Merge pull request #1208 from microbiomedata/automate-github-issues

Create github issue when user submits metadata

Author: pkalita-lbl

nmdc_server/api.py

@@ -1,7 +1,10 @@
+import json
+import logging
 from io import BytesIO
 from typing import Any, Dict, List, Optional
 from uuid import UUID
 
+import requests
 from fastapi import APIRouter, Depends, Header, HTTPException, Response, status
 from fastapi.responses import JSONResponse, PlainTextResponse
 from sqlalchemy.orm import Session
@@ -728,12 +731,16 @@ async def update_submission(
             status_code=400,
             detail="This submission is currently being edited by a different user.",
         )
-
+    # Create Github issue when metadata is being submitted
+    if (
+        submission.status == "in-progress"
+        and body_dict.get("status", None) == "Submitted- Pending Review"
+    ):
+        create_github_issue(submission, user)
     # Merge the submission metadata dicts
     submission.metadata_submission = (
         submission.metadata_submission | body_dict["metadata_submission"]
     )
-
     # Update permissions and status iff the user is an "owner"
     if current_user_role and current_user_role.role == models.SubmissionEditorRole.owner:
         new_permissions = body_dict.get("permissions", None)
@@ -747,6 +754,79 @@ async def update_submission(
     return submission
 
 
+def create_github_issue(submission, user):
+    settings = Settings()
+    gh_url = str(settings.github_issue_url)
+    token = settings.github_authentication_token
+    assignee = settings.github_issue_assignee
+    # If the settings for issue creation weren't supplied return, no need to do anything further
+    if gh_url == None or token == None:
+        return
+
+    # Gathering the fields we want to display in the issue
+    headers = {"Authorization": f"Bearer {token}", "Content-Type": "text/plain; charset=utf-8"}
+    studyform = submission.metadata_submission["studyForm"]
+    contextform = submission.metadata_submission["contextForm"]
+    multiomicsform = submission.metadata_submission["multiOmicsForm"]
+    pi = studyform["piName"]
+    piorcid = studyform["piOrcid"]
+    datagenerated = "Yes" if contextform["dataGenerated"] else "No"
+    omicsprocessingtypes = ", ".join(multiomicsform["omicsProcessingTypes"])
+    sampletype = ", ".join(submission.metadata_submission["templates"])
+    sampledata = submission.metadata_submission["sampleData"]
+    numsamples = 0
+    for key in sampledata:
+        numsamples = max(numsamples, len(sampledata[key]))
+
+    # some variable data to supply depending on if data has been generated or not
+    data_ids = []
+    if contextform["dataGenerated"]:
+        data_ids = [
+            "NCBI ID: " + multiomicsform["NCBIBioProjectId"],
+            "GOLD ID: " + multiomicsform["GOLDStudyId"],
+            "Alternative IDs/Names: " + ", ".join(multiomicsform["alternativeNames"]),
+        ]
+
+    else:
+        data_ids = [
+            "JGI IDs: " + multiomicsform["JGIStudyId"],
+            "EMSL IDs: " + multiomicsform["studyNumber"],
+            "Alternative IDs/Names: " + ", ".join(multiomicsform["alternativeNames"]),
+        ]
+
+    # assemble the body of the API request
+    body_lis = [
+        f"Submitter: {user.name}, {user.orcid}",
+        f"Submission ID: {submission.id}",
+        f"Has data been generated: {datagenerated}",
+        f"PI name: {pi}",
+        f"PI orcid: {piorcid}",
+        "Status: Submitted -Pending Review",
+        f"Data types: {omicsprocessingtypes}",
+        f"Sample type:{sampletype}",
+        f"Number of samples:{numsamples}",
+    ] + data_ids
+    body_string = " \n ".join(body_lis)
+    payload_dict = {
+        "title": f"NMDC Submission: {submission.id}",
+        "body": body_string,
+        "assignees": [assignee],
+    }
+
+    payload = json.dumps(payload_dict)
+
+    # make request and log an error or success depending on reply
+    res = requests.post(url=gh_url, data=payload, headers=headers)
+    if res.status_code != 201:
+        logging.error(f"Github issue creation failed with code {res.status_code}")
+        logging.error(res.reason)
+    else:
+        logging.info(f"Github issue creation successful with code {res.status_code}")
+        logging.info(res.reason)
+
+    return res
+
+
 @router.delete(
     "/metadata_submission/{id}",
     tags=["metadata_submission"],

nmdc_server/config.py

@@ -67,6 +67,11 @@ class Settings(BaseSettings):
     # CORS settings necessary for allowing request from Field Notes app
     cors_allow_origins: Optional[str] = None  # comma separated list of allowed origins
 
+    # Github Issue creation settings. Both are required for automated issue creation.
+    github_issue_url: Optional[str] = None
+    github_authentication_token: Optional[str] = None
+    github_issue_assignee: Optional[str] = None
+
     @property
     def current_db_uri(self) -> str:
         if self.environment == "testing":