portals cleanup; GH-Action on mac

Author: bbest

.github/workflows/render_book.yml

@@ -9,8 +9,8 @@ on:
 jobs:
   build-deploy:
     name: Render & publish Quarto book
-    # runs-on: macOS-latest
-    runs-on: ubuntu-latest
+    runs-on: macOS-latest
+    # runs-on: ubuntu-latest
     permissions:
       contents: write
     steps:
@@ -19,20 +19,20 @@ jobs:
 
       - name: Install Quarto
         uses: quarto-dev/quarto-actions/setup@v2
-        # with:
-        #   tinytex: true  # for pdf but buggy on finding version
+        with:
+          tinytex: true  # for pdf but buggy on finding version
 
-      # - name: Install chromium for Quarto
-      #   # for rendering Mermaid diagrams to pdf: https://quarto.org/docs/authoring/diagrams.html#chrome-install
-      #   run: quarto install chromium
+      - name: Install chromium for Quarto
+        # for rendering Mermaid diagrams to pdf: https://quarto.org/docs/authoring/diagrams.html#chrome-install
+        run: quarto install chromium
 
-      - name: Install TinyTeX
-        uses: r-lib/actions/setup-tinytex@v2
+      # - name: Install TinyTeX
+      #   uses: r-lib/actions/setup-tinytex@v2
 
       - name: Install librsvg
         # convert svg to png for pdf
-        # run: brew install librsvg
-        run: sudo apt-get install librsvg2-bin # librsvg2-dev
+        run: brew install librsvg
+        # run: sudo apt-get install librsvg2-bin # librsvg2-dev
 
       # - name: Install qpdf
       #   # to prevent R install from failing

diagrams/portals_flow.mmd

@@ -4,7 +4,7 @@ graph TD
 
   subgraph calcofi[CalCOFI.io]
     db[(database)]:::database
-    web[calcofi.org]:::website
+    web[CalCOFI.org]:::website
     api[APIs]:::api
     lib[library]:::code
     app[apps]:::code
@@ -35,12 +35,12 @@ graph TD
   portals --> datagov
 
   %% Custom styles
-  classDef source fill:#E0E7FF,stroke:#6366F1,stroke-width:2px
-  classDef database fill:#FEF3C7,stroke:#D97706,stroke-width:2px
-  classDef website fill:#F3E8FF,stroke:#9333EA,stroke-width:2px
-  classDef api fill:#E0E7FF,stroke:#6366F1,stroke-width:2px
-  classDef code fill:#DBEAFE,stroke:#3B82F6,stroke-width:2px
-  classDef portal fill:#F0FDF4,stroke:#22C55E,stroke-width:2px
+  classDef source     fill:#E0E7FF,stroke:#6366F1,stroke-width:2px
+  classDef database   fill:#FEF3C7,stroke:#D97706,stroke-width:2px
+  classDef website    fill:#F3E8FF,stroke:#9333EA,stroke-width:2px
+  classDef api        fill:#E0E7FF,stroke:#6366F1,stroke-width:2px
+  classDef code       fill:#DBEAFE,stroke:#3B82F6,stroke-width:2px
+  classDef portal     fill:#F0FDF4,stroke:#22C55E,stroke-width:2px
   classDef metaportal fill:#FEF2F2,stroke:#DC2626,stroke-width:2px
 
   %% Style subgraphs

diagrams/portals_metadata.mmd

@@ -1,27 +1,31 @@
 graph LR
-    subgraph inputs[Data & Metadata]
+    subgraph dataset[Dataset]
         data([data.csv]):::source
         eml[metadata.eml]:::database
     end
 
-    subgraph portals[Data Portals]
+    subgraph portals[Portals]
         edi[EDI]:::portal
         erddap[ERDDAP]:::portal
         obis[OBIS]:::portal
         ncei[NCEI]:::portal
     end
 
-    data --> eml
-    eml --> edi
-    eml --> erddap
-    eml --> obis
-    eml --> ncei
+    subgraph metaportals[Meta-Portals]
+        odis[ODIS]:::metaportal
+        datagov[data.gov]:::metaportal
+    end
+
+    dataset --> portals
+    eml -->|json-ld| metaportals
 
     %% Custom styles
-    classDef source fill:#E0E7FF,stroke:#6366F1,stroke-width:2px
-    classDef database fill:#FEF3C7,stroke:#D97706,stroke-width:2px
-    classDef portal fill:#F0FDF4,stroke:#22C55E,stroke-width:2px
+    classDef source     fill:#E0E7FF,stroke:#6366F1,stroke-width:2px
+    classDef database   fill:#FEF3C7,stroke:#D97706,stroke-width:2px
+    classDef portal     fill:#F0FDF4,stroke:#22C55E,stroke-width:2px
+    classDef metaportal fill:#FEF2F2,stroke:#DC2626,stroke-width:2px
 
     %% Style subgraphs
-    style inputs fill:#F8FAFC,stroke:#CBD5E1,stroke-width:2px
-    style portals fill:#F8FAFC,stroke:#CBD5E1,stroke-width:2px
+    style dataset     fill:#F8FAFC,stroke:#CBD5E1,stroke-width:2px
+    style portals     fill:#F8FAFC,stroke:#CBD5E1,stroke-width:2px
+    style metaportals fill:#F8FAFC,stroke:#CBD5E1,stroke-width:2px

portals.qmd

@@ -68,7 +68,8 @@ read_csv(portals_csv, show_col_types = F) |>
 ```
 
 
-### EDI (Environmental Data Initiative)
+### EDI
+**Environmental Data Initiative**
 
 -   Complete dataset archives using DataOne software and EML metadata
 -   DOIs issued for all datasets ensuring citability
@@ -80,7 +81,8 @@ read_csv(portals_csv, show_col_types = F) |>
     -   [EDIrepository.org](https://edirepository.org)
     -   CalCOFI datasets: [EDI query "CalCOFI"](http://portal.edirepository.org:80/nis/simpleSearch?defType=edismax&q=CalCOFI&fq=-scope:ecotrends&fq=-scope:lter-landsat*&fl=id,packageid,title,author,organization,pubdate,coordinates&debug=false)
 
-### NCEI (National Centers for Environmental Information)
+### NCEI
+**National Centers for Environmental Information**
 
 -   Long-term archival of oceanographic data
 -   DOIs issued for dataset submissions
@@ -92,7 +94,8 @@ read_csv(portals_csv, show_col_types = F) |>
     -   [NCEI Ocean Archive](https://www.ncei.noaa.gov/products/ocean-archive)
     -   CalCOFI datasets: [NCEI search "CalCOFI"](https://www.ncei.noaa.gov/access/search/index?q=CalCOFI)
 
-### OBIS (Ocean Biodiversity Information System)
+### OBIS
+**Ocean Biodiversity Information System**
 
 -   Specialized in marine biodiversity data
 -   Standardized using DarwinCore fields
@@ -104,7 +107,8 @@ read_csv(portals_csv, show_col_types = F) |>
     -   [OBIS.org](https://obis.org)
     -   CalCOFI datasets: [obis.org/dataset](https://obis.org/datasets) + "calcofi" Keyword
 
-### ERDDAP (Environmental Research Division Data Access Program)
+### ERDDAP
+**Environmental Research Division Data Access Program**
 
 -   Tabular and gridded data server
 -   Advanced subsetting by space, time, and parameters
@@ -146,7 +150,8 @@ This standardized metadata enables automated data transformation and ingestion i
 
 The JSON-LD metadata in the Portal dataset web pages get indexed by [Google Dataset Search](https://datasetsearch.research.google.com/search?query=calcofi) through schema.org metadata. This ensures that CalCOFI data is discoverable through Google search and other search engines.
 
-### ODIS (Ocean Data Information System)
+### ODIS
+**Ocean Data Information System**
 
 ODIS uses the same technology as Google Dataset Search (schema.org, JSON-LD), but focuses on ocean data. CalCOFI curates a sitemap of authoritative datasets to server to [ODIS.org](https://odis.org)