Neuron search and switch to scicrunch _dev #19

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Tehsurfer wants to merge 64 commits into ABI-Software:main from Tehsurfer:scicrunch-doi

README.md

-Original file line number
+Diff line change
@@ Expand Up / @@ -10,7 +10,6 @@ Make sure you have python 3 installed `python3 --version` @@
     python3 -m venv ./venv
     . ./venv/bin/activate
     pip install -r requirements.txt
-    pip install -r requirements-dev.txt
     gunicorn main:app
     ```
@@ Expand All @@
     After the previous steps or if you already have those environment variables setup, run:
     ```
+    export PYTHONPATH=`pwd`
     pip install -r requirements-dev.txt
     pytest
     ```

app/config.py

-Original file line number
+Diff line change
@@ Expand Up / @@ -31,7 +31,7 @@ class Config(object): @@
         KNOWLEDGEBASE_KEY = os.environ.get("KNOWLEDGEBASE_KEY", "secret-key")
         DEPLOY_ENV = os.environ.get("DEPLOY_ENV", "development")
         SPARC_APP_HOST = os.environ.get("SPARC_APP_HOST", "https://sparc-app.herokuapp.com")
-        SCI_CRUNCH_HOST = os.environ.get("SCICRUNCH_HOST", "https://scicrunch.org/api/1/elastic/SPARC_Datasets_pr")
+        SCI_CRUNCH_HOST = os.environ.get("SCICRUNCH_HOST", "https://scicrunch.org/api/1/elastic/SPARC_PortalDatasets_pr")
         MAPSTATE_TABLENAME = os.environ.get("MAPSTATE_TABLENAME", "mapstates")
         SCAFFOLDSTATE_TABLENAME = os.environ.get("SCAFFOLDSTATE_TABLENAME", "scaffoldstates")
         WRIKE_TOKEN = os.environ.get("WRIKE_TOKEN")
@@ Expand All / @@ -42,4 +42,7 @@ class Config(object): @@
         CCB_HEAD_WRIKE_ID = os.environ.get("CCB_HEAD_WRIKE_ID")
         MODERATOR_WRIKE_ID = os.environ.get("MODERATOR_WRIKE_ID")
         MAILCHIMP_API_KEY = os.environ.get("MAILCHIMP_API_KEY")
+        OSPARC_API_URL=os.environ.get("OSPARC_API_URL", "https://api.osparc.io")
+        OSPARC_API_KEY=os.environ.get("OSPARC_API_KEY")
+        OSPARC_API_SECRET=os.environ.get("OSPARC_API_SECRET")

app/main.py

            
                      Original file line number
                      Diff line number
                      Diff line change
                  
    @@ -24,6 +24,9 @@
  
    from requests.auth import HTTPBasicAuth

    import os

    import app.osparc as osparc

    import requests

    # from pymongo import MongoClient

    app = Flask(__name__)

    @@ -210,6 +213,59 @@ def direct_download_url(path):
  
        resource = response["Body"].read()

        return resource

    # /scicrunch/: Returns scicrunch results for a given <search> query

    @app.route("/scicrunch-dataset/<doi1>/<doi2>")

    def sci_doi(doi1,doi2):

        doi = doi1 + '/' + doi2

        print(doi)

        data = create_doi_request(doi)

        try:

            response = requests.post(

                f'{Config.SCI_CRUNCH_HOST}/_search?api_key={Config.KNOWLEDGEBASE_KEY}',

                json=data)

            return response.json()

        except requests.exceptions.HTTPError as err:

            logging.error(err)

            return json.dumps({'error': err})

    # /pubmed/<id> Used as a proxy for making requests to pubmed

    @app.route("/pubmed/<id>")

    @app.route("/pubmed/<id>/")

    def pubmed(id):

        try:

            response = requests.get(f'https://pubmed.ncbi.nlm.nih.gov/{id}/')

            return response.text

        except requests.exceptions.HTTPError as err:

            logging.error(err)

            return json.dumps({'error': err})

    # /scicrunch-query-string/: Returns results for given organ curie. These can be processed by the sidebar

    @app.route("/scicrunch-query-string/")

    def sci_organ():

        fields = request.args.getlist('field')

        curie = request.args.get('curie')

        # field example: "*organ.curie"

        data = {

            "size": 20,

            "from": 0,

            "query": {

                "query_string": {

                    "fields": fields,

                    "query": curie

                }

            }

        }

        try:

            response = requests.post(

                f'{Config.SCI_CRUNCH_HOST}/_search?api_key={Config.KNOWLEDGEBASE_KEY}',

                json=data)

            return process_kb_results(response.json())

        except requests.exceptions.HTTPError as err:

            logging.error(err)

            return json.dumps({'error': err})

    # /search/: Returns scicrunch results for a given <search> query

    @app.route("/search/", defaults={'query': ''})

    @@ -243,9 +299,9 @@ def filter_search(query):
  
            results = process_kb_results(response.json())

        except requests.exceptions.HTTPError as err:

            logging.error(err)

            return jsonify({'error': str(err), 'message': 'Scicrunch is not currently reachable, please try again later'}), 502

            return jsonify({'error': str(err), 'message': 'SciCrunch is not currently reachable, please try again later'}), 502

        except json.JSONDecodeError as e:

            return jsonify({'message': 'Could not parse Scicrunch output, please try again later',

            return jsonify({'message': 'Could not parse SciCrunch output, please try again later',

                            'error': 'JSONDecodeError'}), 502

        return results

    @@ -268,7 +324,7 @@ def get_facets(type):
  
                json_result = response.json()

                results.append(json_result)

            except BaseException as e:

                return jsonify({'message': 'Could not parse Scicrunch output, please try again later',

                return jsonify({'message': 'Could not parse SciCrunch output, please try again later',

                                'error': 'JSONDecodeError'}), 502

        # Select terms from the results

    @@ -565,3 +621,39 @@ def subscribe_to_mailchimp():
  
                return resp.json()

        else:

            abort(400, description="Missing email_address, first_name or last_name")

    @app.route("/simulation", methods=["POST"])

    def simulation():

        data = request.get_json()

        if data and "model_url" in data and "json_config" in data:

            return json.dumps(osparc.run_simulation(data["model_url"], data["json_config"]))

        else:

            abort(400, description="Missing model URL and/or JSON configuration")

    @app.route("/pmr_latest_exposure", methods=["POST"])

    def pmr_latest_exposure():

        data = request.get_json()

        if data and "workspace_url" in data:

            try:

                resp = requests.get(data["workspace_url"],

                                    headers={"Accept": "application/vnd.physiome.pmr2.json.1"})

                if resp.status_code == 200:

                    try:

                        # Return the latest exposure for the given workspace.

                        url = resp.json()["collection"]["items"][0]["links"][0]["href"]

                    except:

                        # There is no latest exposure for the given workspace.

                        url = ""

                    return jsonify(

                        url=url

                    )

                else:

                    return resp.json()

            except:

                abort(400, description="Invalid workspace URL")

        else:

            abort(400, description="Missing workspace URL")

app/osparc.py

-Original file line number
+Diff line change
@@ -0,0 +1,103 @@
+    from app.config import Config
+    import json
+    import osparc
+    import tempfile
+    from time import sleep
+    def run_simulation(model_url, json_config):
+        temp_config_file = tempfile.NamedTemporaryFile(mode="w+")
+        json.dump(json_config, temp_config_file)
+        temp_config_file.seek(0)
+        try:
+            api_client = osparc.ApiClient(osparc.Configuration(
+                host=Config.OSPARC_API_URL,
+                username=Config.OSPARC_API_KEY,
+                password=Config.OSPARC_API_SECRET
+            ))
+            # Upload the configuration file.
+            files_api = osparc.FilesApi(api_client)
+            try:
+                config_file = files_api.upload_file(temp_config_file.name)
+            except:
+                raise Exception(
+                    "the simulation configuration file could not be uploaded")
+            # Create the simulation.
+            solvers_api = osparc.SolversApi(api_client)
+            solver = solvers_api.get_solver_release(
+                "simcore/services/comp/opencor", "1.0.3")
+            job = solvers_api.create_job(
+                solver.id,
+                solver.version,
+                osparc.JobInputs({
+                    "model_url": model_url,
+                    "config_file": config_file
+                })
+            )
+            # Start the simulation job.
+            status = solvers_api.start_job(solver.id, solver.version, job.id)
+            if status.state != "PUBLISHED":
+                raise Exception("the simulation job could not be submitted")
+            # Wait for the simulation job to be complete (or to fail).
+            while True:
+                status = solvers_api.inspect_job(solver.id, solver.version, job.id)
+                if status.progress == 100:
+                    break
+                sleep(1)
+            status = solvers_api.inspect_job(solver.id, solver.version, job.id)
+            if status.state != "SUCCESS":
+                raise Exception("the simulation failed")
+            # Retrieve the simulation job outputs.
+            try:
+                outputs = solvers_api.get_job_outputs(
+                    solver.id, solver.version, job.id)
+            except:
+                raise Exception(
+                    "the simulation job outputs could not be retrieved")
+            # Download the simulation results.
+            try:
+                results_filename = files_api.download_file(
+                    outputs.results["output_1"].id)
+            except:
+                raise Exception("the simulation results could not be retrieved")
+            results_file = open(results_filename, "r")
+            res = {
+                "status": "ok",
+                "results": json.load(results_file)
+            }
+            results_file.close()
+        except Exception as e:
+            res = {
+                "status": "nok",
+                "description": e.args[0] if len(e.args) > 0 else "unknown"
+            }
+        temp_config_file.close()
+        return res

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