Merge pull request #525 from populationgenomics/dev

Release

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 6.1.0
+current_version = 6.2.0
 commit = True
 tag = False
 parse = (?P<major>\d+)\.(?P<minor>\d+)\.(?P<patch>[A-z0-9-]+)

.github/workflows/deploy.yaml

@@ -19,7 +19,7 @@ jobs:
       SM_API_DOCKER: australia-southeast1-docker.pkg.dev/cpg-common/images/sm-api
     defaults:
       run:
-        shell: bash -l {0}
+        shell: bash -eo pipefail -l {0}
     steps:
       - uses: actions/checkout@main
 

.github/workflows/lint.yaml

@@ -6,7 +6,7 @@ jobs:
     runs-on: ubuntu-latest
     defaults:
       run:
-        shell: bash -l {0}
+        shell: bash -eo pipefail -l {0}
 
     steps:
       - uses: actions/checkout@v2
@@ -19,7 +19,6 @@ jobs:
       - name: Install packages
         run: |
           pip install -r requirements-dev.txt
-          pip install -r requirements-server.txt
           pip install .
 
       - name: pre-commit

.github/workflows/test.yaml

@@ -14,7 +14,7 @@ jobs:
       SM_DOCKER: samplemetadata:dev
     defaults:
       run:
-        shell: bash -l {0}
+        shell: bash -eo pipefail -l {0}
     steps:
       - uses: actions/checkout@main
 

api/routes/enum.py

@@ -20,6 +20,12 @@ def _create_route(e: Type[EnumTable]):
     async def get(connection=get_projectless_db_connection) -> list[str]:
         return await e(connection).get()
 
+    @router.post('/' + hyphenated_name, operation_id='post' + camel_case_name + 's')
+    async def post(
+        new_type: str, connection=get_projectless_db_connection
+    ) -> list[str]:
+        return await e(connection).insert(new_type)
+
 
 for enum in enum_tables.__dict__.values():
     if not isclass(enum):

api/server.py

@@ -20,7 +20,7 @@
 from api.settings import PROFILE_REQUESTS, SKIP_DATABASE_CONNECTION
 
 # This tag is automatically updated by bump2version
-_VERSION = '6.1.0'
+_VERSION = '6.2.0'
 
 logger = get_logger()
 

db/python/enum_tables/enums.py

@@ -64,3 +64,4 @@ async def insert(self, value: str):
         await self.connection.execute(_query, {'name': value.lower()})
         # clear the cache so results are up-to-date
         self.get.cache_clear()  # pylint: disable=no-member
+        return value

deploy/python/version.txt

@@ -1 +1 @@
-6.1.0
+6.2.0

regenerate_api.py

@@ -1,15 +1,14 @@
 #!/usr/bin/env python3
 # pylint: disable=logging-not-lazy,subprocess-popen-preexec-fn,consider-using-with
 import logging
-import re
-from typing import Optional, List
-
 import os
+import re
+import shutil
 import signal
+import subprocess
 import tempfile
-import shutil
 import time
-import subprocess
+from typing import List, Optional
 
 import requests
 
@@ -35,6 +34,15 @@ def check_if_server_is_accessible() -> bool:
         return False
 
 
+def assert_server_is_accessible():
+    """Assert that the server is accessible"""
+    if not check_if_server_is_accessible():
+        raise requests.ConnectionError(
+            f'Could not connect to server at {SCHEMA_URL}. '
+            'Please make sure the server is running and accessible.'
+        )
+
+
 def start_server() -> Optional[subprocess.Popen]:
     """Start the API server, and return a process when it's started"""
 
@@ -124,7 +132,9 @@ def check_openapi_version():
     logger.info(f'Got openapi version: {version}')
 
 
-def generate_api_and_copy(output_type, output_copyer, extra_commands: List[str] = None):
+def generate_api_and_copy(
+    output_type, output_copyer, extra_commands: List[str] | None = None
+):
     """
     Use OpenApiGenerator to generate the installable API
     """
@@ -161,15 +171,17 @@ def generate_api_and_copy(output_type, output_copyer, extra_commands: List[str]
             time.sleep(2)
 
     if not succeeded:
-        return
+        raise RuntimeError(
+            f'openapi generation failed after trying {n_attempts} time(s)'
+        )
 
     output_copyer(tmpdir)
     shutil.rmtree(tmpdir)
 
 
 def generate_schema_file():
     """
-    Generate schema file and place int he metamist/graphql/ directory
+    Generate schema file and place in the metamist/graphql/ directory
     """
     command = ['strawberry', 'export-schema', 'api.graphql.schema:schema']
     schema = subprocess.check_output(command, stderr=subprocess.STDOUT).decode()
@@ -299,21 +311,47 @@ def main():
     else:
         process = start_server()
 
+        # Loop until Docker has initialised server and is ready to accept connections
+        startup_tries = 5
+        wait_time_in_seconds = 2
+        while (not check_if_server_is_accessible()) and startup_tries > 0:
+            startup_tries -= 1
+            logger.info(
+                f'Dockerised API server is not ready yet. '
+                + f'Retrying in {wait_time_in_seconds} seconds. '
+                + f'Remaining tries: {startup_tries}'
+            )
+            time.sleep(wait_time_in_seconds)
+
     try:
+        assert_server_is_accessible()
         check_openapi_version()
+
+        # Generate the installable Python API
         generate_api_and_copy(
             'python',
             copy_python_files_from,
             ['--template-dir', 'openapi-templates'],
         )
-        generate_api_and_copy('typescript-axios', copy_typescript_files_from)
 
+        # Generate the Typescript API for React application
+        generate_api_and_copy(
+            'typescript-axios',
+            copy_typescript_files_from,
+        )
+
+        # Generate the GraphQL schema
         generate_schema_file()
+
+        # Copy resources and README
         shutil.copy(
             './resources/muck-the-duck.svg',
             os.path.join('web/src', 'muck-the-duck.svg'),
         )
-        shutil.copy('README.md', os.path.join(OUTPUT_DOCS_DIR, 'index.md'))
+        shutil.copy(
+            'README.md',
+            os.path.join(OUTPUT_DOCS_DIR, 'index.md'),
+        )
 
     # pylint: disable=broad-except
     except BaseException as e:

setup.py

@@ -19,7 +19,7 @@
 setup(
     name=PKG,
     # This tag is automatically updated by bump2version
-    version='6.1.0',
+    version='6.2.0',
     description='Python API for interacting with the Sample API system',
     long_description=readme,
     long_description_content_type='text/markdown',

web/src/pages/project/AnalysisRunnerView/AnalysisRunnerSummary.tsx

@@ -20,7 +20,7 @@ const PAGE_SIZES = [20, 40, 100, 1000]
 const GET_ANALYSIS_RUNNER_LOGS = gql(`
 query AnalysisRunnerLogs($project_name: String!) {
     project(name: $project_name) {
-        analyses(type: { eq: "analysis-runner" }) {
+        analyses(type: { eq: "analysis-runner" }, status: {eq: UNKNOWN}) {
           author
           id
           meta