update helm test

.github/workflows/ci.yaml

@@ -0,0 +1,23 @@
+name: CI
+on:
+  push:
+  pull_request:
+    types: [opened, reopened]
+concurrency:
+  group: '${{ github.workflow }} @ ${{ github.event.pull_request.head.label || github.head_ref || github.ref }}'
+  cancel-in-progress: true
+jobs:
+  Security:
+    name: Security Pipeline
+    uses: uc-cdis/.github/.github/workflows/securitypipeline.yaml@master
+    with:
+       python-poetry: 'false'
+    secrets: inherit
+
+  UnitTest:
+    name: Python Unit Test with Postgres
+    uses: uc-cdis/.github/.github/workflows/python_unit_test.yaml@master
+    with:
+       python-version: '3.9'
+       test-script: 'tests/ci_commands_script.sh'
+       run-coveralls: true

.secrets.baseline

@@ -7,6 +7,9 @@
     {
       "name": "AWSKeyDetector"
     },
+    {
+      "name": "AzureStorageKeyDetector"
+    },
     {
       "name": "Base64HighEntropyString",
       "limit": 4.5
@@ -17,9 +20,15 @@
     {
       "name": "CloudantDetector"
     },
+    {
+      "name": "DiscordBotTokenDetector"
+    },
+    {
+      "name": "GitHubTokenDetector"
+    },
     {
       "name": "HexHighEntropyString",
-      "limit": 3
+      "limit": 3.0
     },
     {
       "name": "IbmCloudIamDetector"
@@ -37,15 +46,24 @@
     {
       "name": "MailchimpDetector"
     },
+    {
+      "name": "NpmDetector"
+    },
     {
       "name": "PrivateKeyDetector"
     },
+    {
+      "name": "SendGridDetector"
+    },
     {
       "name": "SlackDetector"
     },
     {
       "name": "SoftlayerDetector"
     },
+    {
+      "name": "SquareOAuthDetector"
+    },
     {
       "name": "StripeDetector"
     },
@@ -57,10 +75,6 @@
     {
       "path": "detect_secrets.filters.allowlist.is_line_allowlisted"
     },
-    {
-      "path": "detect_secrets.filters.common.is_baseline_file",
-      "filename": ".secrets.baseline"
-    },
     {
       "path": "detect_secrets.filters.common.is_ignored_due_to_verification_policies",
       "min_level": 2
@@ -94,13 +108,22 @@
     }
   ],
   "results": {
+    ".github/workflows/ci.yaml": [
+      {
+        "type": "Secret Keyword",
+        "filename": ".github/workflows/ci.yaml",
+        "hashed_secret": "3e26d6750975d678acb8fa35a0f69237881576b0",
+        "is_verified": false,
+        "line_number": 15
+      }
+    ],
     "bin/settings.py": [
       {
         "type": "Basic Auth Credentials",
         "filename": "bin/settings.py",
         "hashed_secret": "347cd9c53ff77d41a7b22aa56c7b4efaf54658e3",
         "is_verified": false,
-        "line_number": 44
+        "line_number": 46
       }
     ],
     "peregrine/blueprints/coremetadata.py": [
@@ -118,8 +141,7 @@
         "filename": "peregrine/dev_settings.example.py",
         "hashed_secret": "739155dcfcb1fc7f98aa38d18ea3d2213ae62b54",
         "is_verified": false,
-        "line_number": 62,
-        "is_secret": false
+        "line_number": 62
       },
       {
         "type": "Secret Keyword",
@@ -135,8 +157,7 @@
         "filename": "peregrine/dev_settings.py",
         "hashed_secret": "739155dcfcb1fc7f98aa38d18ea3d2213ae62b54",
         "is_verified": false,
-        "line_number": 69,
-        "is_secret": false
+        "line_number": 69
       },
       {
         "type": "Secret Keyword",
@@ -152,8 +173,7 @@
         "filename": "peregrine/test_settings.py",
         "hashed_secret": "27d0f93fe951bda5dc3973ca2a5b420c7dfc387f",
         "is_verified": false,
-        "line_number": 11,
-        "is_secret": false
+        "line_number": 11
       },
       {
         "type": "Secret Keyword",
@@ -183,8 +203,7 @@
         "filename": "tests/data/files.json",
         "hashed_secret": "d13c66cc793960cb8d97a4d64d1deb6d2288e4fc",
         "is_verified": false,
-        "line_number": 6,
-        "is_secret": false
+        "line_number": 6
       }
     ],
     "tests/graphql/data/biospec1.json": [
@@ -193,24 +212,21 @@
         "filename": "tests/graphql/data/biospec1.json",
         "hashed_secret": "78b4db9b2aec0f0f2d3e38f9278be42b861c9dc3",
         "is_verified": false,
-        "line_number": 63,
-        "is_secret": false
+        "line_number": 63
       },
       {
         "type": "Hex High Entropy String",
         "filename": "tests/graphql/data/biospec1.json",
         "hashed_secret": "e65fd5600e42643c6d77f3c5c3a60114e0d3165d",
         "is_verified": false,
-        "line_number": 72,
-        "is_secret": false
+        "line_number": 72
       },
       {
         "type": "Hex High Entropy String",
         "filename": "tests/graphql/data/biospec1.json",
         "hashed_secret": "922282cd0fad4bf8ca1c93de95863177d57a55c1",
         "is_verified": false,
-        "line_number": 81,
-        "is_secret": false
+        "line_number": 81
       }
     ],
     "tests/graphql/data/biospec2.json": [
@@ -219,16 +235,14 @@
         "filename": "tests/graphql/data/biospec2.json",
         "hashed_secret": "78b4db9b2aec0f0f2d3e38f9278be42b861c9dc3",
         "is_verified": false,
-        "line_number": 18,
-        "is_secret": false
+        "line_number": 18
       },
       {
         "type": "Hex High Entropy String",
         "filename": "tests/graphql/data/biospec2.json",
         "hashed_secret": "e65fd5600e42643c6d77f3c5c3a60114e0d3165d",
         "is_verified": false,
-        "line_number": 27,
-        "is_secret": false
+        "line_number": 27
       }
     ],
     "tests/graphql/data/databundle1.json": [
@@ -237,8 +251,7 @@
         "filename": "tests/graphql/data/databundle1.json",
         "hashed_secret": "b87375c47433817ed4310ab448cda0f74670ee71",
         "is_verified": false,
-        "line_number": 28,
-        "is_secret": false
+        "line_number": 28
       }
     ],
     "tests/graphql/data/file.json": [
@@ -247,8 +260,7 @@
         "filename": "tests/graphql/data/file.json",
         "hashed_secret": "78b4db9b2aec0f0f2d3e38f9278be42b861c9dc3",
         "is_verified": false,
-        "line_number": 9,
-        "is_secret": false
+        "line_number": 9
       }
     ],
     "tests/graphql/data/submitted_unaligned_reads.json": [
@@ -257,10 +269,9 @@
         "filename": "tests/graphql/data/submitted_unaligned_reads.json",
         "hashed_secret": "78b4db9b2aec0f0f2d3e38f9278be42b861c9dc3",
         "is_verified": false,
-        "line_number": 10,
-        "is_secret": false
+        "line_number": 10
       }
     ]
   },
-  "generated_at": "2023-05-12T17:31:54Z"
+  "generated_at": "2023-11-01T14:27:13Z"
 }

README.md

@@ -1,8 +1,7 @@
 # Peregrine
 
 [![Build Status](https://travis-ci.org/uc-cdis/peregrine.svg?branch=master)](https://travis-ci.org/uc-cdis/peregrine)
-[![Codacy Badge](https://api.codacy.com/project/badge/Grade/f6128183864d4e5da5093eb72a3c9c97)](https://www.codacy.com/app/uc-cdis/peregrine?utm_source=github.com&utm_medium=referral&utm_content=uc-cdis/peregrine&utm_campaign=Badge_Grade)
-[![Codacy Badge](https://api.codacy.com/project/badge/Coverage/f6128183864d4e5da5093eb72a3c9c97)](https://www.codacy.com/app/uc-cdis/peregrine?utm_source=github.com&utm_medium=referral&utm_content=uc-cdis/peregrine&utm_campaign=Badge_Coverage)
+[![Coverage Status](https://coveralls.io/repos/github/uc-cdis/peregrine/badge.svg)](https://coveralls.io/github/uc-cdis/peregrine)
 
 
 Query interface to get insights into data in Gen3 Commons

peregrine/api.py

@@ -7,7 +7,6 @@
 
 from flask import Flask, jsonify
 from flask_cors import CORS
-from flask_sqlalchemy_session import flask_scoped_session
 from psqlgraph import PsqlGraphDriver
 
 from authutils import AuthError