diff --git a/dev/.gitignore b/dev/.gitignore deleted file mode 100644 index 2dc5e5d..0000000 --- a/dev/.gitignore +++ /dev/null @@ -1,2 +0,0 @@ -#config file -instance/app.cfg \ No newline at end of file diff --git a/dev/Dockerfile b/dev/Dockerfile deleted file mode 100644 index 0cdd64a..0000000 --- a/dev/Dockerfile +++ /dev/null @@ -1,13 +0,0 @@ -FROM hubmap/api-base-image:1.0.0 - -LABEL description="DEV Server for Assayclasses" - -WORKDIR /usr/src/app - -COPY . . - -RUN pip install --upgrade pip -r requirements.txt - -EXPOSE 8181 - -CMD [ "python", "-m" , "app"] diff --git a/dev/README.md b/dev/README.md deleted file mode 100644 index 606a7ad..0000000 --- a/dev/README.md +++ /dev/null @@ -1,95 +0,0 @@ -# Development AssayClasses RESTful service - -## Dev Service -This simple, standalone service is designed for quick changes to the assay class/rule chain information during development to allow for quick testing. The service two endpoints: - - /assayclasses?application_context=HUBMAP - - assayclasses/?application_context=HUBMAP - -## JSON backing file and releasing to UBKG -The [assayclasses.json file](https://github.com/x-atlas-consortia/hs-ontology-api/blob/dev-integrate/dev/assayclasses.json) file is read directly by this service to form the responses. This file can be changed directly in GitHub (in the dev-integrate branch only) to test changes to the associated rule chain/assay class information that normally is sourced from UBKG. To develop using this service and eventually release to UBKG follow this procedure: - - Update the [assayclasses.json file](https://github.com/x-atlas-consortia/hs-ontology-api/blob/dev-integrate/dev/assayclasses.json) directly by merging changes into the `dev-integrate` branch. Test locally or using the HuBMAP DEV infrastructure where this dev service has been put in place. - - After successful tests on the DEV infrastructure make a PR to `main` with the changes in assayclasses.json. Add Alan Simmons as a reviewer on the PR. - - The changes will be added to UBKG and released to the UBKG DEV instance. - - Test the changes on the HuBMAP TEST infrastructure (TEST infrastructure is connected to UBKG DEV instance). - - After successful testing on TEST the changes to UBKG will be released to PROD. - - -### Running the service locally -To run this service, in this directory: - - copy instance/app.cfg.example to instance/app.cfg - - create a python virtual environment with the contents of requirements.txt imported into the environment - - source/activate the virtual environment - - execute `python app.py` -The service will be available on port 8181. -See below for instructions to run with Docker - - -Both endpoints require the `application_context=HUBMAP` parameter. (A future version will allow SENNET context as well, which will read results from a different file). - -### Endpoints -The `/assayclasses` endpoint simply returns the contents of the [assayclasses.json file](https://github.com/x-atlas-consortia/hs-ontology-api/blob/main/dev/assayclasses.json) as a json response. - -The `/assayclasses/` endpoint searches the same [assayclasses.json file](https://raw.githubusercontent.com/x-atlas-consortia/hs-ontology-api/dev-integrate/dev/assayclasses.json) for an assayclass item matching `rule_description.code` and returns the full matching assayclass item as a json response. If the code is not found a 404 is returned. For example if `/assayclasses/C200001?application_context=HUBMAP` is called the return value is: - -``` -{ - "rule_description": { - "application_context": "HUBMAP", - "code": "C200150", - "name": "non-DCWG primary IMC2D" - }, - "value": { - "active_status": "active", - "assaytype": "IMC2D", - "dataset_type": { - "PDR_category": "MxNF", - "dataset_type": "2D Imaging Mass Cytometry", - "fig2": { - "aggregated_assaytype": "LC-MS", - "category": "bulk", - "modality": "Proteomics" - } - }, - "description": "2D Imaging Mass Cytometry", - "dir_schema": "imc-v0", - "is_multiassay": false, - "measurement_assay": { - "codes": [ - { - "code": "SENNET:C006901", - "term": "Imaging Mass Cytometry Measurement Assay" - }, - { - "code": "HUBMAP:C006901", - "term": "Imaging Mass Cytometry Measurement Assay" - }, - { - "code": "OBI:0003096", - "term": "imaging mass cytometry assay" - } - ], - "contains_full_genetic_sequences": false - }, - "must_contain": [], - "pipeline_shorthand": null, - "process_state": "primary", - "provider": "IEC", - "tbl_schema": "imc-v", - "vitessce_hints": [] - } -} -``` - -### Docker Deployment on DEV VM - -First build a new docker image -``` -docker-compose build -``` - -Then spin up the container -``` -docker-compose up -d -``` - -Once the container is up running correctly, you can access at `http://gateway.dev.hubmapconsortium.org:8181/assayclasses` diff --git a/dev/app.py b/dev/app.py deleted file mode 100644 index 481cd76..0000000 --- a/dev/app.py +++ /dev/null @@ -1,125 +0,0 @@ -import os -import json -from flask import Flask, request, Response, abort -from urllib.request import urlopen -from urllib.error import HTTPError -import logging - -# -# This is a RESTful service that exposes two endpoints: -# /assayclasses?application_context=HUBMAP -# /assayclasses/?application_context=HUBMAP -# -# Both endpoints require the application_context=HUBMAP parameter to be included, otherwise they return a 400. -# -# This service is intended to be for development purposes only, so a developer can easily control the output by -# changing the [assayclasses.json file in GitHub], specified in the ASSAYCLASSES_JSON_URL app.conf parameter. -# -# It is intended to mimic the services: -# https://ontology-api.dev.hubmapconsortium.org/assayclasses?application_context=HUBMAP -# https://ontology-api.dev.hubmapconsortium.org/assayclasses/C200150?application_context=HUBMAP -# -# Please see Issue: https://github.com/orgs/hubmapconsortium/projects/40/views/1?filterQuery=kollar&visibleFields=%5B%22Title%22%2C%22Assignees%22%2C%22Status%22%2C%22Labels%22%2C117184707%5D&pane=issue&itemId=74945308 - - -logging.basicConfig(format='[%(asctime)s] %(levelname)s in %(module)s: %(message)s', - level=logging.DEBUG, - datefmt='%Y-%m-%d %H:%M:%S' - ) -logger = logging.getLogger() - - -app = Flask(__name__, - instance_path=os.path.join(os.path.abspath(os.path.dirname(__file__)), 'instance'), - instance_relative_config=True) -app.config.from_pyfile('app.cfg') - - -def get_assayclasses() -> dict: - """ - Download the assayclasses information and return it as a dict. - Since this is done at startup time, on error it will log an error and exit as the app cannot recover from this. - """ - if "ASSAYCLASSES_JSON_URL" not in app.config: - logger.error("app.cfg must contain ASSAYCLASSES_JSON_URL") - exit(1) - assayclasses_json_url: str = app.config["ASSAYCLASSES_JSON_URL"] - try: - response = urlopen(assayclasses_json_url) - data: str = response.read().decode("utf-8") - except HTTPError as he: - logger.error(f"Could not read ASSAYCLASSES_JSON_URL: {assayclasses_json_url}, error: {he}") - exit(1) - try: - json_dict: dict = json.loads(data) - except json.JSONDecodeError as jde: - logger.error(f"Invalid JSON syntax: {jde}") - exit(1) - logger.info(f"successfully downloaded app.cfg:ASSAYCLASSES_JSON_URL={assayclasses_json_url} json as dict") - return json_dict - - -assayclasses_list: dict = get_assayclasses() - - -def find_assayclass_with_rule_description_code(code: str): - """ - Find the assayclass corresponding the rule_description code given or return None. - """ - for ad in assayclasses_list: - if "rule_description" in ad and "code" in ad["rule_description"] and ad["rule_description"]["code"] == code: - return ad - return None - - -def check_for_valid_application_context() -> None: - """ - Check for a valid auery parameter application_context, and if not found abort with a 400. - """ - application_context = request.args.get('application_context') - if application_context is None or application_context.upper() != "HUBMAP": - abort(Response(json.dumps({"message": "A query parameter of application_context=HUBMAP must be specified"}), - 400, - mimetype='application/json')) - - -@app.route('/', methods=['GET']) -def index(): - return "Hello! This is the DEV AssayClass service :)" - - -@app.route('/assayclasses/', methods=['GET']) -def assayclasses_by_code(code): - """ - This endpoint searches the same assayclasses.json file for an assayclass item matching - rule_description.code and returns the full matching assayclass item as a json response. - If the code is not found a 404 is returned. - """ - check_for_valid_application_context() - - assayclass_dict = find_assayclass_with_rule_description_code(code) - - if assayclass_dict is not None: - return Response(json.dumps(assayclass_dict), 200, mimetype='application/json') - - return Response(json.dumps({"message": f"No assayclass corresponding the rule_description code:{code} was found"}), - 404, mimetype='application/json') - - -@app.route('/assayclasses', methods=['GET']) -def assayclass(): - """ - This endpoint returns the contents of the ASSAYCLASSES_JSON_URL as a json response. - """ - check_for_valid_application_context() - - return Response(json.dumps(assayclasses_list), 200, mimetype='application/json') - - -# For development/testing only -if __name__ == '__main__': - try: - port = 8181 - app.run(port=port, host='0.0.0.0') - finally: - pass diff --git a/dev/assayclasses.json b/dev/assayclasses.json deleted file mode 100644 index b2227cc..0000000 --- a/dev/assayclasses.json +++ /dev/null @@ -1,5248 +0,0 @@ -[ - { - "rule_description": { - "application_context": "HUBMAP", - "code": "C200001", - "name": "non-DCWG primary AF" - }, - "value": { - "active_status": "active", - "assaytype": "AF", - "dataset_type": { - "PDR_category": "Single-cycle Flourescence Microscopy", - "dataset_type": "Auto-fluorescence", - "fig2": { - "aggregated_assaytype": null, - "category": "imaging", - "modality": "Label free imaging" - } - }, - "description": "Auto-fluorescence Microscopy", - "dir_schema": "af-v0", - "is_multiassay": false, - "measurement_assay": { - "codes": [ - { - "code": "SENNET:C006002", - "term": "Auto-fluorescence Microscopy Measurement Assay" - }, - { - "code": "HUBMAP:C006002", - "term": "Auto-fluorescence Microscopy Measurement Assay" - }, - { - "code": "OBI:0003088", - "term": "autofluorescence microscopy assay" - } - ], - "contains_full_genetic_sequences": false - }, - "must_contain": [], - "pipeline_shorthand": null, - "process_state": "primary", - "provider": "IEC", - "tbl_schema": "af-v", - "vitessce_hints": [] - } - }, - { - "rule_description": { - "application_context": "HUBMAP", - "code": "C200010", - "name": "derived AF_pyramid" - }, - "value": { - "active_status": "active", - "assaytype": "AF_pyramid", - "dataset_type": { - "PDR_category": "Single-cycle Flourescence Microscopy", - "dataset_type": "Auto-fluorescence", - "fig2": { - "aggregated_assaytype": null, - "category": "imaging", - "modality": "Label free imaging" - } - }, - "description": "Auto-fluorescence Microscopy [Image Pyramid]", - "dir_schema": null, - "is_multiassay": false, - "measurement_assay": { - "codes": [], - "contains_full_genetic_sequences": false - }, - "must_contain": [], - "pipeline_shorthand": "Image Pyramid", - "process_state": "derived", - "provider": "IEC", - "tbl_schema": null, - "vitessce_hints": [ - "is_support", - "pyramid" - ] - } - }, - { - "rule_description": { - "application_context": "HUBMAP", - "code": "C200020", - "name": "non-DCWG primary ATACseq-bulk" - }, - "value": { - "active_status": "active", - "assaytype": "ATACseq-bulk", - "dataset_type": { - "PDR_category": "ATAC Sequencing", - "dataset_type": "ATACseq", - "fig2": { - "aggregated_assaytype": null, - "category": "bulk", - "modality": "Epigenomics" - } - }, - "description": "Bulk ATACseq", - "dir_schema": "bulkatacseq-v0", - "is_multiassay": false, - "measurement_assay": { - "codes": [ - { - "code": "SENNET:C200023", - "term": "ATACseq Measurement Assay" - }, - { - "code": "HUBMAP:C200023", - "term": "ATACseq Measurement Assay" - }, - { - "code": "OBI:0002039", - "term": "assay for transposase-accessible chromatin using sequencing" - } - ], - "contains_full_genetic_sequences": true - }, - "must_contain": [], - "pipeline_shorthand": null, - "process_state": "primary", - "provider": "IEC", - "tbl_schema": "bulkatacseq-v", - "vitessce_hints": [] - } - }, - { - "rule_description": { - "application_context": "HUBMAP", - "code": "C200030", - "name": "derived bulk_atacseq" - }, - "value": { - "active_status": "active", - "assaytype": "bulk_atacseq", - "dataset_type": { - "PDR_category": "ATAC Sequencing", - "dataset_type": "ATACseq", - "fig2": { - "aggregated_assaytype": null, - "category": "bulk", - "modality": "Epigenomics" - } - }, - "description": "Bulk ATAC-seq [BWA + MACS2]", - "dir_schema": null, - "is_multiassay": false, - "measurement_assay": { - "codes": [], - "contains_full_genetic_sequences": false - }, - "must_contain": [], - "pipeline_shorthand": "BWA + MACS2", - "process_state": "derived", - "provider": "IEC", - "tbl_schema": null, - "vitessce_hints": [] - } - }, - { - "rule_description": { - "application_context": "HUBMAP", - "code": "C200040", - "name": "non-DCWG primary cell-dive" - }, - "value": { - "active_status": "active", - "assaytype": "cell-dive", - "dataset_type": { - "PDR_category": "cell", - "dataset_type": "Cell DIVE", - "fig2": { - "aggregated_assaytype": null, - "category": "imaging", - "modality": "Antibody-based imaging" - } - }, - "description": "Cell DIVE", - "dir_schema": "celldive-v0", - "is_multiassay": false, - "measurement_assay": { - "codes": [ - { - "code": "SENNET:C006301", - "term": "Cell DIVE Measurement Assay" - }, - { - "code": "HUBMAP:C006301", - "term": "Cell DIVE Measurement Assay" - }, - { - "code": "OBI:0003092", - "term": "Cell DIVE multiplexed imaging assay" - } - ], - "contains_full_genetic_sequences": false - }, - "must_contain": [], - "pipeline_shorthand": null, - "process_state": "primary", - "provider": "IEC", - "tbl_schema": null, - "vitessce_hints": [] - } - }, - { - "rule_description": { - "application_context": "HUBMAP", - "code": "C200050", - "name": "derived celldive_deepcell" - }, - "value": { - "active_status": "active", - "assaytype": "celldive_deepcell", - "dataset_type": { - "PDR_category": "cell", - "dataset_type": "Cell DIVE", - "fig2": { - "aggregated_assaytype": null, - "category": "imaging", - "modality": "Antibody-based imaging" - } - }, - "description": "Cell DIVE [DeepCell + SPRM]", - "dir_schema": null, - "is_multiassay": false, - "measurement_assay": { - "codes": [], - "contains_full_genetic_sequences": false - }, - "must_contain": [], - "pipeline_shorthand": "DeepCell + SPRM", - "process_state": "derived", - "provider": "IEC", - "tbl_schema": null, - "vitessce_hints": [ - "is_tiled", - "is_image", - "anndata", - "sprm" - ] - } - }, - { - "rule_description": { - "application_context": "HUBMAP", - "code": "C200060", - "name": "non-DCWG primary CODEX" - }, - "value": { - "active_status": "active", - "assaytype": "CODEX", - "dataset_type": { - "PDR_category": "cell", - "dataset_type": "CODEX", - "fig2": { - "aggregated_assaytype": null, - "category": "imaging", - "modality": "Antibody-based imaging" - } - }, - "description": "CODEX", - "dir_schema": "codex-v1", - "is_multiassay": false, - "measurement_assay": { - "codes": [ - { - "code": "SENNET:C006501", - "term": "CO-detection by inDEXing (CODEX) Measurement Assay" - }, - { - "code": "HUBMAP:C006501", - "term": "CO-detection by inDEXing (CODEX) Measurement Assay" - }, - { - "code": "OBI:0003093", - "term": "co-detection by indexing assay" - } - ], - "contains_full_genetic_sequences": false - }, - "must_contain": [], - "pipeline_shorthand": null, - "process_state": "primary", - "provider": "IEC", - "tbl_schema": "codex-v", - "vitessce_hints": [] - } - }, - { - "rule_description": { - "application_context": "HUBMAP", - "code": "C200070", - "name": "non-DCWG primary CODEX2" - }, - "value": { - "active_status": "active", - "assaytype": "CODEX2", - "dataset_type": { - "PDR_category": "cell", - "dataset_type": "CODEX", - "fig2": { - "aggregated_assaytype": null, - "category": "imaging", - "modality": "Antibody-based imaging" - } - }, - "description": "CODEX (CODEX2 assay type)", - "dir_schema": "codex-v1", - "is_multiassay": false, - "measurement_assay": { - "codes": [ - { - "code": "SENNET:C006501", - "term": "CO-detection by inDEXing (CODEX) Measurement Assay" - }, - { - "code": "HUBMAP:C006501", - "term": "CO-detection by inDEXing (CODEX) Measurement Assay" - }, - { - "code": "OBI:0003093", - "term": "co-detection by indexing assay" - } - ], - "contains_full_genetic_sequences": false - }, - "must_contain": [], - "pipeline_shorthand": null, - "process_state": "primary", - "provider": "IEC", - "tbl_schema": "codex-v", - "vitessce_hints": [] - } - }, - { - "rule_description": { - "application_context": "HUBMAP", - "code": "C200080", - "name": "derived codex_cytokit_v1" - }, - "value": { - "active_status": "active", - "assaytype": "codex_cytokit_v1", - "dataset_type": { - "PDR_category": "cell", - "dataset_type": "CODEX", - "fig2": { - "aggregated_assaytype": null, - "category": "imaging", - "modality": "Antibody-based imaging" - } - }, - "description": "CODEX [Cytokit + SPRM]", - "dir_schema": null, - "is_multiassay": false, - "measurement_assay": { - "codes": [], - "contains_full_genetic_sequences": false - }, - "must_contain": [], - "pipeline_shorthand": "Cytokit + SPRM", - "process_state": "derived", - "provider": "IEC", - "tbl_schema": null, - "vitessce_hints": [ - "anndata", - "codex", - "is_tiled", - "is_image" - ] - } - }, - { - "rule_description": { - "application_context": "HUBMAP", - "code": "C200090", - "name": "derived codex_cytokit_v1 json-based" - }, - "value": { - "active_status": "active", - "assaytype": "codex_cytokit_v1", - "dataset_type": { - "PDR_category": "cell", - "dataset_type": "CODEX", - "fig2": { - "aggregated_assaytype": null, - "category": "imaging", - "modality": "Antibody-based imaging" - } - }, - "description": "CODEX [Cytokit + SPRM]", - "dir_schema": null, - "is_multiassay": false, - "measurement_assay": { - "codes": [], - "contains_full_genetic_sequences": false - }, - "must_contain": [], - "pipeline_shorthand": "Cytokit + SPRM", - "process_state": "derived", - "provider": "IEC", - "tbl_schema": null, - "vitessce_hints": [ - "json-based", - "codex", - "is_tiled", - "is_image" - ] - } - }, - { - "rule_description": { - "application_context": "HUBMAP", - "code": "C200100", - "name": "derived codex_cytokit" - }, - "value": { - "active_status": "active", - "assaytype": "codex_cytokit_v1", - "dataset_type": { - "PDR_category": "cell", - "dataset_type": "CODEX", - "fig2": { - "aggregated_assaytype": null, - "category": "imaging", - "modality": "Antibody-based imaging" - } - }, - "description": "CODEX [Cytokit + SPRM]", - "dir_schema": null, - "is_multiassay": false, - "measurement_assay": { - "codes": [], - "contains_full_genetic_sequences": false - }, - "must_contain": [], - "pipeline_shorthand": "Cytokit + SPRM", - "process_state": "derived", - "provider": "IEC", - "tbl_schema": null, - "vitessce_hints": [ - "is_tiled", - "is_image", - "anndata", - "sprm" - ] - } - }, - { - "rule_description": { - "application_context": "HUBMAP", - "code": "C200110", - "name": "non-DCWG primary DART-FISH" - }, - "value": { - "active_status": "active", - "assaytype": "DART-FISH", - "dataset_type": { - "PDR_category": null, - "dataset_type": "DARTFish", - "fig2": { - "aggregated_assaytype": null, - "category": "imaging", - "modality": "Spatial Transcriptomics" - } - }, - "description": "DART-FISH", - "dir_schema": null, - "is_multiassay": false, - "measurement_assay": { - "codes": [ - { - "code": "SENNET:C006701", - "term": "Decoding Amplified taRgeted Transcripts with Fluorescence In Situ Hybridization (DARTFish) Measurement Assay" - }, - { - "code": "HUBMAP:C006701", - "term": "Decoding Amplified taRgeted Transcripts with Fluorescence In Situ Hybridization (DARTFish) Measurement Assay" - }, - { - "code": "OBI:0003095", - "term": "decoding amplified targeted transcripts with fluorescence in situ hybridization assay" - } - ], - "contains_full_genetic_sequences": false - }, - "must_contain": [], - "pipeline_shorthand": null, - "process_state": "primary", - "provider": "IEC", - "tbl_schema": null, - "vitessce_hints": [] - } - }, - { - "rule_description": { - "application_context": "HUBMAP", - "code": "C200120", - "name": "non-DCWG primary DESI" - }, - "value": { - "active_status": "active", - "assaytype": "DESI", - "dataset_type": { - "PDR_category": "IMS", - "dataset_type": "DESI", - "fig2": { - "aggregated_assaytype": null, - "category": "imaging", - "modality": "MS-based imaging" - } - }, - "description": "DESI", - "dir_schema": "ims-v0", - "is_multiassay": false, - "measurement_assay": { - "codes": [ - { - "code": "SENNET:C008001", - "term": "Nanospray Desorption ElectroSpray Ionization (NanoDESI) Measurement Assay" - }, - { - "code": "HUBMAP:C008001", - "term": "Nanospray Desorption ElectroSpray Ionization (NanoDESI) Measurement Assay" - }, - { - "code": "OBI:0003101", - "term": "nanospray desorption electrospray ionization assay" - } - ], - "contains_full_genetic_sequences": false - }, - "must_contain": [], - "pipeline_shorthand": null, - "process_state": "primary", - "provider": "IEC", - "tbl_schema": "ims-v", - "vitessce_hints": [] - } - }, - { - "rule_description": { - "application_context": "HUBMAP", - "code": "C200130", - "name": "derived DESI_pyramid" - }, - "value": { - "active_status": "active", - "assaytype": "DESI_pyramid", - "dataset_type": { - "PDR_category": "IMS", - "dataset_type": "DESI", - "fig2": { - "aggregated_assaytype": null, - "category": "imaging", - "modality": "MS-based imaging" - } - }, - "description": "DESI [Image Pyramid]", - "dir_schema": null, - "is_multiassay": false, - "measurement_assay": { - "codes": [], - "contains_full_genetic_sequences": false - }, - "must_contain": [], - "pipeline_shorthand": "Image Pyramid", - "process_state": "derived", - "provider": "IEC", - "tbl_schema": null, - "vitessce_hints": [ - "is_support", - "pyramid" - ] - } - }, - { - "rule_description": { - "application_context": "HUBMAP", - "code": "C200140", - "name": "derived image_pyramid" - }, - "value": { - "active_status": "active", - "assaytype": "image_pyramid", - "dataset_type": { - "PDR_category": null, - "dataset_type": "UNKNOWN", - "fig2": { - "aggregated_assaytype": null, - "category": null, - "modality": null - } - }, - "description": "Image Pyramid", - "dir_schema": null, - "is_multiassay": false, - "measurement_assay": { - "codes": [], - "contains_full_genetic_sequences": false - }, - "must_contain": [], - "pipeline_shorthand": null, - "process_state": "derived", - "provider": null, - "tbl_schema": null, - "vitessce_hints": [ - "is_support", - "pyramid", - "is_image" - ] - } - }, - { - "rule_description": { - "application_context": "HUBMAP", - "code": "C200150", - "name": "non-DCWG primary IMC2D" - }, - "value": { - "active_status": "active", - "assaytype": "IMC2D", - "dataset_type": { - "PDR_category": "MxNF", - "dataset_type": "2D Imaging Mass Cytometry", - "fig2": { - "aggregated_assaytype": "LC-MS", - "category": "bulk", - "modality": "Proteomics" - } - }, - "description": "2D Imaging Mass Cytometry", - "dir_schema": "imc-v0", - "is_multiassay": false, - 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"application_context": "HUBMAP", - "code": "C201170", - "name": "DCWG music" - }, - "value": { - "active_status": "active", - "assaytype": "music", - "dataset_type": { - "PDR_category": "RNA Sequencing", - "dataset_type": "RNAseq", - "fig2": { - "aggregated_assaytype": null, - "category": "bulk", - "modality": "Transcriptomics" - } - }, - "description": "MUSIC", - "dir_schema": "music-v2", - "is_multiassay": false, - "measurement_assay": { - "codes": [ - { - "code": "HUBMAP:C201172", - "term": "MUSIC Measurement Assay" - } - ], - "contains_full_genetic_sequences": false - }, - "must_contain": [], - "pipeline_shorthand": null, - "process_state": "primary", - "provider": "IEC", - "tbl_schema": null, - "vitessce_hints": [] - } - }, - { - "rule_description": { - "application_context": "HUBMAP", - "code": "C201190", - "name": "non-DCWG primary MS" - }, - "value": { - "active_status": "active", - "assaytype": "MS", - "dataset_type": { - "PDR_category": null, - "dataset_type": "LC-MS", - "fig2": { - 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"category": "bulk", - "modality": "Transcriptomics" - } - }, - "description": "snRNAseq [Salmon]", - "dir_schema": null, - "is_multiassay": false, - "measurement_assay": { - "codes": [], - "contains_full_genetic_sequences": false - }, - "must_contain": [], - "pipeline_shorthand": "Salmon", - "process_state": "derived", - "provider": "IEC", - "tbl_schema": null, - "vitessce_hints": [ - "json-based", - "rna", - "is_sc" - ] - } - }, - { - "rule_description": { - "application_context": "HUBMAP", - "code": "C202010", - "name": "derived salmon_rnaseq_10x json-based" - }, - "value": { - "active_status": "active", - "asssaytype": "salmon_rnaseq_10x", - "dataset_type": { - "PDR_category": "RNA Sequencing", - "dataset_type": "RNAseq", - "fig2": { - "aggregated_assaytype": null, - "category": "bulk", - "modality": "Transcriptomics" - } - }, - "description": "scRNAseq (10x Genomics) [Salmon]", - "dir_schema": null, - "is_multiassay": false, - "measurement_assay": { - "codes": [], - "contains_full_genetic_sequences": false - }, - "must_contain": [], - "pipeline_shorthand": "Salmon", - "process_state": "derived", - "provider": "IEC", - "tbl_schema": null, - "vitessce_hints": [ - "rna", - "is_sc", - "json_based" - ] - } - } -] diff --git a/dev/docker-compose.yml b/dev/docker-compose.yml deleted file mode 100644 index 906423f..0000000 --- a/dev/docker-compose.yml +++ /dev/null @@ -1,13 +0,0 @@ -services: - - assayclasses-dev-server: - build: - context: . - container_name: assayclasses-dev-server - ports: - - "8181:8181" - init: true - restart: always - volumes: - - "./instance:/usr/src/app/instance" - \ No newline at end of file diff --git a/dev/instance/app.cfg.example b/dev/instance/app.cfg.example deleted file mode 100644 index 2a9da04..0000000 --- a/dev/instance/app.cfg.example +++ /dev/null @@ -1,3 +0,0 @@ -# URL to the json file containing the assay class information -ASSAYCLASSES_JSON_URL = 'https://raw.githubusercontent.com/x-atlas-consortia/hs-ontology-api/dev-integrate/dev/assayclasses.json' - diff --git a/dev/requirements.txt b/dev/requirements.txt deleted file mode 100644 index 95fef4e..0000000 --- a/dev/requirements.txt +++ /dev/null @@ -1 +0,0 @@ -Flask==3.0.3 diff --git a/dev/test_api.sh b/dev/test_api.sh deleted file mode 100755 index 7d3b9e8..0000000 --- a/dev/test_api.sh +++ /dev/null @@ -1,52 +0,0 @@ -#!/bin/bash -set -e -set -u - -ASSAYCLASS_URL_LOCAL=http://localhost:8181 -ASSAYCLASS_URL=$ASSAYCLASS_URL_LOCAL - - -curl --request GET \ - --url "${ASSAYCLASS_URL}" -echo -echo - - -echo "Only the last one in the group should succeed..." -curl --request GET \ - --url "${ASSAYCLASS_URL}/assayclasses" \ - --header "Accept: application/json" -echo - -curl --request GET \ - --url "${ASSAYCLASS_URL}/assayclasses?application_context=Wrong" \ - --header "Accept: application/json" -echo - -curl --request GET \ - --url "${ASSAYCLASS_URL}/assayclasses?application_context=HUBMAp" \ - --header "Accept: application/json" -echo -echo - - -echo "Only the last one in the group should succeed..." -curl --request GET \ - --url "${ASSAYCLASS_URL}/assayclasses/C200010" \ - --header "Accept: application/json" -echo - -curl --request GET \ - --url "${ASSAYCLASS_URL}/assayclasses/xyzzy?application_context=NoMap" \ - --header "Accept: application/json" -echo - -curl --request GET \ - --url "${ASSAYCLASS_URL}/assayclasses/xyzzy?application_context=huBMAP" \ - --header "Accept: application/json" -echo - -curl --request GET \ - --url "${ASSAYCLASS_URL}/assayclasses/C200010?application_context=HUbmAP" \ - --header "Accept: application/json" -echo