[22.01] Backport and fix webapps tests

lib/galaxy/config/__init__.py

@@ -60,10 +60,12 @@
 DEFAULT_LOCALE_FORMAT = '%a %b %e %H:%M:%S %Y'
 ISO_DATETIME_FORMAT = "%Y-%m-%d %H:%M:%S"
 
-GALAXY_APP_NAME = 'galaxy'
-GALAXY_SCHEMAS_PATH = files('galaxy.config') / 'schemas'
-GALAXY_CONFIG_SCHEMA_PATH = GALAXY_SCHEMAS_PATH / 'config_schema.yml'
-UWSGI_SCHEMA_PATH = GALAXY_SCHEMAS_PATH / 'uwsgi_schema.yml'
+GALAXY_APP_NAME = "galaxy"
+GALAXY_SCHEMAS_PATH = files("galaxy.config") / "schemas"
+GALAXY_CONFIG_SCHEMA_PATH = GALAXY_SCHEMAS_PATH / "config_schema.yml"
+REPORTS_CONFIG_SCHEMA_PATH = GALAXY_SCHEMAS_PATH / "reports_config_schema.yml"
+TOOL_SHED_CONFIG_SCHEMA_PATH = GALAXY_SCHEMAS_PATH / "tool_shed_config_schema.yml"
+UWSGI_SCHEMA_PATH = GALAXY_SCHEMAS_PATH / "uwsgi_schema.yml"
 LOGGING_CONFIG_DEFAULT: Dict[str, Any] = {
     'disable_existing_loggers': False,
     'version': 1,

lib/galaxy/config/config_manage.py

@@ -24,6 +24,8 @@
 
 from galaxy.config import (
     GALAXY_CONFIG_SCHEMA_PATH,
+    REPORTS_CONFIG_SCHEMA_PATH,
+    TOOL_SHED_CONFIG_SCHEMA_PATH,
     UWSGI_SCHEMA_PATH,
 )
 from galaxy.config.schema import (
@@ -358,16 +360,16 @@ class OptionValue(NamedTuple):
     "9009",
     ["tool_shed.webapp.buildapp:app_factory"],
     "config/tool_shed.yml",
-    "lib/tool_shed/webapp/config_schema.yml",
-    'tool_shed.webapp.buildapp:uwsgi_app()',
+    str(TOOL_SHED_CONFIG_SCHEMA_PATH),
+    "tool_shed.webapp.buildapp:uwsgi_app()",
 )
 REPORTS_APP = App(
     ["reports_wsgi.ini", "config/reports.ini"],
     "9001",
     ["galaxy.webapps.reports.buildapp:app_factory"],
     "config/reports.yml",
-    "lib/galaxy/webapps/reports/config_schema.yml",
-    'galaxy.webapps.reports.buildapp:uwsgi_app()',
+    str(REPORTS_CONFIG_SCHEMA_PATH),
+    "galaxy.webapps.reports.buildapp:uwsgi_app()",
 )
 APPS = {"galaxy": GALAXY_APP, "tool_shed": SHED_APP, "reports": REPORTS_APP}
 

lib/tool_shed/webapp/config.py

@@ -11,23 +11,17 @@
     BaseAppConfiguration,
     CommonConfigurationMixin,
     get_database_engine_options,
+    TOOL_SHED_CONFIG_SCHEMA_PATH,
 )
 from galaxy.config import expand_pretty_datetime_format
 from galaxy.config.schema import AppSchema
 from galaxy.exceptions import ConfigurationError
 from galaxy.util import string_as_bool
 from galaxy.version import VERSION, VERSION_MAJOR, VERSION_MINOR
 
-try:
-    from importlib.resources import files  # type: ignore[attr-defined]
-except ImportError:
-    # Python < 3.9
-    from importlib_resources import files  # type: ignore[no-redef]
-
 log = logging.getLogger(__name__)
 
-TOOLSHED_APP_NAME = 'tool_shed'
-TOOLSHED_CONFIG_SCHEMA_PATH = files('tool_shed.webapp') / 'config_schema.yml'
+TOOLSHED_APP_NAME = "tool_shed"
 
 
 class ToolShedAppConfiguration(BaseAppConfiguration, CommonConfigurationMixin):
@@ -36,7 +30,7 @@ class ToolShedAppConfiguration(BaseAppConfiguration, CommonConfigurationMixin):
     add_sample_file_to_defaults = {'datatypes_config_file'}
 
     def _load_schema(self):
-        return AppSchema(TOOLSHED_CONFIG_SCHEMA_PATH, TOOLSHED_APP_NAME)
+        return AppSchema(TOOL_SHED_CONFIG_SCHEMA_PATH, TOOLSHED_APP_NAME)
 
     def __init__(self, **kwargs):
         super().__init__(**kwargs)

packages/app/requirements.txt

@@ -20,9 +20,10 @@ Markdown
 paramiko!=2.9.0,!=2.9.1
 pulsar-galaxy-lib>=0.14.13
 pydantic
+PyJWT
+pykwalify
 refgenconf>=0.12.0
 sqlitedict
 svgwrite
-tuswsgi
 typing-extensions
 Whoosh

packages/app/setup.py

@@ -30,66 +30,65 @@ def get_var(var_name):
 
 TEST_DIR = 'tests'
 PACKAGES = [
-    'galaxy',
-    'galaxy.actions',
-    'galaxy.app_unittest_utils',
-    'galaxy.authnz',
-    'galaxy.dependencies',
-    'galaxy.forms',
-    'galaxy.jobs',
-    'galaxy.jobs.rules',
-    'galaxy.jobs.runners',
-    'galaxy.jobs.runners.state_handlers',
-    'galaxy.jobs.runners.util',
-    'galaxy.jobs.runners.util.cli',
-    'galaxy.jobs.runners.util.cli.job',
-    'galaxy.jobs.runners.util.cli.shell',
-    'galaxy.jobs.runners.util.condor',
-    'galaxy.jobs.runners.util.job_script',
-    'galaxy.jobs.splitters',
-    'galaxy.managers',
-    'galaxy.schema',
-    'galaxy.tools',
-    'galaxy.tools.actions',
-    'galaxy.tools.data',
-    'galaxy.tools.data_manager',
-    'galaxy.tools.error_reports',
-    'galaxy.tools.expressions',
-    'galaxy.tools.filters',
-    'galaxy.tools.imp_exp',
-    'galaxy.tools.parameters',
-    'galaxy.tools.search',
-    'galaxy.tools.util',
-    'galaxy.tools.util.galaxyops',
-    'galaxy.tool_shed',
-    'galaxy.tool_shed.galaxy_install',
-    'galaxy.tool_shed.galaxy_install.datatypes',
-    'galaxy.tool_shed.galaxy_install.metadata',
-    'galaxy.tool_shed.galaxy_install.repository_dependencies',
-    'galaxy.tool_shed.galaxy_install.tool_dependencies',
-    'galaxy.tool_shed.galaxy_install.tool_dependencies.recipe',
-    'galaxy.tool_shed.galaxy_install.tools',
-    'galaxy.tool_shed.util',
-    'galaxy.tool_shed.metadata',
-    'galaxy.tool_shed.tools',
-    'galaxy.tours',
-    'galaxy.visualization',
-    'galaxy.visualization.data_providers',
-    'galaxy.visualization.data_providers.phyloviz',
-    'galaxy.visualization.genome',
-    'galaxy.visualization.plugins',
-    'galaxy.visualization.tracks',
-    'galaxy.webhooks',
-    'galaxy.work',
-    'galaxy.workflow',
-    'galaxy.workflow.refactor',
-    'galaxy.workflow.reports',
-    'galaxy.workflow.resources',
-    'galaxy.workflow.schedulers',
-    'galaxy_ext',
-    'galaxy_ext.container_monitor',
-    'galaxy_ext.expressions',
-    'galaxy_ext.metadata',
+    "galaxy",
+    "galaxy.actions",
+    "galaxy.app_unittest_utils",
+    "galaxy.authnz",
+    "galaxy.dependencies",
+    "galaxy.forms",
+    "galaxy.jobs",
+    "galaxy.jobs.rules",
+    "galaxy.jobs.runners",
+    "galaxy.jobs.runners.state_handlers",
+    "galaxy.jobs.runners.util",
+    "galaxy.jobs.runners.util.cli",
+    "galaxy.jobs.runners.util.cli.job",
+    "galaxy.jobs.runners.util.cli.shell",
+    "galaxy.jobs.runners.util.condor",
+    "galaxy.jobs.runners.util.job_script",
+    "galaxy.jobs.splitters",
+    "galaxy.managers",
+    "galaxy.tools",
+    "galaxy.tools.actions",
+    "galaxy.tools.data",
+    "galaxy.tools.data_manager",
+    "galaxy.tools.error_reports",
+    "galaxy.tools.expressions",
+    "galaxy.tools.filters",
+    "galaxy.tools.imp_exp",
+    "galaxy.tools.parameters",
+    "galaxy.tools.search",
+    "galaxy.tools.util",
+    "galaxy.tools.util.galaxyops",
+    "galaxy.tool_shed",
+    "galaxy.tool_shed.galaxy_install",
+    "galaxy.tool_shed.galaxy_install.datatypes",
+    "galaxy.tool_shed.galaxy_install.metadata",
+    "galaxy.tool_shed.galaxy_install.repository_dependencies",
+    "galaxy.tool_shed.galaxy_install.tool_dependencies",
+    "galaxy.tool_shed.galaxy_install.tool_dependencies.recipe",
+    "galaxy.tool_shed.galaxy_install.tools",
+    "galaxy.tool_shed.util",
+    "galaxy.tool_shed.metadata",
+    "galaxy.tool_shed.tools",
+    "galaxy.tours",
+    "galaxy.visualization",
+    "galaxy.visualization.data_providers",
+    "galaxy.visualization.data_providers.phyloviz",
+    "galaxy.visualization.genome",
+    "galaxy.visualization.plugins",
+    "galaxy.visualization.tracks",
+    "galaxy.webhooks",
+    "galaxy.work",
+    "galaxy.workflow",
+    "galaxy.workflow.refactor",
+    "galaxy.workflow.reports",
+    "galaxy.workflow.resources",
+    "galaxy.workflow.schedulers",
+    "galaxy_ext",
+    "galaxy_ext.container_monitor",
+    "galaxy_ext.expressions",
+    "galaxy_ext.metadata",
 ]
 ENTRY_POINTS = '''
         [console_scripts]

packages/app/test-requirements.txt

@@ -1,4 +1,3 @@
 mock-ssh-server
-pykwalify
 pytest
 testfixtures

packages/test.sh

@@ -34,8 +34,6 @@ PACKAGE_DIRS=(
     app
     webapps
 )
-RUN_TESTS=(1 1 1 1 1 1 1 1 1 1 1 1 0)
-RUN_MYPY=(1 1 1 1 1 1 1 1 1 1 1 1 1)
 for ((i=0; i<${#PACKAGE_DIRS[@]}; i++)); do
     printf "\n========= TESTING PACKAGE ${PACKAGE_DIRS[$i]} =========\n\n"
     package_dir=${PACKAGE_DIRS[$i]}
@@ -53,11 +51,7 @@ for ((i=0; i<${#PACKAGE_DIRS[@]}; i++)); do
 
     pip install -r test-requirements.txt
 
-    if [[ "${RUN_TESTS[$i]}" == "1" ]]; then
-        pytest --doctest-modules galaxy tests
-    fi
-    if [[ "${RUN_MYPY[$i]}" == "1" ]]; then
-        make mypy
-    fi
+    pytest --doctest-modules galaxy tests
+    make mypy
     cd ..
 done

packages/util/requirements.txt

@@ -2,11 +2,11 @@ bleach
 boltons
 docutils
 importlib_resources
-markupsafe
+MarkupSafe
 packaging
 pycryptodome
-pyyaml
+PyYAML
 requests
-routes
+Routes
 typing-extensions
 zipstream-new

packages/webapps/requirements.txt

@@ -1,14 +1,33 @@
 a2wsgi
 galaxy-app
+galaxy-data
+galaxy-job-execution
+galaxy-tool-util
+galaxy-util
+galaxy-web-framework
+Babel
 Cheetah3
 fastapi>=0.68.2,!=0.69.0,!=0.70.0,!=0.70.1
 fastapi-utils
+gunicorn
+gxformat2
 importlib_resources
 Mako
+MarkupSafe
+Paste
 pydantic
+PyJWT
+python-dateutil
 python-multipart  # required to support form parsing in FastAPI/Starlette
+PyYAML
+requests
+Routes
+SQLAlchemy>=1.4.25,<2
 starlette
 starlette-context
+tuswsgi
 typing-extensions
 uvicorn
+uvloop
+WebOb
 Whoosh

packages/webapps/test-requirements.txt

@@ -1 +1,2 @@
+httpx
 pytest

packages/webapps/tests/webapps

@@ -0,0 +1 @@
+../../../test/unit/webapps/

pyproject.toml

@@ -62,10 +62,12 @@ psutil = "*"
 pulsar-galaxy-lib = ">=0.14.13"
 pycryptodome = "*"
 pydantic = "*"
+PyJWT = "*"
 pykwalify = "*"
 pyparsing = "*"
 pysam = "*"
 python = ">=3.7,<4"
+python-dateutil = "*"
 python-multipart = "*"  # required to support form parsing in FastAPI/Starlette
 pyuwsgi = "*"
 PyYAML = "*"

scripts/release-diff.py

@@ -145,8 +145,6 @@ def main(old_revision, new_revision=None):
     globs = (
         "config/*.yml.sample",
         "lib/galaxy/config/schemas/*schema.yml",
-        "lib/galaxy/webapps/reports/config_schema.yml",
-        "lib/tool_shed/webapp/config_schema.yml",
     )
     files_to_diff = [f for g in globs for f in glob.glob(g)]
     added = {}