Merge from main to gh-pages

CITATION.cff

@@ -14,7 +14,7 @@ authors:
 
 
 repository-code: "https://github.com/caltechlibrary/irdmtools"
-version: 0.0.83
+version: 0.0.84-dev
 license-url: "https://caltechlibrary.github.io/irdmtools/LICENSE"
 keywords: [ "institutional repository", "data
 management", "Invenio", "Invenio-RDM" ]

CaltechAUTHORS_publisher_groups.csv

@@ -189,23 +189,81 @@ American Astronomical Society,Astrophysical Journal,0004-637X,1538-4357,,omit in
 American Astronomical Society,Astrophysical Journal Supplement Series,1538-4365,0067-0049,,omit initial The from journal title
 American Astronomical Society,Planetary Science Journal,,2632-3338,,omit initial The from journal title
 American Astronomical Society,Research Notes of the AAS,,2515-5172,,omit initial The from journal title
-American Chemical Society,Journal of Organic Chemistry,,,,omit initial The from journal title
-American Chemical Society,Journal of Physical Chemistry,,,,omit initial The from journal title
-American Chemical Society,Journal of Physical Chemistry A,,,,omit initial The from journal title
-American Chemical Society,Journal of Physical Chemistry B,,,,omit initial The from journal title
-American Chemical Society,Journal of Physical Chemistry C,,,,omit initial The from journal title
-American Chemical Society,Journal of Physical Chemistry Letters,,,,omit initial The from journal title
+American Chemical Society,Journal of Organic Chemistry,0022-3263,1520-6904,,omit initial The from journal title
+American Chemical Society,Journal of Physical Chemistry,0022-3654,,,omit initial The from journal title
+American Chemical Society,Journal of Physical Chemistry A,1089-5639,1520-5215,,omit initial The from journal title
+American Chemical Society,Journal of Physical Chemistry B,1520-6106,1520-5207,,omit initial The from journal title
+American Chemical Society,Journal of Physical Chemistry C,1932-7447,1932-7455,,omit initial The from journal title
+American Chemical Society,Journal of Physical Chemistry Letters,,1948-7185,,omit initial The from journal title
 American Associaition for the Advancement of Science,Science,,,,
 American Associaition for the Advancement of Science,Science Advances,,,,
 American Associaition for the Advancement of Science,Science Immunology,,,,
 American Associaition for the Advancement of Science,Science Robitics,,,,
 American Associaition for the Advancement of Science,Science Signaling,,,,
 American Associaition for the Advancement of Science,Science Translational Medicine,,,,
-National Academy of Sciences,Proceedings of the National Academy of Sciences,,,,
-National Academy of Sciences,PNAS Nexus,,,,
+National Academy of Sciences,Proceedings of the National Academy of Sciences,0027-8424,1091-6490,,
+National Academy of Sciences,PNAS Nexus,,2752-6542,,
 Seismological Society of America,Bulletin of the Seismological Society of America,0037-1106,0037-1107,,
-Seismological Society of America,Seismological Research Letters,,,,
+Seismological Society of America,Seismological Research Letters,0895-0695,1938-2057,,
 Royal Astronomical Society,Monthly Notice of the Royal Astronomial Society,0035-2966,1365-2966,,
 Royal Astronomical Society,Monthly Notice of the Royal Astronomial Society Letters,1745-3925,1745-3933,,
 Royal Astronomical Society,Geophysical Journal International,0956-540X,1365-246X,,
-Royal Astronomical Society,RAS Techniques and Instruments,,2752-8200,,
+Royal Astronomical Society,RAS Techniques and Instruments,,2752-8200,,
+American Geophysical Union,AGU Advances,,2576-604X,,
+American Geophysical Union,Community Science,2692-9430,2692-9430,,
+American Geophysical Union,Earth's Future,,2328-4277,,
+American Geophysical Union,Earth and Space Science,,2333-5084,,
+American Geophysical Union,"Geochemistry, Geophysics, Geosystems",,1525-2027,,
+American Geophysical Union,GeoHealth,,2471-1403,,
+American Geophysical Union,Geophysical Research Letters,0094-8276,1944-8007,,
+American Geophysical Union,Global Biogeochemical Cycles,0886-6236,1944-9224,,
+American Geophysical Union,Journal of Advances in Modeling Earth System (JAMES),,1942-2466,,
+American Geophysical Union,Paleoceanography and Paleoclimatology,,2572-4525,,
+American Geophysical Union,Perspectives of Earth and Space Scientists,,2637-6989,,
+American Geophysical Union,Radio Science,0048-6604,1944-799X,,
+American Geophysical Union,Reviews of Geophysics,8755-1209,1944-9208,,
+American Geophysical Union,Space Weather,,1542-7390,,
+American Geophysical Union,Space Weather Quarterly,,1539-4964,,
+American Geophysical Union,Tectonics,0278-7407,1944-9194,,
+American Geophysical Union,Water Resources Research,0043-1397,1944-7973,,
+American Geophysical Union,Journal of Geophysical Research: Atmospheres,2169-897X,2169-8996,,
+American Geophysical Union,Journal of Geophysical Research: Biogeosciences,2169-8953,2169-8961,,
+American Geophysical Union,Journal of Geophysical Research: Earth Surface,2169-9011,2169-9003,,
+American Geophysical Union,Journal of Geophysical Research: Machine Learning and Computation,,2993-5210,,
+American Geophysical Union,Journal of Geophysical Research: Oceans,2169-9275,2169-9291,,
+American Geophysical Union,Journal of Geophysical Research: Planets,2169-9097,2169-9100,,
+American Geophysical Union,Journal of Geophysical Research: Solid Earth,2169-9356,2169-9313,,
+American Geophysical Union,Journal of Geophysical Research: Space Physics,2169-9380,2169-9402,,
+American Geophysical Union,Journal of Geophysical Research,2156-2202,0148-0227,,
+International Union of Crystallography,Acta Crystallographica. Section A,0108-7673,2053-2733,,
+International Union of Crystallography,Acta Crystallographica. Section A,1600-5724,0108-7673,,
+International Union of Crystallography,Acta Crystallographica. Section B,2052-5192,2052-5206,,
+International Union of Crystallography,Acta Crystallographica. Section B,0108-7681,,,
+International Union of Crystallography,Acta Crystallographica. Section C,1600-5759,2053-2296,,
+International Union of Crystallography,Acta Crystallographica. Section D,,2059-7983,,
+International Union of Crystallography,Acta Crystallographica. Section E,2056-9890,2056-9890,,
+International Union of Crystallography,Acta Crystallographica. Section F,,2053-230X,,
+International Union of Crystallography,Acta Crystallographica. Section E,1600-5368,,,
+International Union of Crystallography,Journal of Applied Crystallography,,1600-5767,,
+International Union of Crystallography,Journal of Synchrotron Radiation,,1600-5775,,
+International Union of Crystallography,IUCrJ,,2052-2525,,
+International Union of Crystallography,IUCrData,,2414-3146,,
+,,,,,
+,,,,,
+,,,,,
+,,,,,
+,,,,,
+,,,,,
+,,,,,
+,,,,,
+,,,,,
+,,,,,
+,,,,,
+,,,,,
+,,,,,
+,,,,,
+,,,,,
+,,,,,
+,,,,,
+,,,,,
+IUCr,,,,,

INSTALL.html

@@ -31,14 +31,15 @@ <h1 id="install">INSTALL</h1>
 <p>To test the latest version you need the required development
 environment and follow the steps listed below in “Compiling from
 Source”.</p>
-<h2 id="quick-install-using-curl">Quick install using curl</h2>
+<h2 id="quick-install-using-curl-or-irm">Quick install using curl or
+irm</h2>
 <p>The following experimental installer should get the latest stable
 release for macOS and Linux (e.g. Debian, Ubuntu, Raspberry Pi OS).</p>
 <p>Copy and run the following command in your shell (e.g. Terminal)</p>
 <pre><code>curl https://caltechlibrary.github.io/irdmtools/installer.sh | sh</code></pre>
-<p>NOTE: Windows 11 support is via Window’s Sub-System for Linux (aka
-WSL). If you have that available then you can use the installer example
-above.</p>
+<p>For Windows you can use a Powershell script with the following
+command.</p>
+<pre><code>irm https://caltechlibrary.github.io/irdmtools/installer.ps1 | iex</code></pre>
 <h2 id="requirements">Requirements</h2>
 <p>This may change in the future.</p>
 <ul>

INSTALL.md

@@ -6,8 +6,8 @@ irdmtools is an **experimental** Go package and command line tools for working w
 
 To test the latest version you need the required development environment and follow the steps listed below in "Compiling from Source".
 
-Quick install using curl
-------------------------
+Quick install using curl or irm
+-------------------------------
 
 The following experimental installer should get the latest stable release for macOS and Linux (e.g. Debian, Ubuntu, Raspberry Pi OS). 
 
@@ -17,7 +17,11 @@ Copy and run the following command in your shell (e.g. Terminal)
 curl https://caltechlibrary.github.io/irdmtools/installer.sh | sh
 ~~~
 
-NOTE: Windows 11 support is via Window's Sub-System for Linux (aka WSL). If you have that available then you can use the installer example above.
+For Windows you can use a Powershell script with the following command.
+
+~~~
+irm https://caltechlibrary.github.io/irdmtools/installer.ps1 | iex
+~~~
 
 
 Requirements

Makefile

@@ -35,7 +35,7 @@ ifeq ($(OS), Windows)
 	EXT = .exe
 endif
 
-build: version.go $(PROGRAMS) man CITATION.cff about.md installer.sh
+build: version.go $(PROGRAMS) man CITATION.cff about.md installer.sh installer.ps1
 
 version.go: .FORCE
 	@echo '' | pandoc --from t2t --to plain \
@@ -71,10 +71,19 @@ about.md: codemeta.json $(PROGRAMS)
 	@if [ -f _codemeta.json ]; then rm _codemeta.json; fi
 
 installer.sh: .FORCE
-	@echo '' | pandoc --metadata title="Installer" --metadata git_org_or_person="$(GIT_GROUP)" --metadata-file codemeta.json --template codemeta-installer.tmpl >installer.sh
+	@echo '' | pandoc --metadata title="Installer" --metadata git_org_or_person="$(GIT_GROUP)" --metadata-file codemeta.json --template codemeta-bash-installer.tmpl >installer.sh
 	@chmod 775 installer.sh
 	@git add -f installer.sh
 
+<<<<<<< HEAD
+=======
+installer.ps1: .FORCE
+	@echo '' | pandoc --metadata title="Installer" --metadata git_org_or_person="$(GIT_GROUP)" --metadata-file codemeta.json --template codemeta-ps1-installer.tmpl >installer.ps1
+	@chmod 775 installer.ps1
+	@git add -f installer.ps1
+
+
+>>>>>>> 40efc058f9e30a71a08de3f33fa78b223c688882
 test: $(PACKAGE)
 	#go test -timeout 120h
 	go test -test.v -run Test01Config

about.html

@@ -24,7 +24,7 @@
 
 <section>
 <h1 id="about-this-software">About this software</h1>
-<h2 id="irdmtools-0.0.83">irdmtools 0.0.83</h2>
+<h2 id="irdmtools-0.0.84-dev">irdmtools 0.0.84-dev</h2>
 <h3 id="authors">Authors</h3>
 <ul>
 <li>R. S. Doiel</li>

about.md

@@ -14,7 +14,7 @@ authors:
     orcid: "https://orcid.org/0000-0001-9266-5146"
 
 repository-code: "https://github.com/caltechlibrary/irdmtools"
-version: 0.0.83
+version: 0.0.84-dev
 license-url: "https://caltechlibrary.github.io/irdmtools/LICENSE"
 keywords: [ "institutional repository", "data
 management", "Invenio", "Invenio-RDM" ]
@@ -24,7 +24,7 @@ management", "Invenio", "Invenio-RDM" ]
 About this software
 ===================
 
-## irdmtools 0.0.83
+## irdmtools 0.0.84-dev
 
 ### Authors
 

cmd/ep3util/ep3util.go

@@ -137,6 +137,9 @@ with one of the options, e.g. `+"`"+`-all`+"`"+`, you can skip providing the KEY
 -modified START [END]
 : Harvest records modified between start and end dates.
 
+-as-citations
+: This harvests the record into a minimal citation form similar to citeproc
+
 # ACTION_PARAMETERS
 
 Action parameters are the specific optional or required parameters need to complete an aciton.

codemeta-ps1-installer.tmpl

@@ -0,0 +1,48 @@
+#!/usr/bin/env pwsh
+# Generated with codemeta-ps1-installer.tmpl, see https://github.com/caltechlibrary/codemeta-pandoc-examples
+
+#
+# Set the package name and version to install
+#
+$$PACKAGE = "$name$"
+$$VERSION = "$version$"
+$$GIT_GROUP = "$git_org_or_person$"
+$$RELEASE = "https://github.com/$${GIT_GROUP}/$${PACKAGE}/releases/tag/v$${VERSION}"
+$$SYSTEM_TYPE = Get-ComputerInfo -Property CsSystemType
+if ($$SYSTEM_TYPE.CsSystemType.Contains("ARM64")) {
+    $$MACHINE = "arm64"
+} else {
+    $$MACHINE = "x86_64"
+}
+
+# FIGURE OUT Install directory
+$$BIN_DIR = "$${Home}\bin"
+Write-Output "$${PACKAGE} will be installed in $${BIN_DIR}"
+
+#
+# Figure out what the zip file is named
+#
+$$ZIPFILE = "$${PACKAGE}-v$${VERSION}-Windows-$${MACHINE}.zip"
+
+#
+# Check to see if this zip file has been downloaded.
+#
+$$DOWNLOAD_URL = "https://github.com/$${GIT_GROUP}/$${PACKAGE}/releases/download/v$${VERSION}/$${ZIPFILE}"
+
+if (!(Test-Path $$BIN_DIR)) {
+  New-Item $$BIN_DIR -ItemType Directory | Out-Null
+}
+curl.exe -Lo "$${ZIPFILE}" "$${DOWNLOAD_URL}"
+
+tar.exe xf "$${ZIPFILE}" -C "$${Home}"
+
+Remove-Item $$ZIPFILE
+
+$$User = [System.EnvironmentVariableTarget]::User
+$$Path = [System.Environment]::GetEnvironmentVariable('Path', $$User)
+if (!(";$${Path};".ToLower() -like "*;$${BIN_DIR};*".ToLower())) {
+  [System.Environment]::SetEnvironmentVariable('Path', "$${Path};$${BIN_DIR}", $$User)
+  $$Env:Path += ";$${BIN_DIR}"
+}
+
+Write-Output "$${PACKAGE} was installed successfully to $${BIN_DIR}"

codemeta.json

@@ -5,10 +5,10 @@
     "codeRepository": "https://github.com/caltechlibrary/irdmtools",
     "dateCreated": "2022-10-27",
 	"dateRelease": "2024-01-24",
-	"dateModified": "2024-04-29",
+	"dateModified": "2024-06-10",
     "issueTracker": "https://github.com/caltechlibrary/irdmtools/issues",
     "name": "irdmtools",
-    "version": "0.0.83",
+    "version": "0.0.84-dev",
     "description": "Tools for working with institutional repositories and data management systems. Current implementation targets Invenio-RDM.",
     "applicationCategory": "library science",
     "releaseNotes": "Proof of concept and refinements, piloting in production, bug fixes, performance improvements",

config.go

@@ -43,50 +43,54 @@ import (
 
 	// Caltech Library packages
 	"github.com/caltechlibrary/dataset/v2"
+
+	// 3rd Party Libraries
+	"gopkg.in/yaml.v3"
 )
 
 // Config holds the common configuration used by all irdmtools
 type Config struct {
 	// Debug is set true then methods with access to the Config obect
 	// can use this flag to implement addition logging to standard err
-	Debug bool `json:"-"`
+	Debug bool `json:"-", yaml:"-"`
 	// Repository Name, e.g. CaltechAUTHORS, CaltechTHESIS, CaltechDATA
-	RepoName string `json:"repo_name,omitempty"`
+	RepoName string `json:"repo_name,omitempty" yaml:"repo_name,omitempty"`
 	// Repository ID, e.g. caltechauthors, caltechthesis, caltechdata (usually the db name for repository)
 	// NOTE: It should also match the Postgres DB name used by RDM
-	RepoID string `json:"repo_id,omitempty"`
+	RepoID string `json:"repo_id,omitempty" yaml:"repo_id,omitempty"`
 	// InvenioAPI holds the URL to the InvenioAPI
-	InvenioAPI string `json:"rdm_url,omitempty"`
+	InvenioAPI string `json:"rdm_url,omitempty" yaml:"rdm_url,omitempty"`
 	// InvenioToken is holds the token string to access the API
-	InvenioToken string `json:"rdmtok,omitempty"`
+	InvenioToken string `json:"rdmtok,omitempty" yaml:"rdmtok,omitempty"`
 	// Invenio DSN holds the data source name for the Postgres database storing the invenio records
-	InvenioDSN string `json:"rdm_dsn,omitempty"`
+	InvenioDSN string `json:"rdm_dsn,omitempty" yaml:"rdm_dsn,omitempty"`
 	// InvenioStorage holds the URI to the default storage of Invenio RDM objects, e.g. local file system or S3 bucket
-	InvenioStorage string `json:"rdm_storage,omitempty"`
+	InvenioStorage string `json:"rdm_storage,omitempty" yaml:"rdm_storage,omitempty"`
 	// InvenioCommunityID holds the community id for use with the API.
-	InvenioCommunityID string `json:"rdm_community_id,omitempty"`
+	InvenioCommunityID string `json:"rdm_community_id,omitempty" yaml:"rdm_community_id,omitempty"`
 	// InvenioDbHost holds the name of the machine for the Postgres server
-	InvenioDbHost string `json:"rdm_db_host,omitempty"`
+	InvenioDbHost string `json:"rdm_db_host,omitempty" yaml:"rdm_db_host,omitempty"`
 	// InvenioDbUser holds the database username of the machine for the Postgres server
-	InvenioDbUser string `json:"rdm_db_user,omitempty"`
+	InvenioDbUser string `json:"rdm_db_user,omitempty" yaml:"rdm_db_user,omitempty"`
 	// InvenioDbPassword holds the database password of the machine for the Postgres server
-	InvenioDbPassword string `json:"rdm_db_password,omitempty"`
+	InvenioDbPassword string `json:"rdm_db_password,omitempty" yaml:"rdm_db_password,omitempty"`
 
 	// CName holds the dataset collection name used when harvesting content
-	CName string `json:"c_name,omitempty"`
+	CName string `json:"c_name,omitempty" yaml:"c_name,omitempty"`
 	// MailTo holds an email address to use when an email (e.g. CrossRef API access) is needed
-	MailTo string `json:"mailto,omitempty"`
+	MailTo string `json:"mailto,omitempty" yaml:"mailto,omitempty"`
 	// ds his a non-public point to an dataset collection structure
 	ds *dataset.Collection
 
 	// EPrint configuration needed for migration related tools
-	EPrintHost string `json:"eprint_host,omitempty"`
-	EPrintUser string `json:"eprint_user,omitempty"`
-	EPrintPassword string `json:"eprint_password,omitempty"`
-	EPrintArchivesPath string `json:"eprint_archives_path,omitempty"` 
-	EPrintDbHost string `json:"eprint_db_host,omitempty"`
-	EPrintDbUser string `json:"eprint_db_user,omitempty"`
-	EPrintDbPassword string `json:"eprint_db_password,omitempty"`
+	EPrintHost string `json:"eprint_host,omitempty" yaml:"eprint_host,omitempty"`
+	EPrintUser string `json:"eprint_user,omitempty" yaml:"eprint_user,omitempty"`
+	EPrintPassword string `json:"eprint_password,omitempty" yaml:"eprint_password,omitempty"`
+	EPrintArchivesPath string `json:"eprint_archives_path,omitempty" yaml:"eprint_archives_path,omitempty"` 
+	EPrintDbHost string `json:"eprint_db_host,omitempty" yaml:"eprint_db_host,omitempty"`
+	EPrintDbUser string `json:"eprint_db_user,omitempty" yaml:"eprint_db_user,omitempty"`
+	EPrintDbPassword string `json:"eprint_db_password,omitempty" yaml:"eprint_db_password,omitempty"`
+	EPrintBaseURL string`json:"eprint_base_url,omitempty" yaml:"eprint_base_url,omitempty"`
 
 
 	// rl holds rate limiter data for throttling API requests
@@ -252,8 +256,14 @@ func (cfg *Config) LoadConfig(configFName string) error {
 	if err != nil {
 		return err
 	}
-	if err := JSONUnmarshal(src, &cfg); err != nil {
-		return err
+	if strings.HasSuffix(configFName, ".yaml") {
+		if err := yaml.Unmarshal(src, &cfg); err != nil {
+			return err
+		}
+	} else {
+		if err := JSONUnmarshal(src, &cfg); err != nil {
+			return err
+		}
 	}
 	// Build our DSN if not set.
 	if cfg.InvenioDSN == "" {