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'}, \