From dd2e1d3d43bdc4b773b5c95f5247c06110394f0f Mon Sep 17 00:00:00 2001
From: Juan Puerto <=>
Date: Tue, 1 Aug 2023 13:31:48 -0400
Subject: [PATCH] Docs: Add draft specs for new directory schemas (that have
been defined thus far).
---
docs/af/index.md | 3 +++
docs/bulkatacseq/index.md | 3 +++
docs/bulkrnaseq/index.md | 3 +++
docs/celldive/index.md | 3 +++
docs/codex/index.md | 3 +++
docs/histology/index.md | 4 ++++
docs/ims/index.md | 3 +++
docs/mxif/index.md | 3 +++
docs/scatacseq/index.md | 3 +++
docs/scrnaseq-hca/index.md | 3 +++
docs/scrnaseq/index.md | 3 +++
docs/slideseq/index.md | 3 +++
docs/stained/index.md | 3 +++
docs/wgs/index.md | 3 +++
src/ingest_validation_tools/directory-schemas/af-v1.yaml | 4 ++++
.../directory-schemas/bulkatacseq-v1.yaml | 4 ++++
.../directory-schemas/bulkrnaseq-v1.yaml | 4 ++++
.../directory-schemas/celldive-v1.yaml | 5 +++++
.../directory-schemas/codex-v2.yaml | 5 +++++
.../directory-schemas/histology-v0.yaml | 4 ++++
.../directory-schemas/ims-v1.yaml | 4 ++++
.../directory-schemas/mxif-v1.yaml | 4 ++++
.../directory-schemas/scatacseq-v1.yaml | 4 ++++
.../directory-schemas/scrnaseq-hca-v1.yaml | 4 ++++
.../directory-schemas/scrnaseq-v1.yaml | 4 ++++
.../directory-schemas/slideseq-v1.yaml | 4 ++++
.../directory-schemas/stained-v2.yaml | 4 ++++
.../directory-schemas/wgs-v1.yaml | 4 ++++
src/ingest_validation_tools/docs_utils.py | 9 +++++++--
29 files changed, 108 insertions(+), 2 deletions(-)
create mode 100644 src/ingest_validation_tools/directory-schemas/af-v1.yaml
create mode 100644 src/ingest_validation_tools/directory-schemas/bulkatacseq-v1.yaml
create mode 100644 src/ingest_validation_tools/directory-schemas/bulkrnaseq-v1.yaml
create mode 100644 src/ingest_validation_tools/directory-schemas/celldive-v1.yaml
create mode 100644 src/ingest_validation_tools/directory-schemas/codex-v2.yaml
create mode 100644 src/ingest_validation_tools/directory-schemas/histology-v0.yaml
create mode 100644 src/ingest_validation_tools/directory-schemas/ims-v1.yaml
create mode 100644 src/ingest_validation_tools/directory-schemas/mxif-v1.yaml
create mode 100644 src/ingest_validation_tools/directory-schemas/scatacseq-v1.yaml
create mode 100644 src/ingest_validation_tools/directory-schemas/scrnaseq-hca-v1.yaml
create mode 100644 src/ingest_validation_tools/directory-schemas/scrnaseq-v1.yaml
create mode 100644 src/ingest_validation_tools/directory-schemas/slideseq-v1.yaml
create mode 100644 src/ingest_validation_tools/directory-schemas/stained-v2.yaml
create mode 100644 src/ingest_validation_tools/directory-schemas/wgs-v1.yaml
diff --git a/docs/af/index.md b/docs/af/index.md
index e5ba1f7bd..97b7847e8 100644
--- a/docs/af/index.md
+++ b/docs/af/index.md
@@ -15,6 +15,9 @@ Related files:
## Directory schemas
+### v1
+Draft
+
### v0
| pattern | required? | description |
diff --git a/docs/bulkatacseq/index.md b/docs/bulkatacseq/index.md
index a115b7955..9b17a73ab 100644
--- a/docs/bulkatacseq/index.md
+++ b/docs/bulkatacseq/index.md
@@ -15,6 +15,9 @@ Related files:
## Directory schemas
+### v1
+Draft
+
### v0
| pattern | required? | description |
diff --git a/docs/bulkrnaseq/index.md b/docs/bulkrnaseq/index.md
index face5f35c..309df4284 100644
--- a/docs/bulkrnaseq/index.md
+++ b/docs/bulkrnaseq/index.md
@@ -15,6 +15,9 @@ Related files:
## Directory schemas
+### v1
+Draft
+
### v0
| pattern | required? | description |
diff --git a/docs/celldive/index.md b/docs/celldive/index.md
index d8515850d..68e6389e0 100644
--- a/docs/celldive/index.md
+++ b/docs/celldive/index.md
@@ -15,6 +15,9 @@ Related files:
## Directory schemas
+### v1
+Draft
+
### v0
| pattern | required? | description |
diff --git a/docs/codex/index.md b/docs/codex/index.md
index b8aff50ed..392011f9a 100644
--- a/docs/codex/index.md
+++ b/docs/codex/index.md
@@ -15,6 +15,9 @@ Related files:
## Directory schemas
+### v2
+Draft
+
### v1-with-dataset-json
| pattern | required? | description |
diff --git a/docs/histology/index.md b/docs/histology/index.md
index fa0b4a3ec..050fd9a77 100644
--- a/docs/histology/index.md
+++ b/docs/histology/index.md
@@ -14,6 +14,10 @@ Related files:
+## Directory schemas
+### v0
+Draft
+
diff --git a/docs/ims/index.md b/docs/ims/index.md
index 2b5e040fa..f86be2e9e 100644
--- a/docs/ims/index.md
+++ b/docs/ims/index.md
@@ -15,6 +15,9 @@ Related files:
## Directory schemas
+### v1
+Draft
+
### v0
| pattern | required? | description |
diff --git a/docs/mxif/index.md b/docs/mxif/index.md
index 5f2c1f5d6..dfd6d5a6a 100644
--- a/docs/mxif/index.md
+++ b/docs/mxif/index.md
@@ -15,6 +15,9 @@ Related files:
## Directory schemas
+### v1
+Draft
+
### v0
| pattern | required? | description |
diff --git a/docs/scatacseq/index.md b/docs/scatacseq/index.md
index 36a6d6d6a..41d618fea 100644
--- 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
+Draft
+
### v0
| pattern | required? | description |
diff --git a/docs/scrnaseq-hca/index.md b/docs/scrnaseq-hca/index.md
index ad5d3b043..a8f36087f 100644
--- a/docs/scrnaseq-hca/index.md
+++ b/docs/scrnaseq-hca/index.md
@@ -15,6 +15,9 @@ Related files:
## Directory schemas
+### v1
+Draft
+
### v0
| pattern | required? | description |
diff --git a/docs/scrnaseq/index.md b/docs/scrnaseq/index.md
index 1c024a9c9..60255b559 100644
--- a/docs/scrnaseq/index.md
+++ b/docs/scrnaseq/index.md
@@ -15,6 +15,9 @@ Related files:
## Directory schemas
+### v1
+Draft
+
### v0
| pattern | required? | description |
diff --git a/docs/slideseq/index.md b/docs/slideseq/index.md
index 98131b872..e8630c778 100644
--- a/docs/slideseq/index.md
+++ b/docs/slideseq/index.md
@@ -15,6 +15,9 @@ Related files:
## Directory schemas
+### v1
+Draft
+
### v0
| pattern | required? | description |
diff --git a/docs/stained/index.md b/docs/stained/index.md
index 0478efd42..cc2db27ff 100644
--- a/docs/stained/index.md
+++ b/docs/stained/index.md
@@ -15,6 +15,9 @@ Related files:
## Directory schemas
+### v2
+Draft
+
### v1
| pattern | required? | description |
diff --git a/docs/wgs/index.md b/docs/wgs/index.md
index a8225ca40..9c819431d 100644
--- a/docs/wgs/index.md
+++ b/docs/wgs/index.md
@@ -15,6 +15,9 @@ Related files:
## Directory schemas
+### v1
+Draft
+
### 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
new file mode 100644
index 000000000..21507c3c6
--- /dev/null
+++ 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'
\ No newline at end of file
diff --git a/src/ingest_validation_tools/directory-schemas/bulkatacseq-v1.yaml b/src/ingest_validation_tools/directory-schemas/bulkatacseq-v1.yaml
new file mode 100644
index 000000000..8b2138c8b
--- /dev/null
+++ 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'
\ No newline at end of file
diff --git a/src/ingest_validation_tools/directory-schemas/bulkrnaseq-v1.yaml b/src/ingest_validation_tools/directory-schemas/bulkrnaseq-v1.yaml
new file mode 100644
index 000000000..8b2138c8b
--- /dev/null
+++ 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'
\ No newline at end of file
diff --git a/src/ingest_validation_tools/directory-schemas/celldive-v1.yaml b/src/ingest_validation_tools/directory-schemas/celldive-v1.yaml
new file mode 100644
index 000000000..6317af655
--- /dev/null
+++ 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'
\ No newline at end of file
diff --git a/src/ingest_validation_tools/directory-schemas/codex-v2.yaml b/src/ingest_validation_tools/directory-schemas/codex-v2.yaml
new file mode 100644
index 000000000..6317af655
--- /dev/null
+++ 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'
\ No newline at end of file
diff --git a/src/ingest_validation_tools/directory-schemas/histology-v0.yaml b/src/ingest_validation_tools/directory-schemas/histology-v0.yaml
new file mode 100644
index 000000000..21507c3c6
--- /dev/null
+++ 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'
\ No newline at end of file
diff --git a/src/ingest_validation_tools/directory-schemas/ims-v1.yaml b/src/ingest_validation_tools/directory-schemas/ims-v1.yaml
new file mode 100644
index 000000000..4c64912f8
--- /dev/null
+++ 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'
\ No newline at end of file
diff --git a/src/ingest_validation_tools/directory-schemas/mxif-v1.yaml b/src/ingest_validation_tools/directory-schemas/mxif-v1.yaml
new file mode 100644
index 000000000..4a5ee23ac
--- /dev/null
+++ 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'
\ No newline at end of file
diff --git a/src/ingest_validation_tools/directory-schemas/scatacseq-v1.yaml b/src/ingest_validation_tools/directory-schemas/scatacseq-v1.yaml
new file mode 100644
index 000000000..8b2138c8b
--- /dev/null
+++ 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'
\ No newline at end of file
diff --git a/src/ingest_validation_tools/directory-schemas/scrnaseq-hca-v1.yaml b/src/ingest_validation_tools/directory-schemas/scrnaseq-hca-v1.yaml
new file mode 100644
index 000000000..8b2138c8b
--- /dev/null
+++ 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'
\ No newline at end of file
diff --git a/src/ingest_validation_tools/directory-schemas/scrnaseq-v1.yaml b/src/ingest_validation_tools/directory-schemas/scrnaseq-v1.yaml
new file mode 100644
index 000000000..8b2138c8b
--- /dev/null
+++ 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'
\ No newline at end of file
diff --git a/src/ingest_validation_tools/directory-schemas/slideseq-v1.yaml b/src/ingest_validation_tools/directory-schemas/slideseq-v1.yaml
new file mode 100644
index 000000000..affbb91d8
--- /dev/null
+++ 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'
\ No newline at end of file
diff --git a/src/ingest_validation_tools/directory-schemas/stained-v2.yaml b/src/ingest_validation_tools/directory-schemas/stained-v2.yaml
new file mode 100644
index 000000000..21507c3c6
--- /dev/null
+++ 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'
\ No newline at end of file
diff --git a/src/ingest_validation_tools/directory-schemas/wgs-v1.yaml b/src/ingest_validation_tools/directory-schemas/wgs-v1.yaml
new file mode 100644
index 000000000..a1532094d
--- /dev/null
+++ 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'
\ No newline at end of file
diff --git a/src/ingest_validation_tools/docs_utils.py b/src/ingest_validation_tools/docs_utils.py
index 0e3a0cd43..bd8754395 100644
--- 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'Draft'
+
for line in files:
for k in line.keys():
assert k in {'pattern', 'required', 'description', 'example', 'is_qa_qc'}, \