Merge pull request #73 from morphic-bio/esv-fixes-schemaprots

Made changes as requested. @morphic-bio/data-ingestion-development#80
morphic-bio · Oct 3, 2024 · 8de6c0c · 8de6c0c
2 parents 6288fd2 + 952ab0a
commit 8de6c0c
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Showing 6 changed files with 49 additions and 17 deletions.
diff --git a/json_schema/type/biomaterial/differentiated_product.json b/json_schema/type/biomaterial/differentiated_product.json
@@ -46,6 +46,7 @@
             "title": "Content",
             "required": [
                 "label",
+                "differentiated_product_protocol_id",
                 "terminally_differentiated",
                 "timepoint_unit",
                 "timepoint_value"
@@ -71,6 +72,19 @@
                         "KOLF2.2J derived knockout cell line, PAX6/STL2 DKO, differentiated into trophoblasts"
                     ]
                 },
+                "differentiated_product_protocol_id": {
+                    "type": "string",
+                    "format": "regex",
+                    "pattern": "^[a-zA-Z0-9_]*$",
+                    "minLength": 1,
+                    "description": "An ID for the differentiation protocol used. No spaces allowed.",
+                    "title": "Differentiated product protocol ID",
+                    "examples": [
+                        "JAXPD002",
+                        "EB_Protocol_Final_Merged.pdf",
+                        "msk_pancreatic_diff_protocol"
+                  ]
+                },
                 "terminally_differentiated": {
                     "type": "string",
                     "description": "Is the cell line terminally differentiated.",

diff --git a/json_schema/type/biomaterial/library_preparation.json b/json_schema/type/biomaterial/library_preparation.json
@@ -45,7 +45,8 @@
             "type": "object",
             "title": "Content",
             "required": [
-                "label"
+                "label",
+                "library_preparation_protocol_id"
             ],
             "dependentRequired": {
                 "concentration_unit": [
@@ -88,6 +89,19 @@
                         "Run 1, batch 1S, library preparation from KOLF2.2J derived trophoblasts"
                     ]
                 },
+                "library_preparation_protocol_id": {
+                    "type": "string",
+                    "format": "regex",
+                    "pattern": "^[a-zA-Z0-9_]*$",
+                    "minLength": 1,
+                    "description": "An ID for the library preparation protocol used. No spaces allowed.",
+                    "title": "Library preparation protocol ID",
+                    "examples": [
+                        "msk_pooled_wt_transcriptome",
+                        "Library_preparation_bulk.pdf",
+                        "JAXPL001"
+                  ]
+                },
                 "average_fragment_size": {
                     "type": "integer",
                     "description": "Average fragment size for the transcripts in the library preparation, in base pairs.",

diff --git a/json_schema/type/biomaterial/undifferentiated_product.json b/json_schema/type/biomaterial/undifferentiated_product.json
@@ -29,7 +29,8 @@
       "type": "object",
       "title": "Content",
       "required": [
-        "label"
+        "label",
+        "undifferentiated_product_protocol_id"
       ],
       "properties": {
         "label": {
@@ -54,6 +55,18 @@
             "Unmodified \"Grandparent\" KOLF2.2 treated with DMSO"
           ]
         },
+        "undifferentiated_product_protocol_id": {
+          "type": "string",
+          "format": "regex",
+          "pattern": "^[a-zA-Z0-9_]*$",
+          "minLength": 1,
+          "description": "An ID for the protocol applied on the undifferentiated product (if applicable). No spaces allowed.",
+          "title": "Undifferentiated product protocol ID",
+          "examples": [
+            "Auxin_induction_cell_line",
+            "DMSO_treated_iPSC"
+          ]
+        },
         "timepoint_value": {
           "type": "integer",
           "description": "Value of the timepoint. Only integers accepted.",

diff --git a/json_schema/type/file/sequence_file.json b/json_schema/type/file/sequence_file.json
@@ -117,15 +117,6 @@
                         51,
                         150
                     ]
-                },
-                "checksum": {
-                    "type": "string",
-                    "minLength": 1,
-                    "description": "MD5 checksum of the file.",
-                    "title": "Checksum",
-                    "examples": [
-                        "e09a986c2e630130b1849d4bf9a94c06"
-                    ]
                 }
             }
         }

diff --git a/json_schema/type/protocol/expression_alteration.json b/json_schema/type/protocol/expression_alteration.json
@@ -39,7 +39,7 @@
           "pattern": "^[a-zA-Z0-9_]*$",
           "minLength": 1,
           "description": "A unique ID for the gene expression alteration protocol. No spaces allowed.",
-          "title": "Gene expression alteration protocol ID",
+          "title": "Gene expression alteration ID",
           "examples": [
             "JAXPE000E_MEIS1",
             "MSKKI119_MEF2C"

diff --git a/json_schema/versions.json b/json_schema/versions.json
@@ -10,17 +10,17 @@
       },
       "biomaterial": {
         "clonal_cell_line": "3.0.0",
-        "differentiated_product": "2.0.0",
-        "library_preparation": "2.0.0",
+        "differentiated_product": "3.0.0",
+        "library_preparation": "3.0.0",
         "organoid": "1.0.0",
-        "undifferentiated_product": "2.0.0"
+        "undifferentiated_product": "2.1.0"
       },
       "file": {
         "analysis_file": "1.0.0",
-        "sequence_file": "1.0.0"
+        "sequence_file": "2.0.0"
       },
       "protocol": {
-        "expression_alteration": "5.0.0"
+        "expression_alteration": "5.0.1"
       }
     }
   }