Sharing plan issue 106 (#110)

* Fixing unexpected merge (#109)

* build jsonld

* Revert "build jsonld"

This reverts commit 3365dfe.

* Revert "Address typing_extensions issue with ipython"

This reverts commit ce22e3f.

* Revert "Bump schematic to version 24.5.1"

This reverts commit d4e1daa.

* Revert "Collate model CSV and convert to JSON-LD"

This reverts commit 0111969.

* Revert "Update valid values"

This reverts commit 2830a66.

* Revert "Remove unnecessary double quotes"

This reverts commit f791a93.

* Revert "Update annotationProperty.csv"

This reverts commit c0c5409.

* Revert "Removed misspelled Project attribute"

This reverts commit 3122359.

* Revert "Update shared attributes"

This reverts commit 47b324f.

* Revert "Remove Project dependency loop"

This reverts commit 29c6090.

* Revert "Create processLevel.csv"

This reverts commit 22846e7.

* Revert "Change folder reference for DSP"

This reverts commit b755a98.

* Revert "Update and add valid value mappings"

This reverts commit 824437d.

* Revert "Add shared attribute Data Use Codes"

This reverts commit cc73994.

* Revert "Move dataset valid values to shared"

This reverts commit c3e0807.

* Revert "Add DUO terms to model as valid values"

This reverts commit 5a032df.

* Revert "Add initial version of Dataset Sharing Plan model"

This reverts commit 3749b3b.

---------

Co-authored-by: mc2center-bot[bot] <[email protected]>

* Add initial version of Dataset Sharing Plan model

* Add DUO terms to model as valid values

* Move dataset valid values to shared

* Add shared attribute Data Use Codes

* Update and add valid value mappings

- update dataset mappings
- add DSP mappings
- add Data Use Code mapping

* Change folder reference for DSP

* Create processLevel.csv

* Remove Project dependency loop

Project Type dependency on Project is not necessary and is flagged by schematic as circular. Removing produces a true directed acyclic graph (DAG)

* Update shared attributes

* Removed misspelled Project attribute

* Update annotationProperty.csv

* Remove unnecessary double quotes

* Update valid values

* Collate model CSV and convert to JSON-LD

Schematic 24.5.1

* Bump schematic to version 24.5.1

* Address typing_extensions issue with ipython

* build jsonld

* Add DataDSP to template generator

* Replace XLSX templates with CSV

* Update DSP attribute names

* Doc updates issue 106 (#111)

* Update template refs from xlsx --> csv

* Update dataset cv refs to new 'shared' path

* Create DataDSP.md

* Add valid values md for DSP

* Add DSP content to nav config

* Rename Dataset Type to Assay

For consistency with DatasetView model

* Add sharingPlans folder to hooks

* Update Dataset Type to Assay in CV mapping

* Add DSP Url and update schema definition

* Update DataDSP.csv

* Add DSP Data Use Codes as attribute

Instead of using a single Data Use Codes attribute, differentiate for DSP model. This allows it to show up in our documentation

* Update mapping to use DSP Data Use Codes

* Add DSP Data Use Codes to vocab section

---------

Co-authored-by: mc2center-bot[bot] <[email protected]>

.github/workflows/build-jsonld.yml

@@ -16,7 +16,7 @@ jobs:
     runs-on: ubuntu-20.04
     strategy:
       matrix:
-        schematic-version: [ 24.1.1 ]
+        schematic-version: [ 24.5.1 ]
 
     steps:
       - name: Install System Dependencies
@@ -43,7 +43,7 @@ jobs:
           python3.10 -m venv .venv
           chmod 755 .venv/bin/activate
           source .venv/bin/activate
-          pip3.10 install schematicpy==${{ matrix.schematic-version }}
+          pip3.10 install schematicpy==${{ matrix.schematic-version }} ipython==8.18.1
           make CSV=$schema_filename
     
       - name: Commit files

all_valid_values.csv

@@ -991,6 +991,12 @@ assay,Targeted Error Correction Sequencing,TEC-Seq
 assay,Tuba-Seq,
 assay,SDS-PAGE,
 assay,Cell Fractionation,
+processLevel,Level 1,
+processLevel,Level 2,
+processLevel,Level 3,
+processLevel,Level 4,
+processLevel,Auxilliary,
+processLevel,Not Applicable,
 ed_topic,Computational Model Development,
 ed_topic,Computational Resource,
 ed_topic,Diversity/Equity/Inclusion,
@@ -2160,6 +2166,30 @@ project_type,Core,
 project_type,Project,
 publication_accessibility,Open Access,
 publication_accessibility,Restricted Access,
+duo,IRB,
+duo,HMB,
+duo,PUB,
+duo,US,
+duo,NPOA,
+duo,COL,
+duo,NCU,
+duo,NPUNCU,
+duo,RS,
+duo,TS,
+duo,NRES,
+duo,NPU,
+duo,DUM,
+duo,POA,
+duo,MOR,
+duo,GSO,
+duo,RTN,
+duo,CC,
+duo,NMDS,
+duo,IS,
+duo,GS,
+duo,DS,
+duo,GRU,
+duo,PS,
 tool_accessibility,Open Access,
 tool_accessibility,Open Access (With Restrictions),
 tool_accessibility,Restricted Access,

docs/model/DataDSP.md

@@ -0,0 +1,3 @@
+[⤓ Download template](https://github.com/mc2-center/data-models/raw/main/templates/DataDSP.csv)
+
+{{ read_csv('sharingPlans/template.csv') }}

docs/model/dataset.md

@@ -1,3 +1,3 @@
-[⤓ Download template](https://github.com/mc2-center/data-models/raw/main/templates/DatasetView.xlsx)
+[⤓ Download template](https://github.com/mc2-center/data-models/raw/main/templates/DatasetView.csv)
 
 {{ read_csv('dataset/template.csv') }}

docs/model/education.md

@@ -1,3 +1,3 @@
-[⤓ Download template](https://github.com/mc2-center/data-models/raw/main/templates/EducationalResource.xlsx)
+[⤓ Download template](https://github.com/mc2-center/data-models/raw/main/templates/EducationalResource.csv)
 
 {{ read_csv('education/template.csv') }}

docs/model/grant.md

@@ -1,3 +1,3 @@
-[⤓ Download template](https://github.com/mc2-center/data-models/raw/main/templates/GrantView.xlsx)
+[⤓ Download template](https://github.com/mc2-center/data-models/raw/main/templates/GrantView.csv)
 
 {{ read_csv('grant/template.csv') }}

docs/model/person.md

@@ -1,3 +1,3 @@
-[⤓ Download template](https://github.com/mc2-center/data-models/raw/main/templates/PersonView.xlsx)
+[⤓ Download template](https://github.com/mc2-center/data-models/raw/main/templates/PersonView.csv)
 
 {{ read_csv('person/template.csv') }}

docs/model/publication.md

@@ -1,3 +1,3 @@
-[⤓ Download template](https://github.com/mc2-center/data-models/raw/main/templates/PublicationView.xlsx)
+[⤓ Download template](https://github.com/mc2-center/data-models/raw/main/templates/PublicationView.csv)
 
 {{ read_csv('publication/template.csv') }}

docs/model/tool.md

@@ -1,3 +1,3 @@
-[⤓ Download template](https://github.com/mc2-center/data-models/raw/main/templates/ToolView.xlsx)
+[⤓ Download template](https://github.com/mc2-center/data-models/raw/main/templates/ToolView.csv)
 
 {{ read_csv('tool/template.csv') }}

docs/valid_values/dataset.md

@@ -13,7 +13,7 @@ List of standard terms for the [Dataset Data Model](../model/dataset.md).
 
 <div style="max-height:650px; overflow-x: hidden; overflow-y: auto;">
 
-{{ read_csv('dataset/dataset_file_format.csv', header=0, names=['Valid Value','Description'], usecols=['Valid Value','Description'], tablefmt='html') }}
+{{ read_csv('shared/dataset_file_format.csv', header=0, names=['Valid Value','Description'], usecols=['Valid Value','Description'], tablefmt='html') }}
 
 </div>
 
@@ -31,7 +31,7 @@ List of standard terms for the [Dataset Data Model](../model/dataset.md).
 
 <div style="max-height:650px; overflow-x: hidden; overflow-y: auto;">
 
-{{ read_csv('dataset/dataset_species.csv', header=0, names=['Valid Value','Description'], usecols=['Valid Value','Description'], tablefmt='html') }}
+{{ read_csv('shared/dataset_species.csv', header=0, names=['Valid Value','Description'], usecols=['Valid Value','Description'], tablefmt='html') }}
 
 </div>
 

docs/valid_values/sharingPlans.md

@@ -0,0 +1,71 @@
+List of standard terms for the [Dataset Sharing Plan Model](../model/DataDSP.md).
+
+## Attribute: `DSP Data Use Codes`
+
+<div style="max-height:650px; overflow-x: hidden; overflow-y: auto;">
+
+{{ read_csv('shared/duo.csv', header=0, names=['Valid Value','Description'], usecols=['Valid Value','Description'], tablefmt='html') }}
+
+</div>
+
+
+## Attribute: `DSP Dataset Assay`
+
+<div style="max-height:650px; overflow-x: hidden; overflow-y: auto;">
+
+{{ read_csv('shared/assay.csv', header=0, names=['Valid Value','Description'], usecols=['Valid Value','Description'], tablefmt='html') }}
+
+</div>
+
+
+## Attribute: `DSP Dataset File Formats`
+
+<div style="max-height:650px; overflow-x: hidden; overflow-y: auto;">
+
+{{ read_csv('shared/dataset_file_format.csv', header=0, names=['Valid Value','Description'], usecols=['Valid Value','Description'], tablefmt='html') }}
+
+</div>
+
+
+## Attribute: `DSP Dataset Grant Number`
+
+<div style="max-height:650px; overflow-x: hidden; overflow-y: auto;">
+
+{{ read_csv('grant/grant_number.csv', header=0, names=['Valid Value','Description'], usecols=['Valid Value','Description'], tablefmt='html') }}
+
+</div>
+
+## Attribute: `DSP Dataset Level`
+
+<div style="max-height:650px; overflow-x: hidden; overflow-y: auto;">
+
+{{ read_csv('shared/processLevel.csv', header=0, names=['Valid Value','Description'], usecols=['Valid Value','Description'], tablefmt='html') }}
+
+</div>
+
+## Attribute: `DSP Dataset Species`
+
+<div style="max-height:650px; overflow-x: hidden; overflow-y: auto;">
+
+{{ read_csv('shared/dataset_species.csv', header=0, names=['Valid Value','Description'], usecols=['Valid Value','Description'], tablefmt='html') }}
+
+</div>
+
+
+## Attribute: `DSP Dataset Tissue`
+
+<div style="max-height:650px; overflow-x: hidden; overflow-y: auto;">
+
+{{ read_csv('shared/tissue.csv', header=0, names=['Valid Value','Description'], usecols=['Valid Value','Description'], tablefmt='html') }}
+
+</div>
+
+
+
+## Attribute: `DSP Dataset Tumor Type`
+
+<div style="max-height:650px; overflow-x: hidden; overflow-y: auto;">
+
+{{ read_csv('shared/tumorType.csv', header=0, names=['Valid Value','Description'], usecols=['Valid Value','Description'], tablefmt='html') }}
+
+</div>