Merge branch 'master' into 4-create-taxon-pattern

iodepo · Apr 19, 2024 · 1993414 · 1993414
2 parents b63e870 + a99682c
commit 1993414
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diff --git a/.github/dependabot.yml b/.github/dependabot.yml
@@ -0,0 +1,8 @@
+# https://docs.github.com/code-security/dependabot/dependabot-version-updates/configuration-options-for-the-dependabot.yml-file
+
+version: 2
+updates:
+  - package-ecosystem: "github-actions" # See documentation for possible values
+    directory: "/" # Location of package manifests
+    schedule:
+      interval: "weekly"
diff --git a/.github/workflows/check-crlf.yml b/.github/workflows/check-crlf.yml
@@ -0,0 +1,20 @@
+# check for Windows CRLF in files
+# homepage: https://github.com/marketplace/actions/check-crlf
+
+name: Check CRLF
+
+on: [push, pull_request]
+
+jobs:
+  Check-CRLF:
+    name: verify that only LF linefeeds are used
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout repository contents
+        uses: actions/checkout@v4
+
+      - name: Use action to check for CRLF endings
+        uses: erclu/[email protected]
+        with: # ignore directories containing *.csv & data
+          exclude: /testData/
diff --git a/.github/workflows/irc_notify.yml b/.github/workflows/irc_notify.yml
@@ -0,0 +1,46 @@
+# send build notifications to the #odis IRC channel
+# homepage: https://github.com/marketplace/actions/notify-irc
+
+name: "IRC Push Notification"
+on: 
+  push:
+    branches:
+      - master
+  pull_request:
+    branches:
+      - master
+
+jobs:
+  irc_notify:
+    runs-on: ubuntu-latest
+    #if: github.repository == 'iodepo/odis-in'
+    steps:
+      - name: irc push
+        uses: rectalogic/notify-irc@v2
+        if: github.event_name == 'push'
+        with:
+          channel: "#odis"
+          server: "irc.libera.chat"
+          nickname: odis-github-notifier
+          message: |
+            ${{ github.actor }} pushed ${{ github.event.ref }} ${{ github.event.compare }}
+            ${{ join(github.event.commits.*.message) }}
+      - name: irc pull request
+        uses: rectalogic/notify-irc@v2
+        if: github.event_name == 'pull_request'
+        with:
+          channel: "#odis"
+          server: "irc.libera.chat"
+          nickname: odis-github-notifier
+          message: |
+            ${{ github.actor }} opened PR ${{ github.event.pull_request.html_url }}
+            ${{ github.event.pull_request.title }}
+      - name: irc tag created
+        uses: rectalogic/notify-irc@v2
+        if: github.event_name == 'create' && github.event.ref_type == 'tag'
+        with:
+          channel: "#odis"
+          server: "irc.libera.chat"
+          nickname: odis-github-notifier
+          message: |
+            ${{ github.actor }} tagged ${{ github.repository }} ${{ github.event.ref }}
diff --git a/.github/workflows/json-yaml-validate.yml b/.github/workflows/json-yaml-validate.yml
@@ -0,0 +1,23 @@
+# validate JSON and YAML files
+# homepage: https://github.com/GrantBirki/json-yaml-validate
+
+name: Validate JSON and YAML files
+
+on: [push, pull_request]
+
+jobs:
+  json-yaml-validate:
+    name: json-yaml-validate
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout repository contents
+        uses: actions/checkout@v4
+
+      - name: json-yaml-validate
+        uses: GrantBirki/[email protected]
+        with:
+          base_dir: "./dataGraphs/thematics"        
+
+
+
diff --git a/dataGraphs/thematics/dataset/graphs/krillMetadata.json b/dataGraphs/thematics/dataset/graphs/krillMetadata.json
@@ -0,0 +1,179 @@
+{
+  "@context": {
+    "@vocab": "https://schema.org/",
+    "geosparql": "http://www.opengis.net/ont/geosparql#"
+  },
+  "@type": "Dataset",
+  "@id": "https://registry.org/permanentUrlToThisJsonDoc",
+  "name": "D20220226-T144737.raw",
+  "description": "An extended, free-text description of what's in the dataset, who created it, and other attributes",
+  "url": "https://urlToTheDatasetOrLandingPage.org/",
+  "license": "This work is licensed under a  Creative Commons Attribution (CC-BY) 4.0 License",
+  "sameAs": [
+    "https://URLforAnyEquivalentPages.org/"
+  ],
+  "citation": [
+    "Citation to other work relevant to this dataset",
+    "Citation to other work relevant to this dataset",
+    "Citation to other work relevant to this dataset"
+  ],
+  "version": "2021-04-24T06:34:56.000Z",
+  "keywords": [
+    "Keyword 1",
+    "Keyword 2",
+    "Keyword 3"
+  ],
+  "encoding": {
+    "@type": "MediaObject",
+    "encodingFormat": "text/plain",
+    "contentSize": "54960000"
+  },
+  "distribution": {
+    "@type": "DataDownload",
+    "contentUrl": "http://urlToDirectDownloadOfThisDataset.org/",
+    "encodingFormat": "application/octet-stream"
+  },
+  "potentialAction": {
+    "@type": "Action",
+    "name": "Use My API",
+    "description": "Use the API to retrieve data from my organization.",
+    "@id": "https://us-central1-top-operand-112611.cloudfunctions.net/function-1",
+    "result": {
+      "@type": "DataDownload",
+      "encodingFormat": "text/plain",
+      "description": "a simple text result for the RGB counts"
+    },
+    "target": {
+      "@type": "EntryPoint",
+      "urlTemplate": "https://us-central1-top-operand-112611.cloudfunctions.net/function-1",
+      "httpMethod": "POST",
+      "contentType": [
+        "image/jpeg",
+        "image/png"
+      ]
+    },
+    "object": {
+      "@type": "ImageObject",
+      "description": "A JPEG or PNG to analyze the RGB counts"
+    }
+  },
+  "identifier": {
+    "@id": "https://doi.org/10.5066/F7VX0DMQ",
+    "@type": "PropertyValue",
+    "name": "DOI: 10.5066/F7VX0DMQ",
+    "propertyID": "https://registry.identifiers.org/registry/doi",
+    "value": "doi:10.5066/F7VX0DMQ",
+    "url": "https://doi.org/10.5066/F7VX0DMQ"
+  },
+  "geosparql:hasGeometry": {
+    "@type": "http://www.opengis.net/ont/sf#Point",
+    "geosparql:asWKT": {
+      "@type": "http://www.opengis.net/ont/geosparql#wktLiteral",
+      "@value": "POINT (-45.70008 -60.04339)"
+    },
+    "geosparql:crs": {
+      "@id": "http://www.opengis.net/def/crs/OGC/1.3/CRS84"
+    }
+  },
+  "provider": [
+    {
+      "@type": "Organization",
+      "legalName": "Legal Name of Organisation which generated the dataset",
+      "name": "Other Name of Organisation which generated the dataset",
+      "url": "https://organisationWebsite.org/"
+    }
+  ],
+  "includedInDataCatalog": {
+    "@id": "https://registryOfCatalogs.org/permanentUrlIdentifiyingCatalog",
+    "@type": "DataCatalog",
+    "url": "https://urlOfDataCatalog.org"
+  },
+  "temporalCoverage": "2007/2007",
+  "additionalProperty": [
+    {
+      "@type": "PropertyValue",
+      "propertyID": "krill.akerbiomarine.com/vessel",
+      "value": "Saga Sea"
+    },
+    {
+      "@type": "PropertyValue",
+      "propertyID": "krill.akerbiomarine.com/sonarModel",
+      "value": "ES80"
+    },
+    {
+      "@type": "PropertyValue",
+      "propertyID": "krill.akerbiomarine.com/sonarType",
+      "value": "echosounder"
+    },
+    {
+      "@type": "PropertyValue",
+      "propertyID": "krill.akerbiomarine.com/frequencies",
+      "value": "[38, 120]"
+    },
+    {
+      "@type": "PropertyValue",
+      "propertyID": "krill.akerbiomarine.com/surveyTime",
+      "value": "2022-02-26T14:47:37"
+    },
+    {
+      "@type": "PropertyValue",
+      "propertyID": "krill.akerbiomarine.com/startTime",
+      "value": "2022-02-26 14:47:37.473999872"
+    },
+    {
+      "@type": "PropertyValue",
+      "propertyID": "krill.akerbiomarine.com/endTime",
+      "value": "2022-02-26 15:01:23.320000"
+    }
+  ],
+  "variableMeasured": [
+    {
+      "@type": "PropertyValue",
+      "name": "Name of a variable in the dataset",
+      "url": "http://ontology.org/uriToSemanticDescriptorOfThisVariable",
+      "description": "Extended description of this variable"
+    },
+    {
+      "@type": "PropertyValue",
+      "name": "Name of a variable in the dataset",
+      "url": "http://ontology.org/uriToSemanticDescriptorOfThisVariable",
+      "description": "Extended description of this variable?"
+    },
+    {
+      "@type": "PropertyValue",
+      "name": "SamplingDeviceApertureSurfaceArea",
+      "url": "http://ontology.org/uriToSemanticDescriptorOfThisVariable",
+      "description": "Extended description of this variable"
+    }
+  ],
+  "about": {
+    "@type": "Event",
+    "description": "Describe the event which is the subject of this dataset. For example, a cruise ID.",
+    "name": "Concise and descriptive name of the Event",
+    "potentialAction": {
+      "@type": "Action",
+      "name": "Concise but descriptive name of action that was part of an Event. For example, the name of a CTD cast",
+      "agent": [
+        "Name or permanent ID of person or thing that performed this action",
+        "Name or permanent ID of person or thing that performed this action",
+        "Name or permanent ID of person or thing that performed this action"
+      ],
+      "startTime": "2007-03-11T14:45UTC",
+      "endTime": "2007-03-11T15:42UTC",
+      "instrument": {
+        "@type": "Thing",
+        "name": "The name of the instrument used in the action. For example, the specific model of a CTD, a glider, a moored sensor",
+        "url": "http://ontology.org/uriToSemanticDescriptorOfThisInstrument",
+        "description": "Extended description of the sampling instrument"
+      }
+    }
+  },
+  "publishingPrinciples": [
+    {
+      "@type": "CreativeWork",
+      "url": "http://example.org/id/doc/ID",
+      "name": "Recommendations for assessing protected area status in US national waters",
+      "description": "This dataset was generated following the recommendations of ..."
+    }
+  ]
+}
diff --git a/dataGraphs/thematics/projects/graphs/proj.json b/dataGraphs/thematics/projects/graphs/proj.json
@@ -13,14 +13,12 @@
     "url": "https://www.example-data-repository.org/logo.jpg"
   },
   "identifier": {
-    "@id": "https://grid.ac/institutes/grid.475727.4",
     "@type": "PropertyValue",
     "description": "UN Department of Economic and Social Affairs Sustainable Development",
     "propertyID": "https://registry.identifiers.org/registry/grid",
     "url": "https://grid.ac/institutes/grid.475727.4"
   },
   "contactPoint": {
-    "@id": "https://www.example-data-repository.org/about-us",
     "@type": "ContactPoint",
     "name": "Support",
     "email": "[email protected]",
@@ -29,13 +27,11 @@
   },
   "funder": {
     "@type": "FundingAgency",
-    "@id": "https://dx.doi.org/10.13039/10000001",
     "name": "National Science Foundation",
     "legalName": "National Science Foundation",
     "alternateName": "NSF",
     "url": "https://www.nsf.gov/",
     "identifier": {
-      "@id": "https://example.org/id/resproj/X",
       "@type": "PropertyValue",
       "propertyID": "https://registry.identifiers.org/registry/doi",
       "value": "DOI value expressed as doi:{doi}",
@@ -44,33 +40,33 @@
   },
   "funding": [
     {
-      "@id": "{odo:hasAward -> odo:osprey_page}",
       "@type": "MonetaryGrant",
       "url": "http://www.someinstitute.edu",
       "name": "{odo:hasAward -> odo:hasAwardNumber}",
       "identifier": "{odo:hasAward -> odo:hasAwardNumber}",
       "funder": [
-        {
-          "@id": "https://dx.doi.org/10.13039/10000001"
-        },
         {
           "@type": "FundingAgency",
           "name": "Some other org",
-          "url": "https://example.funder.org/"
+          "url": "https://example.funder.org/",
+          "identifier": {
+            "@type": "PropertyValue",
+            "propertyID": "https://registry.identifiers.org/registry/doi",
+            "value": "DOI value expressed as doi:{doi}",
+            "url": "https://dio.org/id/XYZ"
+          }
         }
       ]
     }
   ],
   "ethicsPolicy": {
     "@type": "CreativeWork",
-    "@id": "https://example.org/id/XYZ",
     "name": "Name or title of the document",
     "description": "Description of the creative work ",
     "url": "https://www.foo.org/creativework/ethicsPolicy.pdf"
   },
   "diversityPolicy": {
     "@type": "CreativeWork",
-    "@id": "https://example.org/id/ABC",
     "name": "Name or title of the document",
     "description": "Description of the creative work",
     "url": "https://www.foo.org/creativework/diversityPolicy.pdf"
@@ -83,12 +79,9 @@
         "latitude": 39.3280,
         "longitude": 120.1633
       },
+      "name": "Textual name of the area served",
       "description": "Description of the area served"
     },
-    {
-      "@type": "Text",
-      "description": "Textual description of area served"
-    },
     {
       "@type": "AdministrativeArea",
       "geo": {
@@ -101,7 +94,6 @@
   ],
   "parentOrganization": {
     "@type": "Organization",
-    "@id": "http://www.someinstitute.edu",
     "legalName": "Some Institute",
     "name": "SI",
     "url": "http://www.someinstitute.edu",