Merge latest to main (#5)

* Add tapis token retrieval and usage of the token in the api request (#4)

* initial rough draft commit
* Added auth_check to subjects data pull and wrote the function to return a boolean so that it's more modular.
* Passed coresessionid correctly and tried to remove an overlyverbose debug statement
* Correcting headers to be passed according to requests library, not flask
* Requiring tapis token to get data through APIs, still need to add requirement for local data
* Making flask more verbose
* Setup github actions for latest

---------

Co-authored-by: Frank Netscher <[email protected]>

.github/workflows/build-latest.yml

@@ -0,0 +1,41 @@
+name: Build on push to latest
+on:
+  push:
+    branches: [ latest ]
+
+jobs:
+  build_commit:
+    runs-on: ubuntu-latest
+    environment: docker
+    steps:
+      - uses: actions/checkout@v2
+      - name: Get shortsha
+        id: vars
+        run: |
+          if [ -z "$EVENT_SHA" ]; then SHORT_SHA=${GITHUB_SHA::8}; else SHORT_SHA=${EVENT_SHA::8}; fi
+          echo ::set-output name=sha_short::${SHORT_SHA}
+        env:
+          EVENT_SHA: ${{ github.event.client_payload.sha }} 
+      - name: Print shortsha
+        run: |
+          echo $SHORTSHA
+        env: 
+          SHORTSHA: ${{ steps.vars.outputs.sha_short }}     
+      - uses: mr-smithers-excellent/docker-build-push@v3
+        name: Build & push commit tagged Docker image
+        with:
+          image: ${{ secrets.DOCKERHUB_REPO }}
+          tag: ${{ steps.vars.outputs.sha_short }}   
+          registry: docker.io
+          dockerfile: Dockerfile
+          username: ${{ secrets.DOCKERHUB_USERNAME }}
+          password: ${{ secrets.DOCKERHUB_TOKEN }}
+      - uses: mr-smithers-excellent/docker-build-push@v3
+        name: Build & push commit tagged Docker image
+        with:
+          image: ${{ secrets.DOCKERHUB_REPO }}
+          tag: latest   
+          registry: docker.io
+          dockerfile: Dockerfile
+          username: ${{ secrets.DOCKERHUB_USERNAME }}
+          password: ${{ secrets.DOCKERHUB_TOKEN }}

src/app.py

@@ -1,28 +1,18 @@
-from flask import Flask, jsonify
-from os import environ
+from flask import Flask, jsonify, request
 import os
 import pandas as pd
-import json
 import csv
 
 # from data_processing import *
 from data_loading import *
 
-## Demonstrate that app is accessing the env variables properly
-SECRET_KEY = environ.get("SECRET_KEY")
-print("SECRET KEY", SECRET_KEY)
-
 # ----------------------------------------------------------------------------
 # DATA PARAMETERS
 # ----------------------------------------------------------------------------
 current_folder = os.path.dirname(__file__)
 DATA_PATH = os.path.join(current_folder,'data')
 ASSETS_PATH = os.path.join(current_folder,'assets')
 
-
-# Path to Report files at TACC
-api_root = environ.get("API_ROOT") #'https://api.a2cps.org/files/v2/download/public/system/a2cps.storage.community/reports'
-
 # ----------------------------------------------------------------------------
 # LOAD ASSETS FILES
 # ----------------------------------------------------------------------------
@@ -127,11 +117,11 @@
 }
 
 app = Flask(__name__)
+app.debug = True
 
 # APIS: try to load new data, if doesn't work, get most recent
 @app.route("/api/apis")
 def api_apis():
-    print(api_data_index)
     return jsonify(api_data_index)
 
 @app.route("/api/imaging")
@@ -142,7 +132,7 @@ def api_imaging():
     try:
         if not api_data_index['imaging'] or not check_data_current(datetime.strptime(api_data_index['imaging'], datetime_format)):
             api_date = datetime.now().strftime(datetime_format)
-            imaging_data = get_api_imaging_data()
+            imaging_data = get_api_imaging_data(request)
             if imaging_data:
                 api_data_cache['imaging'] = imaging_data
                 api_data_index['imaging'] = api_date
@@ -159,7 +149,7 @@ def api_consort():
     # try:
     if not api_data_index['consort'] or not check_data_current(datetime.strptime(api_data_index['consort'], datetime_format)):
         api_date = datetime.now().strftime(datetime_format)
-        consort_data_json = get_api_consort_data()
+        consort_data_json = get_api_consort_data(request)
         if consort_data_json:
             api_data_cache['consort'] = consort_data_json
             api_data_index['consort'] = api_date
@@ -177,7 +167,7 @@ def api_blood():
     try:
         if not api_data_index['blood'] or not check_data_current(datetime.strptime(api_data_index['blood'], datetime_format)):
             api_date = datetime.now().strftime(datetime_format)
-            blood_data, blood_data_request_status = get_api_blood_data()
+            blood_data, blood_data_request_status = get_api_blood_data(request)
             if blood_data:
                 api_data_index['blood'] = api_date
                 api_data_cache['blood'] = blood_data
@@ -204,7 +194,7 @@ def api_subjects():
     try:
         if not api_data_index['subjects'] or not check_data_current(datetime.strptime(api_data_index['subjects'], datetime_format)):
             api_date = datetime.now().strftime(datetime_format)
-            latest_subjects_json = get_api_subjects_json()
+            latest_subjects_json = get_api_subjects_json(request)
             if latest_subjects_json:
                 # latest_data = create_clean_subjects(latest_subjects_json, screening_sites, display_terms_dict, display_terms_dict_multi)
                 latest_data = process_subjects_data(latest_subjects_json,subjects_raw_cols_for_reports,screening_sites, display_terms_dict, display_terms_dict_multi)
@@ -247,7 +237,5 @@ def api_simple():
         return jsonify('not found')
 
 
-
-
 if __name__ == "__main__":
     app.run(host='0.0.0.0')