General: Update docs

hubmapconsortium · Aug 2, 2023 · 2dee3bd · 2dee3bd
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Showing 11 changed files with 72 additions and 30 deletions.
diff --git a/docs/10x-multiome/index.md b/docs/10x-multiome/index.md
@@ -1,16 +1,16 @@
 ---
-title: 10x-multiome
+title: 10x Multiome
 schema_name: 10x-multiome
-category: Other TSVs
+category: Sequence Assays
 all_versions_deprecated: False
 exclude_from_index: False
 layout: default
 ---
 
 Related files:
 
-- [📝 Excel template](https://raw.githubusercontent.com/hubmapconsortium/ingest-validation-tools/main/docs/10x-multiome/10x-multiome-metadata.xlsx): For metadata entry.
-- [📝 TSV template](https://raw.githubusercontent.com/hubmapconsortium/ingest-validation-tools/main/docs/10x-multiome/10x-multiome-metadata.tsv): Alternative for metadata entry.
+- [📝 Excel template](): For metadata entry.
+- [📝 TSV template](): Alternative for metadata entry.
 
 
 
@@ -20,7 +20,7 @@ Related files:
 
 
 
-
+In the portal: 10x Multiome not in Portal
 
 ## Metadata schema
 

diff --git a/docs/bodyct/index.md b/docs/bodyct/index.md
@@ -1,16 +1,16 @@
 ---
-title: bodyct
+title: Body CT
 schema_name: bodyct
-category: Other TSVs
+category: Clinical Imaging Modalities
 all_versions_deprecated: False
 exclude_from_index: False
 layout: default
 ---
 
 Related files:
 
-- [📝 Excel template](https://raw.githubusercontent.com/hubmapconsortium/ingest-validation-tools/main/docs/bodyct/bodyct-metadata.xlsx): For metadata entry.
-- [📝 TSV template](https://raw.githubusercontent.com/hubmapconsortium/ingest-validation-tools/main/docs/bodyct/bodyct-metadata.tsv): Alternative for metadata entry.
+- [📝 Excel template](): For metadata entry.
+- [📝 TSV template](): Alternative for metadata entry.
 
 
 
@@ -24,7 +24,7 @@ Related files:
 
 
 
-
+In the portal: Body CT not in Portal
 
 ## Metadata schema
 

diff --git a/docs/bulkatacseq/index.md b/docs/bulkatacseq/index.md
@@ -1,16 +1,16 @@
 ---
-title: bulkatacseq
+title: bulkATACseq
 schema_name: bulkatacseq
-category: Other TSVs
+category: Sequence Assays
 all_versions_deprecated: False
 exclude_from_index: False
 layout: default
 ---
 
 Related files:
 
-- [📝 Excel template](https://raw.githubusercontent.com/hubmapconsortium/ingest-validation-tools/main/docs/bulkatacseq/bulkatacseq-metadata.xlsx): For metadata entry.
-- [📝 TSV template](https://raw.githubusercontent.com/hubmapconsortium/ingest-validation-tools/main/docs/bulkatacseq/bulkatacseq-metadata.tsv): Alternative for metadata entry.
+- [📝 Excel template](): For metadata entry.
+- [📝 TSV template](): Alternative for metadata entry.
 
 
 
@@ -27,7 +27,7 @@ Related files:
 
 
 
-
+In the portal: bulkATACseq not in Portal
 
 ## Metadata schema
 

diff --git a/docs/bulkrnaseq/index.md b/docs/bulkrnaseq/index.md
@@ -1,16 +1,16 @@
 ---
-title: bulkrnaseq
+title: bulk-RNA
 schema_name: bulkrnaseq
-category: Other TSVs
+category: Sequence Assays
 all_versions_deprecated: False
 exclude_from_index: False
 layout: default
 ---
 
 Related files:
 
-- [📝 Excel template](https://raw.githubusercontent.com/hubmapconsortium/ingest-validation-tools/main/docs/bulkrnaseq/bulkrnaseq-metadata.xlsx): For metadata entry.
-- [📝 TSV template](https://raw.githubusercontent.com/hubmapconsortium/ingest-validation-tools/main/docs/bulkrnaseq/bulkrnaseq-metadata.tsv): Alternative for metadata entry.
+- [📝 Excel template](): For metadata entry.
+- [📝 TSV template](): Alternative for metadata entry.
 
 
 
@@ -27,7 +27,7 @@ Related files:
 
 
 
-
+In the portal: bulk-RNA not in Portal
 
 ## Metadata schema
 

diff --git a/docs/celldive/index.md b/docs/celldive/index.md
@@ -1,16 +1,16 @@
 ---
-title: celldive
+title: Cell Dive
 schema_name: celldive
-category: Other TSVs
+category: MxFBE
 all_versions_deprecated: False
 exclude_from_index: False
 layout: default
 ---
 
 Related files:
 
-- [📝 Excel template](https://raw.githubusercontent.com/hubmapconsortium/ingest-validation-tools/main/docs/celldive/celldive-metadata.xlsx): For metadata entry.
-- [📝 TSV template](https://raw.githubusercontent.com/hubmapconsortium/ingest-validation-tools/main/docs/celldive/celldive-metadata.tsv): Alternative for metadata entry.
+- [📝 Excel template](): For metadata entry.
+- [📝 TSV template](): Alternative for metadata entry.
 
 
 
@@ -30,7 +30,7 @@ Related files:
 
 
 
-
+In the portal: Cell Dive not in Portal
 
 ## Metadata schema
 

diff --git a/src/ingest_validation_tools/enums.py b/src/ingest_validation_tools/enums.py
@@ -27,11 +27,13 @@
 
 shared_enums: Dict[str, List[str]] = {
     'assay_type': [
+        '10x Multiome',
         '3D Imaging Mass Cytometry',
         'AF',
         'bulk-RNA',
         'bulkATACseq',
         'Cell DIVE',
+        'Cell Dive',
         'cell-dive',
         'CE-MS',
         'CODEX',

diff --git a/src/ingest_validation_tools/table-schemas/assays/10x-multiome-v2.yaml b/src/ingest_validation_tools/table-schemas/assays/10x-multiome-v2.yaml
@@ -2,4 +2,12 @@ draft: true
 fields:
 - name: is_cedar
   description: 'Identifies whether the version is hosted by CEDAR'
-  example: 'https://docs.google.com/spreadsheets/d/1YNyMWvDTZzuj8m4fgdwLI6Wht1C3zb_s2kTONEVkZmo'
+  example: 'https://docs.google.com/spreadsheets/d/1YNyMWvDTZzuj8m4fgdwLI6Wht1C3zb_s2kTONEVkZmo'
+- name: assay_category
+  constraints:
+    enum:
+      - sequence
+- name: assay_type
+  constraints:
+    enum:
+      - 10x Multiome
diff --git a/src/ingest_validation_tools/table-schemas/assays/bodyct-v2.yaml b/src/ingest_validation_tools/table-schemas/assays/bodyct-v2.yaml
@@ -2,4 +2,12 @@ draft: true
 fields:
 - name: is_cedar
   description: 'Identifies whether the version is hosted by CEDAR'
-  example: 'https://docs.google.com/spreadsheets/d/114DmeiACGQzA8C5ZY3mWh-338XNe7Zy7'
+  example: 'https://docs.google.com/spreadsheets/d/114DmeiACGQzA8C5ZY3mWh-338XNe7Zy7'
+- name: assay_category
+  constraints:
+    enum:
+      - clinical_imaging
+- name: assay_type
+  constraints:
+    enum:
+      - Body CT
diff --git a/src/ingest_validation_tools/table-schemas/assays/bulkatacseq-v2.yaml b/src/ingest_validation_tools/table-schemas/assays/bulkatacseq-v2.yaml
@@ -2,4 +2,12 @@ draft: true
 fields:
 - name: is_cedar
   description: 'Identifies whether the version is hosted by CEDAR'
-  example: 'https://docs.google.com/spreadsheets/d/1YNyMWvDTZzuj8m4fgdwLI6Wht1C3zb_s2kTONEVkZmo'
+  example: 'https://docs.google.com/spreadsheets/d/1YNyMWvDTZzuj8m4fgdwLI6Wht1C3zb_s2kTONEVkZmo'
+- name: assay_category
+  constraints:
+    enum:
+      - sequence
+- name: assay_type
+  constraints:
+    enum:
+      - bulkATACseq
diff --git a/src/ingest_validation_tools/table-schemas/assays/bulkrnaseq-v2.yaml b/src/ingest_validation_tools/table-schemas/assays/bulkrnaseq-v2.yaml
@@ -2,4 +2,12 @@ draft: true
 fields:
 - name: is_cedar
   description: 'Identifies whether the version is hosted by CEDAR'
-  example: 'https://docs.google.com/spreadsheets/d/1YNyMWvDTZzuj8m4fgdwLI6Wht1C3zb_s2kTONEVkZmo'
+  example: 'https://docs.google.com/spreadsheets/d/1YNyMWvDTZzuj8m4fgdwLI6Wht1C3zb_s2kTONEVkZmo'
+- name: assay_category
+  constraints:
+    enum:
+      - sequence
+- name: assay_type
+  constraints:
+    enum:
+      - bulk-RNA
diff --git a/src/ingest_validation_tools/table-schemas/assays/celldive-v2.yaml b/src/ingest_validation_tools/table-schemas/assays/celldive-v2.yaml
@@ -2,4 +2,12 @@ draft: true
 fields:
 - name: is_cedar
   description: 'Identifies whether the version is hosted by CEDAR'
-  example: 'https://docs.google.com/spreadsheets/d/1GKh4x8HIoQ3eKi2WWtWa2eWann3FG1pfaqxGKkUK1Wo'
+  example: 'https://docs.google.com/spreadsheets/d/1GKh4x8HIoQ3eKi2WWtWa2eWann3FG1pfaqxGKkUK1Wo'
+- name: assay_category
+  constraints:
+    enum:
+      - mxfbe
+- name: assay_type
+  constraints:
+    enum:
+      - Cell Dive