From 00bf092eb836d25ba5f3978b464ac5d22608610e Mon Sep 17 00:00:00 2001
From: Orion Banks <49208907+Bankso@users.noreply.github.com>
Date: Fri, 19 Jul 2024 15:54:45 -0400
Subject: [PATCH] Docs update (#124)
* Create file.md
* Create study.md
* Create valid values file.md
* Add file and study to hooks
* Add study and file markdown to nav
* Create FileView.csv
* Create Study.csv
---
docs/model/file.md | 3 ++
docs/model/study.md | 3 ++
docs/valid_values/file.md | 63 +++++++++++++++++++++++++++++++++++++++
mkdocs.yml | 4 +++
scripts/hooks.py | 2 ++
templates/FileView.csv | 2 ++
templates/Study.csv | 2 ++
7 files changed, 79 insertions(+)
create mode 100644 docs/model/file.md
create mode 100644 docs/model/study.md
create mode 100644 docs/valid_values/file.md
create mode 100644 templates/FileView.csv
create mode 100644 templates/Study.csv
diff --git a/docs/model/file.md b/docs/model/file.md
new file mode 100644
index 0000000..b8ceb1c
--- /dev/null
+++ b/docs/model/file.md
@@ -0,0 +1,3 @@
+[⤓ Download template](https://github.com/mc2-center/data-models/raw/main/templates/FileView.csv)
+
+{{ read_csv('file/template.csv') }}
\ No newline at end of file
diff --git a/docs/model/study.md b/docs/model/study.md
new file mode 100644
index 0000000..e26b290
--- /dev/null
+++ b/docs/model/study.md
@@ -0,0 +1,3 @@
+[⤓ Download template](https://github.com/mc2-center/data-models/raw/main/templates/Study.csv)
+
+{{ read_csv('study/template.csv') }}
\ No newline at end of file
diff --git a/docs/valid_values/file.md b/docs/valid_values/file.md
new file mode 100644
index 0000000..1990970
--- /dev/null
+++ b/docs/valid_values/file.md
@@ -0,0 +1,63 @@
+List of standard terms for the [Dataset Sharing Plan Model](../model/file.md).
+
+## Attribute: `File Level`
+
+
+
+{{ read_csv('shared/processLevel.csv', header=0, names=['Valid Value','Description'], usecols=['Valid Value','Description'], tablefmt='html') }}
+
+
+
+
+## Attribute: `File Assay`
+
+
+
+{{ read_csv('shared/assay.csv', header=0, names=['Valid Value','Description'], usecols=['Valid Value','Description'], tablefmt='html') }}
+
+
+
+
+## Attribute: `File Species`
+
+
+
+{{ read_csv('shared/dataset_species.csv', header=0, names=['Valid Value','Description'], usecols=['Valid Value','Description'], tablefmt='html') }}
+
+
+
+
+## Attribute: `File Tumor Type`
+
+
+
+{{ read_csv('shared/tumorType.csv', header=0, names=['Valid Value','Description'], usecols=['Valid Value','Description'], tablefmt='html') }}
+
+
+
+
+## Attribute: `File Tissue`
+
+
+
+{{ read_csv('shared/tissue.csv', header=0, names=['Valid Value','Description'], usecols=['Valid Value','Description'], tablefmt='html') }}
+
+
+
+
+## Attribute: `File Format`
+
+
+
+{{ read_csv('shared/dataset_file_format.csv', header=0, names=['Valid Value','Description'], usecols=['Valid Value','Description'], tablefmt='html') }}
+
+
+
+
+## Attribute: `Data Use Codes`
+
+
+
+{{ read_csv('shared/duo.csv', header=0, names=['Valid Value','Description'], usecols=['Valid Value','Description'], tablefmt='html') }}
+
+
\ No newline at end of file
diff --git a/mkdocs.yml b/mkdocs.yml
index fe35a26..77d91ca 100644
--- a/mkdocs.yml
+++ b/mkdocs.yml
@@ -14,16 +14,20 @@ nav:
- Dataset Data Model: model/dataset.md
- Dataset Sharing Plan: model/DataDSP.md
- Education Resource Data Model: model/education.md
+ - File Data Model: model/file.md
- Grant Data Model: model/grant.md
- Person Data Model: model/person.md
- Publication Data Model: model/publication.md
+ - Study Data Model: model/study.md
- Tool Data Model: model/tool.md
+
- Standard Terms:
- All terms: valid_values/all_terms.md
- Terms by model:
- Dataset: valid_values/dataset.md
- Dataset Sharing Plan: valid_values/sharingPlans.md
- Education Resource: valid_values/education.md
+ - File: valid_values/file.md
- Grant: valid_values/grant.md
- Person: valid_values/person.md
- Publication: valid_values/publication.md
diff --git a/scripts/hooks.py b/scripts/hooks.py
index 24a21c6..3f8df65 100644
--- a/scripts/hooks.py
+++ b/scripts/hooks.py
@@ -5,9 +5,11 @@
"dataset",
"sharingPlans",
"education",
+ "file",
"grant",
"person",
"publication",
+ "study",
"tool",
]
diff --git a/templates/FileView.csv b/templates/FileView.csv
new file mode 100644
index 0000000..e38076e
--- /dev/null
+++ b/templates/FileView.csv
@@ -0,0 +1,2 @@
+Component,FileView_id,Biospecimen Key,Study Key,DatasetView Key,Filename,File Alias,File Description,File Design,File Level,File Assay,File Species,File Tumor Type,File Tissue,File Url,File Format,Data Use Codes
+FileView,,,,,,,,,,,,,,,,
\ No newline at end of file
diff --git a/templates/Study.csv b/templates/Study.csv
new file mode 100644
index 0000000..492e226
--- /dev/null
+++ b/templates/Study.csv
@@ -0,0 +1,2 @@
+Component,Study_id,GrantView Key,ProjectView Key,Study Name,Study Description,Study Investigator,PersonView Key,Study Reuse Statement
+Study,,,,,,,,
\ No newline at end of file