Card: simplify How this dataset is built section; link to source for full payloads

README.md

@@ -30,7 +30,7 @@ National Cancer Institute (NCI) Genomic Data Commons (GDC). One HuggingFace
 (HF) subset per TCGA project; one row per patient.
 
 - **Projects included:** `TCGA-CHOL`, `TCGA-DLBC`, `TCGA-LUAD`
-- **Generated:** 2026-05-05 06:12:43 UTC
+- **Generated:** 2026-05-05 15:19:38 UTC
 - **Source:** GDC `/cases` endpoint, open-access tier only.
 - **Schema:** derived from the [GDC Data Dictionary][gdc-dict]; the live
   dictionary the GDC was serving when the data was fetched is hashed into
@@ -84,147 +84,59 @@ tree:
 
 ## How this dataset is built
 
-Three GDC REST endpoints feed every row in this dataset. Both endpoints
-and payloads below are reproduced verbatim from the build code; the
-on-disk `gdc_status.json` for each project additionally pins the GDC
-data release and dictionary SHA-256 the data was fetched against.
-
-### `POST /cases` — clinical entities
-
-One paginated POST per build, returning the nested case JSON for every
-patient in the requested projects.
-
-```json
-{
-  "filters": {
-    "op": "in",
-    "content": {
-      "field": "project.project_id",
-      "value": [
-        "TCGA-CHOL",
-        "TCGA-DLBC",
-        "TCGA-LUAD"
-      ]
-    }
-  },
-  "fields": "case_id,submitter_id,primary_site,disease_type,index_date,consent_type,days_to_consent,days_to_lost_to_followup,lost_to_followup",
-  "expand": "demographic,diagnoses,diagnoses.treatments,follow_ups,exposures,family_histories,project,samples,samples.portions,samples.portions.analytes,samples.portions.analytes.aliquots",
-  "format": "JSON",
-  "size": 200,
-  "from": 0
-}
-```
+Three GDC REST endpoints feed every row, with filters and field lists
+constructed in [`src/tcga2hf/clinical.py`][src-clinical] (the `cases`
+table) and [`src/tcga2hf/genomic.py`][src-genomic] (molecular and
+provenance tables) of the [`tcga2hf` repo][repo].
 
-The full nested response (top-level scalars + `demographic` + `diagnoses[]`
-with `treatments[]` inside + `follow_ups[]` + `exposures[]` +
-`family_histories[]` + `samples[]` with `portions[].analytes[].aliquots[]`
-inside) is written to `<data-dir>/raw/<project>/cases.json` and feeds the
-`cases` config (and the consolidated patient row).
-
-### `POST /files` — molecular file discovery
-
-One POST per (project, modality) pair, listing every open-access file of
-that modality. Each modality is identified by a `data_type` plus a small
-set of clauses that lock the format / experimental strategy / workflow
-type so future GDC additions can't silently ship under the same
-`data_type`:
-
-- `data_type='Masked Somatic Mutation'` AND `data_format='MAF'` AND `data_category='Simple Nucleotide Variation'` AND `experimental_strategy='WXS'` AND `analysis.workflow_type='Aliquot Ensemble Somatic Variant Merging and Masking'`
-- `data_type='Gene Expression Quantification'` AND `data_format='TSV'` AND `data_category='Transcriptome Profiling'` AND `experimental_strategy='RNA-Seq'` AND `analysis.workflow_type='STAR - Counts'`
-
-Below is the full request shape for `Masked Somatic Mutation` against
-`TCGA-LUAD`; the build runs the same shape with the
-`Gene Expression Quantification` clauses too. Responses are written to
-`<data-dir>/raw/<project>/<modality>/manifest.json` and feed the `files`
-config.
-
-```json
-{
-  "filters": {
-    "op": "and",
-    "content": [
-      {
-        "op": "=",
-        "content": {
-          "field": "cases.project.project_id",
-          "value": "TCGA-LUAD"
-        }
-      },
-      {
-        "op": "=",
-        "content": {
-          "field": "access",
-          "value": "open"
-        }
-      },
-      {
-        "op": "=",
-        "content": {
-          "field": "data_type",
-          "value": "Masked Somatic Mutation"
-        }
-      },
-      {
-        "op": "=",
-        "content": {
-          "field": "data_format",
-          "value": "MAF"
-        }
-      },
-      {
-        "op": "=",
-        "content": {
-          "field": "data_category",
-          "value": "Simple Nucleotide Variation"
-        }
-      },
-      {
-        "op": "=",
-        "content": {
-          "field": "experimental_strategy",
-          "value": "WXS"
-        }
-      },
-      {
-        "op": "=",
-        "content": {
-          "field": "analysis.workflow_type",
-          "value": "Aliquot Ensemble Somatic Variant Merging and Masking"
-        }
-      }
-    ]
-  },
-  "fields": "file_id,file_name,file_size,md5sum,access,data_category,data_type,data_format,experimental_strategy,analysis.workflow_type,cases.case_id,cases.submitter_id,cases.samples.portions.analytes.aliquots.aliquot_id",
-  "format": "JSON",
-  "size": 500,
-  "from": 0
-}
-```
+**Projects fetched in this build:** `TCGA-CHOL`, `TCGA-DLBC`, `TCGA-LUAD`.
 
-### `POST /data` — file bytes
+### `POST /cases` → `cases` table
 
-For every file UUID returned by `/files`, the build batches up to 50
-UUIDs per request:
+Filter: `project.project_id IN [<projects above>]`. The request `expand`s
+the full nested `case` structure (demographic + diagnoses → treatments +
+follow_ups + exposures + family_histories + samples → portions →
+analytes → aliquots), and the response is captured verbatim into
+`<data-dir>/raw/<project>/cases.json` per project. See
+`tcga2hf.clinical.TOP_LEVEL_FIELDS` and `tcga2hf.clinical.EXPANSIONS`
+for the exact field/expand lists.
 
-```json
-{"ids": ["<file_uuid_1>", "<file_uuid_2>", "..."]}
-```
+### `POST /files` → `masked_somatic_mutation`, `gene_expression_quantification`, `files` tables
+
+One POST per (project, modality). All requests share
+`cases.project.project_id = <project>` AND `access = open`. The
+remaining clauses lock the format / experimental strategy / workflow
+type so future GDC additions can't silently ship a different pipeline
+under the same `data_type`:
+
+| Table | data_type | data_format | data_category | experimental_strategy | analysis.workflow_type |
+|---|---|---|---|---|---|
+| `masked_somatic_mutation` | `Masked Somatic Mutation` | `MAF` | `Simple Nucleotide Variation` | `WXS` | `Aliquot Ensemble Somatic Variant Merging and Masking` |
+| `gene_expression_quantification` | `Gene Expression Quantification` | `TSV` | `Transcriptome Profiling` | `RNA-Seq` | `STAR - Counts` |
+
+The combined `/files` responses (one per modality per project) feed the
+`files` table. See `tcga2hf.genomic.MODALITY_FILTERS` and
+`tcga2hf.genomic.FILE_FIELDS` for the full request payload.
+
+### `POST /data` → file bytes
+
+UUIDs returned by `/files` are batched (≤50 per request) into `POST
+/data`; the response is a tar.gz of those files. Mutations files are
+parsed row-by-row into the `masked_somatic_mutation` config; expression
+files are parsed gene-row-by-gene-row into the
+`gene_expression_quantification` config. See
+`tcga2hf.gdc.bulk_download` for the batching and retry logic.
+
+### Provenance pinned per build
+
+- `GET /status` → `data_release` / `tag` / `commit` saved in each
+  project's `gdc_status.json`.
+- `GET /v0/submission/_dictionary/_all` → schema dictionary snapshot
+  saved alongside the raw data; its SHA-256 is recorded in
+  `gdc_status.json`.
 
-The response is a tar.gz of the files. Mutations files are parsed
-row-by-row into the `masked_somatic_mutation` config; expression files
-are parsed gene-row-by-gene-row into the
-`gene_expression_quantification` config. (See `tcga2hf.gdc.bulk_download`
-for the batching + retry logic.)
-
-### Other GDC calls captured for provenance
-
-- `GET /status` — once at the top of every build; `data_release` /
-  `tag` / `commit` are saved in each project's `gdc_status.json`.
-- `GET /v0/submission/_dictionary/_all` — once at the top of every build;
-  written to `<data-dir>/raw/gdc_dictionary.<major>.<minor>.json` and its
-  SHA-256 is recorded in `gdc_status.json`. The static schema in
-  `tcga2hf.schema` is regenerated from this dictionary; see the package
-  `scripts/regenerate_clinical_fields.py`.
+[src-clinical]: https://github.com/galtay/tcga2hf/blob/main/src/tcga2hf/clinical.py
+[src-genomic]: https://github.com/galtay/tcga2hf/blob/main/src/tcga2hf/genomic.py
 
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