Docs: Add draft specs for new directory schemas (that have been defin…

…ed thus far).
hubmapconsortium · Aug 1, 2023 · dd2e1d3 · dd2e1d3
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diff --git a/docs/af/index.md b/docs/af/index.md
@@ -15,6 +15,9 @@ Related files:
 
 
 ## Directory schemas
+### v1
+<summary><a href="https://docs.google.com/spreadsheets/d/1_fMJrZVgx8g80uduxfr1HcIHz52_fpRfwFWFrA40tlg">Draft</a></summary>
+
 ### v0
 
 | pattern | required? | description |

diff --git a/docs/bulkatacseq/index.md b/docs/bulkatacseq/index.md
@@ -15,6 +15,9 @@ Related files:
 
 
 ## Directory schemas
+### v1
+<summary><a href="https://docs.google.com/spreadsheets/d/10Om2iinTwfLn1ySWtovmcm35cQnyg0Pm-rRd0a-eMjc">Draft</a></summary>
+
 ### v0
 
 | pattern | required? | description |

diff --git a/docs/bulkrnaseq/index.md b/docs/bulkrnaseq/index.md
@@ -15,6 +15,9 @@ Related files:
 
 
 ## Directory schemas
+### v1
+<summary><a href="https://docs.google.com/spreadsheets/d/10Om2iinTwfLn1ySWtovmcm35cQnyg0Pm-rRd0a-eMjc">Draft</a></summary>
+
 ### v0
 
 | pattern | required? | description |

diff --git a/docs/celldive/index.md b/docs/celldive/index.md
@@ -15,6 +15,9 @@ Related files:
 
 
 ## Directory schemas
+### v1
+<summary><a href="https://docs.google.com/spreadsheets/d/1pZD2e51e4QkxzIk6xjHPPu1RBZpx5mzoykMmlaDK8rA/edit#gid=158547256">Draft</a></summary>
+
 ### v0
 
 | pattern | required? | description |

diff --git a/docs/codex/index.md b/docs/codex/index.md
@@ -15,6 +15,9 @@ Related files:
 
 
 ## Directory schemas
+### v2
+<summary><a href="https://docs.google.com/spreadsheets/d/1pZD2e51e4QkxzIk6xjHPPu1RBZpx5mzoykMmlaDK8rA/edit#gid=158547256">Draft</a></summary>
+
 ### v1-with-dataset-json
 
 | pattern | required? | description |

diff --git a/docs/histology/index.md b/docs/histology/index.md
@@ -14,6 +14,10 @@ Related files:
 
 
 
+## Directory schemas
+### v0
+<summary><a href="https://docs.google.com/spreadsheets/d/1_fMJrZVgx8g80uduxfr1HcIHz52_fpRfwFWFrA40tlg">Draft</a></summary>
+
 
 
 

diff --git a/docs/ims/index.md b/docs/ims/index.md
@@ -15,6 +15,9 @@ Related files:
 
 
 ## Directory schemas
+### v1
+<summary><a href="https://docs.google.com/spreadsheets/d/1I2aXIpOQHBjeLbKsVn0qJTOH7vtByeQ9t_1EnlTAPL4">Draft</a></summary>
+
 ### v0
 
 | pattern | required? | description |

diff --git a/docs/mxif/index.md b/docs/mxif/index.md
@@ -15,6 +15,9 @@ Related files:
 
 
 ## Directory schemas
+### v1
+<summary><a href="https://docs.google.com/spreadsheets/d/1pZD2e51e4QkxzIk6xjHPPu1RBZpx5mzoykMmlaDK8rA/edit#gid=158547256">Draft</a></summary>
+
 ### v0
 
 | pattern | required? | description |

diff --git a/docs/scatacseq/index.md b/docs/scatacseq/index.md
@@ -17,6 +17,9 @@ Related files:
 ## Directory schemas
 The HIVE will process each dataset with
 [scATACseq Pipeline 1.4.3](https://github.com/hubmapconsortium/sc-atac-seq-pipeline/releases/tag/1.4.3).
+### v1
+<summary><a href="https://docs.google.com/spreadsheets/d/10Om2iinTwfLn1ySWtovmcm35cQnyg0Pm-rRd0a-eMjc">Draft</a></summary>
+
 ### v0
 
 | pattern | required? | description |

diff --git a/docs/scrnaseq-hca/index.md b/docs/scrnaseq-hca/index.md
@@ -15,6 +15,9 @@ Related files:
 
 
 ## Directory schemas
+### v1
+<summary><a href="https://docs.google.com/spreadsheets/d/10Om2iinTwfLn1ySWtovmcm35cQnyg0Pm-rRd0a-eMjc">Draft</a></summary>
+
 ### v0
 
 | pattern | required? | description |

diff --git a/docs/scrnaseq/index.md b/docs/scrnaseq/index.md
@@ -15,6 +15,9 @@ Related files:
 
 
 ## Directory schemas
+### v1
+<summary><a href="https://docs.google.com/spreadsheets/d/10Om2iinTwfLn1ySWtovmcm35cQnyg0Pm-rRd0a-eMjc">Draft</a></summary>
+
 ### v0
 
 | pattern | required? | description |

diff --git a/docs/slideseq/index.md b/docs/slideseq/index.md
@@ -15,6 +15,9 @@ Related files:
 
 
 ## Directory schemas
+### v1
+<summary><a href="https://docs.google.com/spreadsheets/d/1LE-iyY2E6eP4E8jhgP6rhsvjESrdHXWYrMwKTvNkI5Y">Draft</a></summary>
+
 ### v0
 
 | pattern | required? | description |

diff --git a/docs/stained/index.md b/docs/stained/index.md
@@ -15,6 +15,9 @@ Related files:
 
 
 ## Directory schemas
+### v2
+<summary><a href="https://docs.google.com/spreadsheets/d/1_fMJrZVgx8g80uduxfr1HcIHz52_fpRfwFWFrA40tlg">Draft</a></summary>
+
 ### v1
 
 | pattern | required? | description |

diff --git a/docs/wgs/index.md b/docs/wgs/index.md
@@ -15,6 +15,9 @@ Related files:
 
 
 ## Directory schemas
+### v1
+<summary><a href="https://docs.google.com/spreadsheets/d/10Om2iinTwfLn1ySWtovmcm35cQnyg0Pm-rRd0a-eMjc/edit#gid=37240204">Draft</a></summary>
+
 ### v0
 
 | pattern | required? | description |

diff --git a/src/ingest_validation_tools/directory-schemas/af-v1.yaml b/src/ingest_validation_tools/directory-schemas/af-v1.yaml
@@ -0,0 +1,4 @@
+draft: true
+files:
+  -
+    draft_link: 'https://docs.google.com/spreadsheets/d/1_fMJrZVgx8g80uduxfr1HcIHz52_fpRfwFWFrA40tlg'
diff --git a/src/ingest_validation_tools/directory-schemas/bulkatacseq-v1.yaml b/src/ingest_validation_tools/directory-schemas/bulkatacseq-v1.yaml
@@ -0,0 +1,4 @@
+draft: true
+files:
+  -
+    draft_link: 'https://docs.google.com/spreadsheets/d/10Om2iinTwfLn1ySWtovmcm35cQnyg0Pm-rRd0a-eMjc'
diff --git a/src/ingest_validation_tools/directory-schemas/bulkrnaseq-v1.yaml b/src/ingest_validation_tools/directory-schemas/bulkrnaseq-v1.yaml
@@ -0,0 +1,4 @@
+draft: true
+files:
+  -
+    draft_link: 'https://docs.google.com/spreadsheets/d/10Om2iinTwfLn1ySWtovmcm35cQnyg0Pm-rRd0a-eMjc'
diff --git a/src/ingest_validation_tools/directory-schemas/celldive-v1.yaml b/src/ingest_validation_tools/directory-schemas/celldive-v1.yaml
@@ -0,0 +1,5 @@
+#  GE CellDIVE Directory Schema
+draft: true
+files:
+  -
+    draft_link: 'https://docs.google.com/spreadsheets/d/1pZD2e51e4QkxzIk6xjHPPu1RBZpx5mzoykMmlaDK8rA/edit#gid=158547256'
diff --git a/src/ingest_validation_tools/directory-schemas/codex-v2.yaml b/src/ingest_validation_tools/directory-schemas/codex-v2.yaml
@@ -0,0 +1,5 @@
+#  GE CellDIVE Directory Schema
+draft: true
+files:
+  -
+    draft_link: 'https://docs.google.com/spreadsheets/d/1pZD2e51e4QkxzIk6xjHPPu1RBZpx5mzoykMmlaDK8rA/edit#gid=158547256'
diff --git a/src/ingest_validation_tools/directory-schemas/histology-v0.yaml b/src/ingest_validation_tools/directory-schemas/histology-v0.yaml
@@ -0,0 +1,4 @@
+draft: true
+files:
+  -
+    draft_link: 'https://docs.google.com/spreadsheets/d/1_fMJrZVgx8g80uduxfr1HcIHz52_fpRfwFWFrA40tlg'
diff --git a/src/ingest_validation_tools/directory-schemas/ims-v1.yaml b/src/ingest_validation_tools/directory-schemas/ims-v1.yaml
@@ -0,0 +1,4 @@
+draft: true
+files:
+  -
+    draft_link: 'https://docs.google.com/spreadsheets/d/1I2aXIpOQHBjeLbKsVn0qJTOH7vtByeQ9t_1EnlTAPL4'
diff --git a/src/ingest_validation_tools/directory-schemas/mxif-v1.yaml b/src/ingest_validation_tools/directory-schemas/mxif-v1.yaml
@@ -0,0 +1,4 @@
+draft: true
+files:
+  -
+    draft_link: 'https://docs.google.com/spreadsheets/d/1pZD2e51e4QkxzIk6xjHPPu1RBZpx5mzoykMmlaDK8rA/edit#gid=158547256'
diff --git a/src/ingest_validation_tools/directory-schemas/scatacseq-v1.yaml b/src/ingest_validation_tools/directory-schemas/scatacseq-v1.yaml
@@ -0,0 +1,4 @@
+draft: true
+files:
+  -
+    draft_link: 'https://docs.google.com/spreadsheets/d/10Om2iinTwfLn1ySWtovmcm35cQnyg0Pm-rRd0a-eMjc'
diff --git a/src/ingest_validation_tools/directory-schemas/scrnaseq-hca-v1.yaml b/src/ingest_validation_tools/directory-schemas/scrnaseq-hca-v1.yaml
@@ -0,0 +1,4 @@
+draft: true
+files:
+  -
+    draft_link: 'https://docs.google.com/spreadsheets/d/10Om2iinTwfLn1ySWtovmcm35cQnyg0Pm-rRd0a-eMjc'
diff --git a/src/ingest_validation_tools/directory-schemas/scrnaseq-v1.yaml b/src/ingest_validation_tools/directory-schemas/scrnaseq-v1.yaml
@@ -0,0 +1,4 @@
+draft: true
+files:
+  -
+    draft_link: 'https://docs.google.com/spreadsheets/d/10Om2iinTwfLn1ySWtovmcm35cQnyg0Pm-rRd0a-eMjc'
diff --git a/src/ingest_validation_tools/directory-schemas/slideseq-v1.yaml b/src/ingest_validation_tools/directory-schemas/slideseq-v1.yaml
@@ -0,0 +1,4 @@
+draft: true
+files:
+  -
+    draft_link: 'https://docs.google.com/spreadsheets/d/1LE-iyY2E6eP4E8jhgP6rhsvjESrdHXWYrMwKTvNkI5Y'
diff --git a/src/ingest_validation_tools/directory-schemas/stained-v2.yaml b/src/ingest_validation_tools/directory-schemas/stained-v2.yaml
@@ -0,0 +1,4 @@
+draft: true
+files:
+  -
+    draft_link: 'https://docs.google.com/spreadsheets/d/1_fMJrZVgx8g80uduxfr1HcIHz52_fpRfwFWFrA40tlg'
diff --git a/src/ingest_validation_tools/directory-schemas/wgs-v1.yaml b/src/ingest_validation_tools/directory-schemas/wgs-v1.yaml
@@ -0,0 +1,4 @@
+draft: true
+files:
+  -
+    draft_link: 'https://docs.google.com/spreadsheets/d/10Om2iinTwfLn1ySWtovmcm35cQnyg0Pm-rRd0a-eMjc/edit#gid=37240204'
diff --git a/src/ingest_validation_tools/docs_utils.py b/src/ingest_validation_tools/docs_utils.py
@@ -502,13 +502,14 @@ def _make_dir_descriptions(dir_schemas, pipeline_infos):
         f'### v{v}\n'
         + _make_dir_description(
             schema['files'],
-            schema.get('deprecated', False))
+            schema.get('deprecated', False),
+            schema.get('draft', False))
         + '\n\n'  # Trailing blankline needed for correct gh-pages rendering.
         for v, schema in sorted_items
     )
 
 
-def _make_dir_description(files, is_deprecated=False):
+def _make_dir_description(files, is_deprecated=False, is_draft=False):
     '''
     QA and Required flags are handled:
 
@@ -573,6 +574,10 @@ def _make_dir_description(files, is_deprecated=False):
     ...
     AssertionError: Unexpected key "bad" in {'bad': 'schema'}
     '''
+
+    if is_draft and files[0].get("draft_link", None):
+        return f'<summary><a href="{files[0].get("draft_link")}">Draft</a></summary>'
+
     for line in files:
         for k in line.keys():
             assert k in {'pattern', 'required', 'description', 'example', 'is_qa_qc'}, \