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Updated swagger and endpoints doc #549

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Feb 15, 2023
Merged

Updated swagger and endpoints doc #549

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19 changes: 0 additions & 19 deletions docs/ENDPOINTS.md
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Original file line number Diff line number Diff line change
Expand Up @@ -235,25 +235,6 @@ curl -s -H "Authorization: Bearer $PORTAL_TOKEN" "https://api.data.prod.umccr.or

Similarly, you can filter request parameters on `run_id`, `lane`.

### Reports Endpoint

_(*potentially large JSON response)_

_List Report entries:_
```
curl -s -H "Authorization: Bearer $PORTAL_TOKEN" "https://api.data.prod.umccr.org/reports" | jq > reports.json
```

_Get a Report record by Subject:_
```
curl -s -H "Authorization: Bearer $PORTAL_TOKEN" "https://api.data.prod.umccr.org/reports?subject_id=SBJ01146" | jq > reports_SBJ01146.json
```

_Get a Report record by Subject, Report Type:_
```
curl -s -H "Authorization: Bearer $PORTAL_TOKEN" "https://api.data.prod.umccr.org/reports?subject_id=SBJ01146&type=hrd_hrdetect" | jq > reports_SBJ01146_hrd_hrdetect.json
```

### Pairing Endpoint

_Create T/N Pairing by SequenceRuns:_
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255 changes: 48 additions & 207 deletions swagger/swagger.json
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Expand Up @@ -558,6 +558,51 @@
}
]
},
"/manops/": {
"get": {
"operationId": "manops_list",
"description": "You have hit GET /manops. This is placeholder only list endpoint. Nothing here yet.\nPlease use POST /manops endpoint and path with appropriate payload to run manual operations.",
"parameters": [],
"responses": {
"200": {
"description": ""
}
},
"tags": [
"manops"
]
},
"post": {
"operationId": "manops_create",
"description": "Need more specific path, POST /manops endpoint does not exist.\nPlease hit with the correct path with appropriate payload to run the /manops endpoint.",
"parameters": [],
"responses": {
"201": {
"description": ""
}
},
"tags": [
"manops"
]
},
"parameters": []
},
"/manops/rnasum/": {
"post": {
"operationId": "manops_rnasum",
"description": "Expected payload:\n{\n \"wfr_id\": \"wfr.<umccrise_wfr_id>\",\n \"subject_id\": \"SBJ00000\",\n \"dataset\": \"BRCA\" See: https://github.com/umccr/RNAsum/blob/master/TCGA_projects_summary.md#pan-cancer-dataset\n}\nwfr_id takes precedence over subject_id",
"parameters": [],
"responses": {
"201": {
"description": ""
}
},
"tags": [
"manops"
]
},
"parameters": []
},
"/metadata/": {
"get": {
"operationId": "metadata_list",
Expand Down Expand Up @@ -823,105 +868,6 @@
},
"parameters": []
},
"/reports/": {
"get": {
"operationId": "reports_list",
"description": "",
"parameters": [
{
"name": "ordering",
"in": "query",
"description": "Which field to use when ordering the results.",
"required": false,
"type": "string"
},
{
"name": "search",
"in": "query",
"description": "A search term.",
"required": false,
"type": "string"
},
{
"name": "page",
"in": "query",
"description": "A page number within the paginated result set.",
"required": false,
"type": "integer"
},
{
"name": "rowsPerPage",
"in": "query",
"description": "Number of results to return per page.",
"required": false,
"type": "integer"
}
],
"responses": {
"200": {
"description": "",
"schema": {
"required": [
"count",
"results"
],
"type": "object",
"properties": {
"count": {
"type": "integer"
},
"next": {
"type": "string",
"format": "uri",
"x-nullable": true
},
"previous": {
"type": "string",
"format": "uri",
"x-nullable": true
},
"results": {
"type": "array",
"items": {
"$ref": "#/definitions/Report"
}
}
}
}
}
},
"tags": [
"reports"
]
},
"parameters": []
},
"/reports/{id}/": {
"get": {
"operationId": "reports_read",
"description": "",
"parameters": [],
"responses": {
"200": {
"description": "",
"schema": {
"$ref": "#/definitions/Report"
}
}
},
"tags": [
"reports"
]
},
"parameters": [
{
"name": "id",
"in": "path",
"required": true,
"type": "string"
}
]
},
"/runs/": {
"get": {
"operationId": "runs_list",
Expand Down Expand Up @@ -2155,7 +2101,6 @@
"LabMetadataModel": {
"required": [
"library_id",
"sample_name",
"sample_id",
"phenotype",
"quality",
Expand All @@ -2181,7 +2126,7 @@
"title": "Sample name",
"type": "string",
"maxLength": 255,
"minLength": 1
"x-nullable": true
},
"sample_id": {
"title": "Sample id",
Expand Down Expand Up @@ -2366,7 +2311,8 @@
"2019",
"2020",
"2021",
"2022"
"2022",
"2023"
]
},
"truncate": {
Expand All @@ -2376,111 +2322,6 @@
}
}
},
"Report": {
"required": [
"subject_id",
"sample_id",
"library_id",
"type"
],
"type": "object",
"properties": {
"id": {
"title": "Id",
"type": "string",
"format": "uuid",
"readOnly": true
},
"subject_id": {
"title": "Subject id",
"type": "string",
"maxLength": 255,
"minLength": 1
},
"sample_id": {
"title": "Sample id",
"type": "string",
"maxLength": 255,
"minLength": 1
},
"library_id": {
"title": "Library id",
"type": "string",
"maxLength": 255,
"minLength": 1
},
"type": {
"title": "Type",
"type": "string",
"enum": [
"msi",
"tmb",
"tmb_trace",
"fusion_caller_metrics",
"failed_exon_coverage_qc",
"sample_analysis_results",
"target_region_coverage",
"qc_summary",
"multiqc",
"report_inputs",
"hrd_chord",
"hrd_hrdetect",
"purple_cnv_germ",
"purple_cnv_som",
"purple_cnv_som_gene",
"sigs_dbs",
"sigs_indel",
"sigs_snv_2015",
"sigs_snv_2020",
"sv_unmelted",
"sv_melted",
"sv_bnd_main",
"sv_bnd_purpleinf",
"sv_nobnd_main",
"sv_nobnd_other",
"sv_nobnd_manygenes",
"sv_nobnd_manytranscripts"
]
},
"created_by": {
"title": "Created by",
"type": "string",
"maxLength": 255,
"x-nullable": true
},
"data": {
"title": "Data",
"type": "object",
"x-nullable": true
},
"s3_object_id": {
"title": "S3 object id",
"type": "integer",
"maximum": 9223372036854776000,
"minimum": -9223372036854776000,
"x-nullable": true
},
"gds_file_id": {
"title": "Gds file id",
"type": "integer",
"maximum": 9223372036854776000,
"minimum": -9223372036854776000,
"x-nullable": true
},
"report_uri": {
"title": "Report uri",
"type": "string",
"minLength": 1
},
"unique_hash": {
"title": "Unique hash",
"type": "string",
"maxLength": 64,
"minLength": 1,
"x-nullable": true
}
}
},
"S3ObjectModel": {
"required": [
"bucket",
Expand Down