diff --git a/.project b/.project
new file mode 100644
index 0000000..aa1aa32
--- /dev/null
+++ b/.project
@@ -0,0 +1,18 @@
+
+
+ hs-ontology-api
+
+
+ ubkg-api
+
+
+
+ org.python.pydev.PyDevBuilder
+
+
+
+
+
+ org.python.pydev.pythonNature
+
+
diff --git a/.pydevproject b/.pydevproject
new file mode 100644
index 0000000..08475ee
--- /dev/null
+++ b/.pydevproject
@@ -0,0 +1,13 @@
+
+
+
+ python interpreter
+
+ Default
+
+
+ /${PROJECT_DIR_NAME}/src
+ /${PROJECT_DIR_NAME}/dev
+
+
+
diff --git a/dev/.gitignore b/dev/.gitignore
new file mode 100644
index 0000000..2dc5e5d
--- /dev/null
+++ b/dev/.gitignore
@@ -0,0 +1,2 @@
+#config file
+instance/app.cfg
\ No newline at end of file
diff --git a/dev/README.md b/dev/README.md
new file mode 100644
index 0000000..fb4d66a
--- /dev/null
+++ b/dev/README.md
@@ -0,0 +1,67 @@
+## Development AssayClasses RESTful service
+
+The service contained within this directory exposes two endpoints:
+ - /assayclasses?application_context=HUBMAP
+ - assayclasses/?application_context=HUBMAP
+
+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/activage the virtual environment
+ - execute `python app.py`
+The service will be available on port 8181.
+
+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).
+
+The `/assayclasses` endpoint simply returns the contents of the file https://raw.githubusercontent.com/x-atlas-consortia/hs-ontology-api/dev-integrate/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": []
+ }
+}
+```
\ No newline at end of file
diff --git a/dev/app.py b/dev/app.py
new file mode 100644
index 0000000..678617f
--- /dev/null
+++ b/dev/app.py
@@ -0,0 +1,40 @@
+import os
+import json
+from flask import Flask, Response
+
+# Specify the absolute path of the instance folder and use the config file relative to the instance path
+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')
+
+@app.route('/', methods=['GET'])
+def index():
+ return "Hello! This is the DEV AssayClass service :)"
+
+@app.route('/assayclasses/', methods=['GET'])
+def assayclasses(code):
+ response_code = 200
+ response_data = {
+ 'message': f'This endpoint not yet implemented code: {code}'
+ }
+
+ return Response(json.dumps(response_data), response_code, mimetype='application/json')
+
+@app.route('/assayclasses', methods=['GET'])
+def assayclass_by_code():
+ response_code = 200
+ response_data = {
+ 'message': 'This endpoint not yet implemented'
+ }
+
+ return Response(json.dumps(response_data), response_code, 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
new file mode 100644
index 0000000..3a2b380
--- /dev/null
+++ b/dev/assayclasses.json
@@ -0,0 +1,5211 @@
+[
+ {
+ "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,
+ "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"
+ }
+ ],
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+ "dataset_type": "Second Harmonic Generation (SHG)",
+ "fig2": {
+ "aggregated_assaytype": null,
+ "category": "imaging",
+ "modality": "Label free imaging"
+ }
+ },
+ "description": "Second Harmonic Generation (SHG)",
+ "dir_schema": "second-harmonic-generation-v2",
+ "is_multiassay": false,
+ "measurement_assay": {
+ "codes": [
+ {
+ "code": "HUBMAP:C201113",
+ "term": "Second Harmonic Generation Microscopy 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": "C201120",
+ "name": "DCWG enhanced-srs"
+ },
+ "value": {
+ "active_status": "active",
+ "assaytype": "enhanced-srs",
+ "dataset_type": {
+ "PDR_category": null,
+ "dataset_type": "Enhanced Stimulated Raman Spectroscopy (SRS)",
+ "fig2": {
+ "aggregated_assaytype": null,
+ "category": "imaging",
+ "modality": "Label free imaging"
+ }
+ },
+ "description": "Enhanced Stimulated Raman Spectroscopy (SRS)",
+ "dir_schema": "enhanced-srs-v2",
+ "is_multiassay": false,
+ "measurement_assay": {
+ "codes": [
+ {
+ "code": "SENNET:C201123",
+ "term": "Enhanced Stimulated Raman Spectroscopy Measurement Assay"
+ },
+ {
+ "code": "HUBMAP:C201123",
+ "term": "Enhanced Stimulated Raman Spectroscopy Measurement Assay"
+ },
+ {
+ "code": "CHV:0000011571",
+ "term": "raman spectroscopy"
+ },
+ {
+ "code": "LCH_NW:sh85111278",
+ "term": "Raman spectroscopy"
+ },
+ {
+ "code": "NCI:C17157",
+ "term": "Raman Spectroscopy"
+ },
+ {
+ "code": "CSP:0633-0213",
+ "term": "Raman spectrometry"
+ }
+ ],
+ "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": "C201130",
+ "name": "DCWG molecular-cartography"
+ },
+ "value": {
+ "active_status": "active",
+ "assaytype": "molecular-cartography",
+ "dataset_type": {
+ "PDR_category": null,
+ "dataset_type": "Molecular Cartography",
+ "fig2": {
+ "aggregated_assaytype": null,
+ "category": "imaging",
+ "modality": "Spatial Transcriptomics"
+ }
+ },
+ "description": "Molecular Cartography",
+ "dir_schema": "mc-v2",
+ "is_multiassay": false,
+ "measurement_assay": {
+ "codes": [
+ {
+ "code": "HUBMAP:C201133",
+ "term": "Molecular Cartography Measurement Assay"
+ }
+ ],
+ "contains_full_genetic_sequences": false
+ },
+ "must_contain": [],
+ "pipeline_shorthand": null,
+ "process_state": "primary",
+ "provider": null,
+ "tbl_schema": null,
+ "vitessce_hints": []
+ }
+ },
+ {
+ "rule_description": {
+ "application_context": "HUBMAP",
+ "code": "C201140",
+ "name": "derived visium-no-probes"
+ },
+ "value": {
+ "active_status": "active",
+ "assaytype": "visium-no-probes",
+ "dataset_type": {
+ "PDR_category": "Spatial Transcriptomics",
+ "dataset_type": "Visium (no probes)",
+ "fig2": {
+ "aggregated_assaytype": null,
+ "category": "imaging",
+ "modality": "Spatial Transcriptomics"
+ }
+ },
+ "description": "Visium (no probes) [Salmon + Scanpy]",
+ "dir_schema": null,
+ "is_multiassay": true,
+ "measurement_assay": {
+ "codes": [],
+ "contains_full_genetic_sequences": false
+ },
+ "must_contain": [],
+ "pipeline_shorthand": "Salmon + Scanpy",
+ "process_state": "derived",
+ "provider": "IEC",
+ "tbl_schema": null,
+ "vitessce_hints": [
+ "spatial",
+ "anndata",
+ "is_image",
+ "rna"
+ ]
+ }
+ },
+ {
+ "rule_description": {
+ "application_context": "HUBMAP",
+ "code": "C201150",
+ "name": "derived multiome snare-seq2"
+ },
+ "value": {
+ "active_status": "active",
+ "assaytype": "multiome-snare-seq2",
+ "dataset_type": {
+ "PDR_category": "RNA Sequencing",
+ "dataset_type": "RNAseq",
+ "fig2": {
+ "aggregated_assaytype": null,
+ "category": "bulk",
+ "modality": "Transcriptomics"
+ }
+ },
+ "description": "SNAREseq2 [Salmon + ArchR + Muon]",
+ "dir_schema": null,
+ "is_multiassay": true,
+ "measurement_assay": {
+ "codes": [
+ {
+ "code": "SENNET:C001024",
+ "term": "Single-nucleus chromatin accessibility and mRNA expression sequencing (SNARE-seq) assay"
+ },
+ {
+ "code": "HUBMAP:C001024",
+ "term": "Single-nucleus chromatin accessibility and mRNA expression sequencing (SNARE-seq) assay"
+ },
+ {
+ "code": "OBI:0003108",
+ "term": "single-nucleus chromatin accessibility and mRNA expression sequencing assay"
+ }
+ ],
+ "contains_full_genetic_sequences": true
+ },
+ "must_contain": [],
+ "pipeline_shorthand": "Salmon + ArchR + Muon",
+ "process_state": "derived",
+ "provider": "IEC",
+ "tbl_schema": null,
+ "vitessce_hints": [
+ "atac",
+ "spatial",
+ "anndata",
+ "is_image",
+ "rna"
+ ]
+ }
+ },
+ {
+ "rule_description": {
+ "application_context": "HUBMAP",
+ "code": "C201160",
+ "name": "derived multiome 10x"
+ },
+ "value": {
+ "active_status": "active",
+ "assaytype": "10x-multiome",
+ "dataset_type": {
+ "PDR_category": "RNA Sequencing",
+ "dataset_type": "RNAseq",
+ "fig2": {
+ "aggregated_assaytype": null,
+ "category": "bulk",
+ "modality": "Transcriptomics"
+ }
+ },
+ "description": "10x Multiome [Salmon + ArchR + Muon]",
+ "dir_schema": null,
+ "is_multiassay": true,
+ "measurement_assay": {
+ "codes": [
+ {
+ "code": "SENNET:C200772",
+ "term": "10x Multiome Measurement Assay"
+ },
+ {
+ "code": "HUBMAP:C200772",
+ "term": "10x Multiome Measurement Assay"
+ },
+ {
+ "code": "EFO:0030059",
+ "term": "10x multiome"
+ }
+ ],
+ "contains_full_genetic_sequences": true
+ },
+ "must_contain": [],
+ "pipeline_shorthand": "Salmon + ArchR + Muon",
+ "process_state": "derived",
+ "provider": "IEC",
+ "tbl_schema": null,
+ "vitessce_hints": [
+ "anndata",
+ "atac",
+ "rna",
+ "is_sc"
+ ]
+ }
+ },
+ {
+ "rule_description": {
+ "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": {
+ "aggregated_assaytype": null,
+ "category": "bulk",
+ "modality": "Proteomics"
+ }
+ },
+ "description": "MS",
+ "dir_schema": "lcms-v0",
+ "is_multiassay": false,
+ "measurement_assay": {
+ "codes": [
+ {
+ "code": "SENNET:C001001",
+ "term": "Mass Spectrometry Measurement Assay"
+ },
+ {
+ "code": "HUBMAP:C001001",
+ "term": "Mass Spectrometry Measurement Assay"
+ },
+ {
+ "code": "OBI:0000470",
+ "term": "mass spectrometry assay"
+ }
+ ],
+ "contains_full_genetic_sequences": false
+ },
+ "must_contain": [],
+ "pipeline_shorthand": null,
+ "process_state": "primary",
+ "provider": "IEC",
+ "tbl_schema": "lcms-v",
+ "vitessce_hints": []
+ }
+ },
+ {
+ "rule_description": {
+ "application_context": "HUBMAP",
+ "code": "C202000",
+ "name": "derived salmon_sn_rnaseq_10x json-based"
+ },
+ "value": {
+ "active_status": "active",
+ "assaytype": "salmon_sn_rnaseq_10x",
+ "dataset_type": {
+ "PDR_category": "RNA Sequencing",
+ "dataset_type": "RNAseq",
+ "fig2": {
+ "aggregated_assaytype": null,
+ "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"
+ ]
+ }
+ }
+]
diff --git a/dev/instance/app.cfg.example b/dev/instance/app.cfg.example
new file mode 100644
index 0000000..2a9da04
--- /dev/null
+++ b/dev/instance/app.cfg.example
@@ -0,0 +1,3 @@
+# 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
new file mode 100644
index 0000000..95fef4e
--- /dev/null
+++ b/dev/requirements.txt
@@ -0,0 +1 @@
+Flask==3.0.3