Merge pull request #9 from smrgeoinfo/main

updates to github.io page

Author: smrgeoinfo

.github/workflows/quarto-pages.yml

@@ -19,25 +19,40 @@ jobs:
 
       # Install any computing dependency you may need, usually either python and Jupyter or R
       # More specific examples will be shared on quarto-dev/quarto-actions project
+      # plantUML can be used to dynamically generate UML diagrams to insert in model documentation
+      # 
+      #- name: Install plantuml deps
+      #  run: sudo apt-get install -y default-jre graphviz
 
-      - name: Install plantuml deps
-        run: sudo apt-get install -y default-jre graphviz
-
-      - name: Install plantuml
-        run: wget -O plantuml.jar "https://github.com/plantuml/plantuml/releases/download/v1.2022.4/plantuml-1.2022.4.jar" 
+      #- name: Install plantuml
+      #  run: wget -O plantuml.jar "https://github.com/plantuml/plantuml/releases/download/v1.2022.4/plantuml-1.2022.4.jar" 
 
+      # this just inserts some information in the action log
       - name: Whereami
-        run: pwd; ls -lah; java -version; java -jar plantuml.jar -version
+        run: pwd; ls -lah; java -version    # java -jar plantuml.jar -version
 
       - uses: actions/setup-python@v3
       - name: "Install Python deps"
         run: |
           pip install -r requirements.txt      
+      
+      - name: "install pipx"
+        run: pip install pipx
+
+      - name: "install vocab_tools"
+        #run: pipx install git+https://github.com/isamplesorg/vocab_tools.git@main
+        run: pipx install git+https://github.com/smrgeoinfo/vocab_tools.git@main
+          # sets up python code to convert skos to markdown; code is run
+          # in generate_vocab_docs.sh
 
       - name: Render book to all format
         # Add any command line argument needed
-        env: 
-          PLANTUML_BIN: "java -jar ${{ github.workspace }}/plantuml.jar"
+        #env: 
+        #  PLANTUML_BIN: "java -jar ${{ github.workspace }}/plantuml.jar"
+        
+        # ttl to markdown python code is called from the generate_vocab_docs script
+        # Quarto render uses site configuration defined in the _quarto.yml file,
+        #  individual page content in the web site is defined by various xxx.qmd files.
         run: |
           scripts/generate_vocab_docs.sh; quarto render
       - name: Deploy 🚀

.github/workflows/quarto-pagesbkuyml

@@ -0,0 +1,51 @@
+name: Render using Quarto and push to GH-pages
+
+on: workflow_dispatch
+
+jobs:
+  build-deploy:
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v2
+
+      - name: Install Quarto
+        uses: quarto-dev/quarto-actions/install-quarto@v1
+        with:
+          # To install LaTeX to build PDF book 
+          tinytex: false
+          # uncomment below and fill to pin a version
+          # version: 0.9.105
+
+      # Install any computing dependency you may need, usually either python and Jupyter or R
+      # More specific examples will be shared on quarto-dev/quarto-actions project
+
+      - name: Install plantuml deps
+        run: sudo apt-get install -y default-jre graphviz
+
+      - name: Install plantuml
+        run: wget -O plantuml.jar "https://github.com/plantuml/plantuml/releases/download/v1.2022.4/plantuml-1.2022.4.jar" 
+
+      - name: Whereami
+        run: pwd; ls -lah; java -version; java -jar plantuml.jar -version
+
+      - uses: actions/setup-python@v3
+      - name: "Install Python deps"
+        run: |
+          pip install -r requirements.txt      
+
+      - name: Render book to all format
+        # Add any command line argument needed
+        env: 
+          PLANTUML_BIN: "java -jar ${{ github.workspace }}/plantuml.jar"
+        run: |
+          scripts/generate_vocab_docs.sh; quarto render
+      - name: Deploy 🚀
+        # only deploy when push to main
+        if: github.event_name != 'pull_request'
+        uses: JamesIves/github-pages-deploy-action@v4
+        with:
+          # The branch the action should deploy to.
+          branch: gh-pages
+          # The folder the action should deploy. Adapt if you changed in Quarto config
+          folder: docs

README.md

@@ -5,7 +5,7 @@ subtitle: README for the isamples.github.io source
 
 # isamplesorg.github.io
 
-This repository provides the source for [isamplesorg.github.io](https://isamplesorg.github.io). 
+This repository provides the source for [SMR fork isamplesorg.github.io](https://smrgeoinfo.github.io/isamplesorg.github.io/). 
 
 The site uses the [Quarto](https://quarto.org/) and is built using GitHub actions.
 
@@ -39,4 +39,4 @@ The output is placed under `models/generated/vocabularies`
 
 After editing, push the sources to GitHub. The rendered pages are generated using the `Render using Quarto and push to GH-pages` GitHub action that is currently manually triggered.
 
-Updating dependencies using `pip -U <<package name>>` and regenerate `requirements.txt` with `pip freeze > requirements.txt`.
+Updating dependencies using `pip -U <<package name>>` and regenerate `requirements.txt` with `pip freeze > requirements.txt`.

_quarto.yml

@@ -28,6 +28,8 @@ website:
         contents:
           - design/index.qmd
           - design/requirements.md
+          - text: Metadata Model
+            href: "https://isamplesorg.github.io/metadata/"
           - models/index.qmd
       - section: "Resources"
         contents:
@@ -38,8 +40,9 @@ website:
           href: "https://github.com/isamplesorg/"
 
 
-
-  repo-url: https://github.com/isamplesorg/isamples.github.io
+# configure for correct source repository
+#  repo-url: https://github.com/isamples.org/isamples.github.io
+  repo-url: https://github.com/smrgeoinfo/isamples.github.io
   repo-actions: [edit, issue]
 
   page-footer: 
@@ -55,9 +58,14 @@ website:
   
 format:
   html:
-    theme: cosmo
+    toc: true
+    toc-depth: 4
+    number-sections: true
+    anchor-sections: false
+    number-depth: 8
+    theme: sandstone
     css: styles.css
 
-filters:
-  - pandoc-plantuml
-
+#filters:
+#  - pandoc-plantuml
+#  comment out for testing

about.qmd

@@ -37,9 +37,9 @@ The iSamples project will:
 
 # Principal Investigators
 
-* Kerstin Lehnert, Columbia University
-* Ramona Walls, University of Arizona
-* Neil Davies, The Regents of the University of California, Berkeley
-* David Vieglais, University of Kansas Biodiversity Institute
+* [Kerstin Lehnert](https://orcid.org/0000-0001-7036-1977), Columbia University
+* [Andrea Thomer](https://orcid.org/0000-0001-6238-3498), University of Arizona
+* [Neil Davies](https://orcid.org/0000-0001-8085-5014), The Regents of the University of California, Berkeley
+* [David Vieglais](https://orcid.org/0000-0002-6513-4996), University of Kansas Biodiversity Institute
 
 

design/index.qmd

@@ -19,37 +19,4 @@ iSamples has defined a profile applicable to all physical samples.
 
 iSamples has defined a programmatic interface
 
-
-
-```{.plantuml}
-!include https://raw.githubusercontent.com/datadavev/C4-PlantUML/master/C4_Component.puml
-
-System(isa, "iSamples", "iSamples Infrastructure")
-System_Ext(coll, "Collection", "Collection of records")
-Rel_U(isa, coll, "Synchronize records from")
- 
-System_Ext(ont, "Ontologies", "Community maintained ontologies and vocabularies")
-Rel_L(isa, ont, "Uses")
- 
-Person(admin, "Admin", "Administrator")
-Rel(admin, isa, "Manage systems")
-
-Person(user, "User", "Consumer\nContributor")
-Rel(user, isa, "Discover, Retrieve, Annotate, [Create, Update if authorized]")
-
-Person(curator, "Curator", "Curator")
-Rel(curator, isa, "Create, Manage, Annotate content")
-
-
- System_Ext(pid, "Id Authority", "Identifier authorities (IGSN, ARK, DOI, ROR, ...)")
- Rel(isa, pid, "Get allocation of identifier value range from")
- 
- System_Ext(identity, "Identity", "User identity service (ORCID, GitHub, ...)")
-Rel(isa, identity, "Get user metadata and authenticate using")
- 
-System_Ext(publisher, "Publisher", "Source of identifier appareance in publications")
-Rel(isa, publisher, "Get identifier appearances from")
-
-SHOW_LEGEND()
-```
-
+PlantUML diagram removed for testing [SMR 2024-01-04]

design/indexbkuqmd

@@ -0,0 +1,55 @@
+---
+title: "Overview"
+subtitle: "iSamples use cases, requirements, architecture, and data models"
+---    
+
+Physical samples are represented by a digital record.
+
+Each digital record is addressable by at least one identifier that is unique to the record.
+
+A collection of digital records can be represented by a list of the record identifiers.
+
+A list of all physical sample digital record identifiers (global record list) can be constructed from the collection lists.
+
+Digital records may be presented in different serializations (media type).
+
+Digital records of a serialization may present different views of the same information (profile).
+
+iSamples has defined a profile applicable to all physical samples.
+
+iSamples has defined a programmatic interface
+
+
+
+```{.plantuml}
+!include https://raw.githubusercontent.com/datadavev/C4-PlantUML/master/C4_Component.puml
+
+System(isa, "iSamples", "iSamples Infrastructure")
+System_Ext(coll, "Collection", "Collection of records")
+Rel_U(isa, coll, "Synchronize records from")
+ 
+System_Ext(ont, "Ontologies", "Community maintained ontologies and vocabularies")
+Rel_L(isa, ont, "Uses")
+ 
+Person(admin, "Admin", "Administrator")
+Rel(admin, isa, "Manage systems")
+
+Person(user, "User", "Consumer\nContributor")
+Rel(user, isa, "Discover, Retrieve, Annotate, [Create, Update if authorized]")
+
+Person(curator, "Curator", "Curator")
+Rel(curator, isa, "Create, Manage, Annotate content")
+
+
+ System_Ext(pid, "Id Authority", "Identifier authorities (IGSN, ARK, DOI, ROR, ...)")
+ Rel(isa, pid, "Get allocation of identifier value range from")
+ 
+ System_Ext(identity, "Identity", "User identity service (ORCID, GitHub, ...)")
+Rel(isa, identity, "Get user metadata and authenticate using")
+ 
+System_Ext(publisher, "Publisher", "Source of identifier appareance in publications")
+Rel(isa, publisher, "Get identifier appearances from")
+
+SHOW_LEGEND()
+```
+

index.qmd

@@ -10,5 +10,6 @@ The Internet of Samples (iSamples) is a multi-disciplinary and multi-institution
 
 * [Recording of project presentation at the 2020 SPNHC & ICOM NATHIST Conference](https://youtu.be/eRUw5NMksFo?t=105)
 * [Zenodo Community](https://zenodo.org/communities/isamples)
+  * [presentation of iSamples metadata model](https://zenodo.org/records/7434185/files/2022-11_iSamplesMetadata.pdf?download=1)
 
 

models/generated/extensions/readme.md

@@ -0,0 +1 @@
+this folder contains markdown output for extension vocabularies