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Various show page PDF bug fixes.

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- In FastAPI mode GET /api/pages/{id}.pdf was being masked by /api/pages/{id} and the tested 400 was an invalid ID error.
- trans.response was being used in the service layer and was unavailable under FastAPI - moved setting response type back up into the controller.
- API tests should skip if the Galaxy configuration is invalid - it wasn't doing this.

While I was in there I also tweaked the exception handling a bit to indicate that this is not a USER FORBIDDEN (403) operation so much as an optional SERVER configuration NOT IMPLEMENTED (501).
This commit is contained in:
John Chilton
2021-10-16 15:00:59 -04:00
parent 0c1c0be38b
commit 5cd46c3d5e
8 changed files with 61 additions and 28 deletions
Download Patch File Download Diff File Expand all files Collapse all files
lib/galaxy/exceptions/__init__.py
+7
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@@ -241,6 +241,13 @@ class ReferenceDataError(MessageException):
err_code = error_codes_by_name['REFERENCE_DATA_ERROR']
class ServerNotConfiguredForRequest(MessageException):
# A bit like ConfigDoesNotAllowException but it has nothing to do with the user of the
# request being "forbidden". It just isn't configured.
status_code = 501
err_code = error_codes_by_name['SERVER_NOT_CONFIGURED_FOR_REQUEST']
# non-web exceptions
class ContainerCLIError(Exception):
lib/galaxy/exceptions/error_codes.json
+5
View File
@@ -173,5 +173,10 @@
"name": "NOT_IMPLEMENTED",
"code": 501001,
"message": "Method is not implemented."
},
{
"name": "SERVER_NOT_CONFIGURED_FOR_REQUEST",
"code": 501002,
"message": "Server not configured for the request. The Galaxy admin may be able to resolve the problem by installing additional dependencies or setting up new infrastructure."
}
]
lib/galaxy/managers/configuration.py
+2 -1
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@@ -18,10 +18,10 @@ from typing import (
from galaxy.app import MinimalManagerApp
from galaxy.managers import base
from galaxy.managers.context import ProvidesUserContext
from galaxy.managers.markdown_util import weasyprint_available
from galaxy.schema.fields import EncodedDatabaseIdField
from galaxy.schema.types import SerializationParams
from galaxy.web.framework.base import server_starttime
log = logging.getLogger(__name__)
VERSION_JSON_FILE = 'version.json'
@@ -167,6 +167,7 @@ class ConfigSerializer(base.ModelSerializer):
'ga_code': _use_config,
'plausible_server': _use_config,
'plausible_domain': _use_config,
'markdown_to_pdf_available': lambda config, key, **context: weasyprint_available(),
'matomo_server': _use_config,
'matomo_site_id': _use_config,
'enable_unique_workflow_defaults': _use_config,
lib/galaxy/managers/markdown_util.py
+7 -3
View File
@@ -28,7 +28,7 @@ except Exception:
from galaxy.exceptions import (
MalformedContents,
MessageException,
ServerNotConfiguredForRequest,
)
from galaxy.managers.hdcas import HDCASerializer
from galaxy.managers.jobs import (
@@ -595,10 +595,14 @@ def to_pdf(trans, basic_markdown, css_paths=None) -> bytes:
shutil.rmtree(directory)
def weasyprint_available() -> bool:
return weasyprint is not None
def _check_can_convert_to_pdf_or_raise():
"""Checks if the HTML to PDF converter is available."""
if not weasyprint:
raise MessageException("PDF conversion service not available.")
if not weasyprint_available():
raise ServerNotConfiguredForRequest("PDF conversion service not available.")
def internal_galaxy_markdown_to_pdf(trans, internal_galaxy_markdown, document_type) -> bytes:
lib/galaxy/managers/pages.py
-1
View File
@@ -283,7 +283,6 @@ class PagesService:
if page.latest_revision.content_format != PageContentFormat.markdown.value:
raise exceptions.RequestParameterInvalidException("PDF export only allowed for Markdown based pages")
internal_galaxy_markdown = page.latest_revision.content
trans.response.set_content_type("application/pdf")
return internal_galaxy_markdown_to_pdf(trans, internal_galaxy_markdown, 'page')
lib/galaxy/webapps/galaxy/api/pages.py
+15 -14
View File
@@ -101,19 +101,6 @@ class FastAPIPages:
self.service.delete(trans, id)
return Response(status_code=status.HTTP_204_NO_CONTENT)
@router.get(
'/api/pages/{id}',
summary="Return a page summary and the content of the last revision.",
response_description="The page summary information.",
)
async def show(
self,
trans: ProvidesUserContext = DependsOnTrans,
id: EncodedDatabaseIdField = PageIdPathParam,
) -> PageDetails:
"""Return summary information about a specific Page and the content of the last revision."""
return self.service.show(trans, id)
@router.get(
'/api/pages/{id}.pdf',
summary="Return a PDF document of the last revision of the Page.",
@@ -123,7 +110,7 @@ class FastAPIPages:
"description": "PDF document with the last revision of the page.",
"content": {"application/pdf": {}},
},
400: {
501: {
"description": "PDF conversion service not available."
}
},
@@ -140,6 +127,19 @@ class FastAPIPages:
pdf_bytes = self.service.show_pdf(trans, id)
return StreamingResponse(io.BytesIO(pdf_bytes), media_type="application/pdf")
@router.get(
'/api/pages/{id}',
summary="Return a page summary and the content of the last revision.",
response_description="The page summary information.",
)
async def show(
self,
trans: ProvidesUserContext = DependsOnTrans,
id: EncodedDatabaseIdField = PageIdPathParam,
) -> PageDetails:
"""Return summary information about a specific Page and the content of the last revision."""
return self.service.show(trans, id)
@router.get(
'/api/pages/{id}/sharing',
summary="Get the current sharing status of the given Page.",
@@ -309,6 +309,7 @@ class PagesController(BaseGalaxyAPIController):
:rtype: dict
:returns: Dictionary return of the Page.to_dict call with the 'content' field populated by the most recent revision
"""
trans.response.set_content_type("application/pdf")
return self.service.show_pdf(trans, id)
@expose_api
lib/galaxy_test/api/test_pages.py
+19 -9
View File
@@ -1,7 +1,10 @@
from unittest import SkipTest
from requests import delete
from galaxy.exceptions import error_codes
from galaxy_test.api.sharable import SharingApiTests
from galaxy_test.base import api_asserts
from galaxy_test.base.populators import DatasetPopulator, skip_without_tool, WorkflowPopulator
from ._framework import ApiTestCase
@@ -41,6 +44,11 @@ class PageApiTestCase(BasePageApiTestCase, SharingApiTests):
api_name = "pages"
def setUp(self):
super().setUp()
self.dataset_populator = DatasetPopulator(self.galaxy_interactor)
self.workflow_populator = WorkflowPopulator(self.galaxy_interactor)
def create(self, name: str) -> str:
response_json = self._create_valid_page_with_slug(name)
return response_json["id"]
@@ -51,15 +59,13 @@ class PageApiTestCase(BasePageApiTestCase, SharingApiTests):
@skip_without_tool("cat")
def test_create_from_report(self):
dataset_populator = DatasetPopulator(self.galaxy_interactor)
workflow_populator = WorkflowPopulator(self.galaxy_interactor)
test_data = """
input_1:
value: 1.bed
type: File
"""
with dataset_populator.test_history() as history_id:
summary = workflow_populator.run_workflow("""
with self.dataset_populator.test_history() as history_id:
summary = self.workflow_populator.run_workflow("""
class: GalaxyWorkflow
inputs:
input_1: data
@@ -75,7 +81,7 @@ steps:
workflow_id = summary.workflow_id
invocation_id = summary.invocation_id
report_json = workflow_populator.workflow_report_json(workflow_id, invocation_id)
report_json = self.workflow_populator.workflow_report_json(workflow_id, invocation_id)
assert "markdown" in report_json
self._assert_has_keys(report_json, "markdown", "render_format")
assert report_json["render_format"] == "markdown"
@@ -172,8 +178,7 @@ steps:
self._assert_error_code_is(page_response, error_codes.MALFORMED_ID)
def test_400_on_invalid_embedded_content(self):
dataset_populator = DatasetPopulator(self.galaxy_interactor)
valid_id = dataset_populator.new_history()
valid_id = self.dataset_populator.new_history()
page_request = self._test_page_payload(slug="invalid-embed-content")
page_request["content"] = f'''<p>Page!<div class="embedded-item" id="CoolObject-{valid_id}"></div></p>'''
page_response = self._post("pages", page_request, json=True)
@@ -205,13 +210,18 @@ steps:
self._assert_status_code_is(show_response, 403)
self._assert_error_code_is(show_response, error_codes.USER_CANNOT_ACCESS_ITEM)
def test_400_on_download_pdf_when_service_unavailable(self):
def test_501_on_download_pdf_when_service_unavailable(self):
configuration = self.dataset_populator.get_configuration()
can_produce_markdown = configuration["markdown_to_pdf_available"]
if can_produce_markdown:
raise SkipTest("Skipping test because server does implement markdown conversion to PDF")
page_request = self._test_page_payload(slug="md-page-to-pdf", content_format="markdown")
page_response = self._post("pages", page_request, json=True)
self._assert_status_code_is(page_response, 200)
page_id = page_response.json()['id']
pdf_response = self._get(f"pages/{page_id}.pdf")
self._assert_status_code_is(pdf_response, 400)
api_asserts.assert_status_code_is(pdf_response, 501)
api_asserts.assert_error_code_is(pdf_response, error_codes.error_codes_by_name["SERVER_NOT_CONFIGURED_FOR_REQUEST"])
def test_400_on_download_pdf_when_unsupported_content_format(self):
page_request = self._test_page_payload(slug="html-page-to-pdf", content_format="html")
lib/galaxy_test/base/populators.py
+6
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@@ -586,6 +586,12 @@ class BaseDatasetPopulator(BasePopulator):
assert roles_response.status_code == 200
return roles_response.json()
def get_configuration(self, admin=False) -> Dict[str, Any]:
response = self._get("configuration", admin=admin)
api_asserts.assert_status_code_is_ok(response)
configuration = response.json()
return configuration
def user_email(self) -> str:
users_response = self._get("users")
users = users_response.json()