 59, 60], "value1": [12, 17], "value2": [12, 17], "value_set": [1, 12, 17, 39, 41], "value_set_descript": [12, 22, 46, 54], "value_set_nam": [12, 22, 46, 54], "value_set_str": [12, 22, 46, 54], "value_str": [46, 52, 53], "valueerror": [12, 15, 18, 46, 48, 49], "valueset": [1, 12, 17, 22, 39, 41, 46, 54], "variabl": [1, 12, 15, 16, 17, 21, 22, 59], "variat": [12, 21, 46, 50], "variou": 2, "venv": 59, "veri": [59, 60], "verifi": 59, "version": [2, 5, 6, 12, 15, 16, 46, 48, 59, 60], "via": 59, "viabl": [12, 22], "visit": 59, "wa": 60, "wagner": 60, "wai": [59, 60], "want": 59, "warn": [1, 12, 15, 17, 18, 39, 41, 46, 48, 49, 60], "we": [12, 22, 59, 60], "websit": [59, 60], "well": 60, "when": [1, 12, 17, 18, 39, 41, 46, 49], "where": [2, 3, 12, 21, 36, 37, 46, 51, 59], "whether": [1, 12, 15, 17, 21, 39, 41, 46, 48, 50], "which": [12, 17, 21, 23, 26, 46, 50, 51, 59, 60], "while": [12, 21, 60], "who": 60, "width": [12, 17], "win": 59, "window": 59, "within": [12, 17, 60], "word": 60, "work": [12, 17, 46, 53, 59], "would": 60, "wrapper": [46, 53], "write": [32, 35, 36, 37, 39, 42], "write_to_fil": [36, 37], "written": 59, "wrong": [36, 45], "www": [2, 6, 59], "x": 60, "x86_64": 59, "xcode": 59, "xlsx": [39, 40], "xml": [39, 40, 44], "y": [59, 60], "year": [12, 21], "year_str": [12, 21], "yet": 59, "you": [59, 60, 61], "your": 59, "yournam": 59, "z": [12, 17, 21], "zero": [12, 21]}, "titles": ["API reference", "phenopacket_mapper package", "phenopacket_mapper.api_requests package", "phenopacket_mapper.api_requests.api_request_super_class module", "phenopacket_mapper.api_requests.get module", "phenopacket_mapper.api_requests.hpo_api_request module", "phenopacket_mapper.api_requests.orpha_api_request module", "phenopacket_mapper.cli package", "phenopacket_mapper.cli.main module", "phenopacket_mapper.cli.mapping_command module", "phenopacket_mapper.cli.quickstart_command module", "phenopacket_mapper.cli.validate_command module", "phenopacket_mapper.data_standards package", "phenopacket_mapper.data_standards.DataModel2PhenopacketSchema module", "phenopacket_mapper.data_standards.cardinality module", "phenopacket_mapper.data_standards.code module", "phenopacket_mapper.data_standards.code_system module", "phenopacket_mapper.data_standards.data_model module", "phenopacket_mapper.data_standards.data_models package", "phenopacket_mapper.data_standards.data_models.erdri_cds module", "phenopacket_mapper.data_standards.data_models.rarelink_datamodel module", "phenopacket_mapper.data_standards.date module", "phenopacket_mapper.data_standards.value_set module", "phenopacket_mapper.mapping package", "phenopacket_mapper.mapping.map_field module", "phenopacket_mapper.mapping.mapper module", "phenopacket_mapper.mapping.phenopacket_building_block module", "phenopacket_mapper.pipeline package", "phenopacket_mapper.pipeline.input module", "phenopacket_mapper.pipeline.mapper module", "phenopacket_mapper.pipeline.output module", "phenopacket_mapper.pipeline.validate module", "phenopacket_mapper.preprocessing package", "phenopacket_mapper.preprocessing.preprocess module", "phenopacket_mapper.preprocessing.preprocess_dict module", "phenopacket_mapper.preprocessing.preprocess_method module", "phenopacket_mapper.utils package", "phenopacket_mapper.utils.create_ipynb_in_code module", "phenopacket_mapper.utils.get_field_name module", "phenopacket_mapper.utils.io package", "phenopacket_mapper.utils.io.data_reader module", "phenopacket_mapper.utils.io.input module", "phenopacket_mapper.utils.io.output module", "phenopacket_mapper.utils.io.read_json module", "phenopacket_mapper.utils.io.read_xml module", "phenopacket_mapper.utils.pandas_utils module", "phenopacket_mapper.utils.parsing package", "phenopacket_mapper.utils.parsing.get_codesystem_by_namespace_prefix module", "phenopacket_mapper.utils.parsing.parse_coding module", "phenopacket_mapper.utils.parsing.parse_data_type module", "phenopacket_mapper.utils.parsing.parse_date module", "phenopacket_mapper.utils.parsing.parse_ordinal module", "phenopacket_mapper.utils.parsing.parse_primitive_data_value module", "phenopacket_mapper.utils.parsing.parse_value module", "phenopacket_mapper.utils.parsing.parse_value_set module", "phenopacket_mapper.utils.str_to_valid_id module", "phenopacket_mapper.validate package", "phenopacket_mapper.validate.validate module", "Welcome to Phenopacket Mapper\u2019s documentation!", "Installation", "Introduction", "Quickstart", "User Guides", "Create a Data Model in Code", "Read a Data Model from a File"], "titleterms": {"": 58, "about": 58, "anaconda": 59, "api": 0, "api_request": [2, 3, 4, 5, 6], "api_request_super_class": 3, "ar": 60, "cardin": 14, "cli": [7, 8, 9, 10, 11], "code": [15, 63], "code_system": 16, "content": [58, 62], "creat": [59, 63], "create_ipynb_in_cod": 37, "data": [63, 64], "data_model": [17, 18, 19, 20], "data_read": 40, "data_standard": [12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22], "datamodel2phenopacketschema": 13, "date": 21, "document": 58, "environ": 59, "erdri_cd": 19, "featur": 60, "file": 64, "from": 64, "get": 4, "get_codesystem_by_namespace_prefix": 47, "get_field_nam": 38, "git": 59, "guid": 62, "hpo_api_request": 5, "indic": 58, "input": [28, 41], "instal": 59, "introduct": 60, "io": [39, 40, 41, 42, 43, 44], "java": 59, "local": 59, "main": 8, "map": [23, 24, 25, 26], "map_field": 24, "mapper": [25, 29, 58, 59], "mapping_command": 9, "model": [63, 64], "modul": [3, 4, 5, 6, 8, 9, 10, 11, 13, 14, 15, 16, 17, 19, 20, 21, 22, 24, 25, 26, 28, 29, 30, 31, 33, 34, 35, 37, 38, 40, 41, 42, 43, 44, 45, 47, 48, 49, 50, 51, 52, 53, 54, 55, 57], "motiv": 60, "orpha_api_request": 6, "output": [30, 42], "packag": [1, 2, 7, 12, 18, 23, 27, 32, 36, 39, 46, 56], "pandas_util": 45, "pars": [46, 47, 48, 49, 50, 51, 52, 53, 54], "parse_cod": 48, "parse_d": 50, "parse_data_typ": 49, "parse_ordin": 51, "parse_primitive_data_valu": 52, "parse_valu": 53, "parse_value_set": 54, "phenopacket": [58, 59, 60], "phenopacket_building_block": 26, "phenopacket_mapp": [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57], "pip": 59, "pipelin": [27, 28, 29, 30, 31], "preprocess": [32, 33, 34, 35], "preprocess_dict": 34, "preprocess_method": 35, "public": 60, "python": 59, "quickstart": 61, "quickstart_command": 10, "rarelink_datamodel": 20, "read": 64, "read_json": 43, "read_xml": 44, "refer": 0, "resourc": 60, "standard": 59, "str_to_valid_id": 55, "submodul": [2, 7, 12, 18, 23, 27, 32, 36, 39, 46, 56], "subpackag": [1, 12, 36], "tabl": 58, "tldr": 60, "us": 59, "user": 62, "util": [36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55], "valid": [31, 56, 57], "validate_command": 11, "value_set": 22, "virtual": 59, "welcom": 58, "what": 60, "why": 60, "wip": 59}}) \ No newline at end of file