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docs: enhance score set create/patch endpoints with detailed OpenAPI schema for file uploads
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‎src/mavedb/routers/score_sets.py‎

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@@ -1691,6 +1691,40 @@ async def create_score_set(
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response_model_exclude_none=True,
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responses={**BASE_400_RESPONSE, **ACCESS_CONTROL_ERROR_RESPONSES},
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summary="Upload score and variant count files for a score set",
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openapi_extra={
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"requestBody": {
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"content": {
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"multipart/form-data": {
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"schema": {
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"type": "object",
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"properties": {
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"scores_file": {
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"type": "string",
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"format": "binary",
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"description": "CSV file containing variant scores. This file is required, and should have at least one score column.",
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},
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"counts_file": {
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"type": "string | null",
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"format": "binary",
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"description": "CSV file containing variant counts. If provided, this file should have the same index and variant columns as the scores file.",
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},
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"score_columns_metadata": {
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"type": "string | null",
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"format": "binary",
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"description": "JSON file containing metadata for score columns. If provided, this file should have metadata for one or more score columns in the scores file. This JSON file should provide a dictionary mapping column names to metadata objects. Metadata objects should follow the DatasetColumnMetadata schema: `{'description': string, 'details': string}`.",
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},
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"count_columns_metadata": {
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"type": "string | null",
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"format": "binary",
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"description": "JSON file containing metadata for count columns. If provided, this file should have metadata for one or more count columns in the counts file. This JSON file should provide a dictionary mapping column names to metadata objects. Metadata objects should follow the DatasetColumnMetadata schema: `{'description': string, 'details': string}`.",
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},
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},
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}
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},
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},
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"description": "Score files, to be uploaded as multipart form data. The `scores_file` is required, while the `counts_file`, `score_columns_metadata`, and `count_columns_metadata` are optional.",
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}
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},
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)
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async def upload_score_set_variant_data(
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*,
@@ -1763,6 +1797,41 @@ async def upload_score_set_variant_data(
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response_model_exclude_none=True,
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responses={**BASE_400_RESPONSE, **ACCESS_CONTROL_ERROR_RESPONSES},
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summary="Update score ranges / calibrations for a score set",
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openapi_extra={
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"requestBody": {
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"content": {
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"multipart/form-data": {
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"schema": {
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"type": "object",
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"properties": {
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**score_set.ScoreSetUpdateAllOptional.model_json_schema(by_alias=False)["properties"],
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"scores_file": {
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"type": "string | null",
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"format": "binary",
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"description": "CSV file containing variant scores. If provided, this file should have at least one score column.",
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},
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"counts_file": {
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"type": "string | null",
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"format": "binary",
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"description": "CSV file containing variant counts. If provided, this file should have the same index and variant columns as the scores file.",
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},
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"score_columns_metadata": {
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"type": "string | null",
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"format": "binary",
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"description": "JSON file containing metadata for score columns. If provided, this file should have metadata for one or more score columns in the scores file. This JSON file should provide a dictionary mapping column names to metadata objects. Metadata objects should follow the DatasetColumnMetadata schema: `{'description': string, 'details': string}`.",
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},
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"count_columns_metadata": {
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"type": "string | null",
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"format": "binary",
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"description": "JSON file containing metadata for count columns. If provided, this file should have metadata for one or more count columns in the counts file. This JSON file should provide a dictionary mapping column names to metadata objects. Metadata objects should follow the DatasetColumnMetadata schema: `{'description': string, 'details': string}`.",
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},
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},
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}
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},
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},
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"description": "Score set properties and score files, to be uploaded as multipart form data. All fields here are optional, and only those provided will be updated.",
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}
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},
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)
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async def update_score_set_with_variants(
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*,
@@ -1780,6 +1849,13 @@ async def update_score_set_with_variants(
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"""
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logger.info(msg="Began score set with variants update.", extra=logging_context())
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# TODO#629: Use `flexible_model_loader` utility here to support both form data and JSON body.
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# See: https://github.com/VariantEffect/mavedb-api/pull/589/changes/d1641de7e4bee43e8a0c9f9283e022c5b56830ff
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# Currently, only form data is supported but this would allow us to also support JSON bodies
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# in cases where no files are being uploaded. My view is accepting score set calibration
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# information via a single form field is also more straightforward than handling all the score
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# set update fields as separate form fields and parsing them into an object. Doing so will also
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# simplify the OpenAPI schema for this endpoint.
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try:
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# Get all form data from the request
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form_data = await request.form()

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