Neuron search and switch to scicrunch _dev

README.md

@@ -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
 ```
 
@@ -24,6 +23,7 @@ If you do not have the NIH SPARC portal user environment variables setup already
 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

@@ -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")
@@ -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

@@ -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

@@ -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