Mount test data dir read-only in docker#1327
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jmchilton merged 6 commits intogalaxyproject:masterfrom Nov 29, 2022
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That's an easy fix for data managers that access (test) reference data.
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bernt-matthias
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I might be wrong, but are the tests skipped? In test (3.7, unit-quick) I found
tests/test_cmd_test.py::CmdTestTestCase::test_data_manager SKIPPED (...) [ 10%]
tests/test_cmd_test.py::CmdTestTestCase::test_data_manager_docker_mount SKIPPED [ 11%]
Also wondering if the following might be related:
galaxy.util ERROR 2022-11-28 15:45:20,548 [pN:main,p:3073228,tN:MainThread] Error parsing file /tmp/tmpdzfmq09t/galaxy-dev/config
Traceback (most recent call last):
File "/tmp/tmpdzfmq09t/galaxy-dev/lib/galaxy/util/__init__.py", line 271, in parse_xml
tree = etree.parse(fname, parser=parser)
File "src/lxml/etree.pyx", line 3536, in lxml.etree.parse
File "src/lxml/parser.pxi", line 1875, in lxml.etree._parseDocument
File "src/lxml/parser.pxi", line 1901, in lxml.etree._parseDocumentFromURL
File "src/lxml/parser.pxi", line 1805, in lxml.etree._parseDocFromFile
File "src/lxml/parser.pxi", line 1177, in lxml.etree._BaseParser._parseDocFromFile
File "src/lxml/parser.pxi", line 615, in lxml.etree._ParserContext._handleParseResultDoc
File "src/lxml/parser.pxi", line 725, in lxml.etree._handleParseResult
File "src/lxml/parser.pxi", line 654, in lxml.etree._raiseParseError
File "/tmp/tmpdzfmq09t/galaxy-dev/config", line 1
lxml.etree.XMLSyntaxError: Document is empty, line 1, column 1
galaxy.tools.data_manager.manager ERROR 2022-11-28 15:45:20,550 [pN:main,p:3073228,tN:MainThread] There was an error parsing your Data Manager config file "/tmp/tmpdzfmq09t/galaxy-dev/config": Document is empty, line 1, column 1 (config, line 1)
I see this during all my recent tool tests (no data managers).
TIL you can extend a list with tuples Co-authored-by: M Bernt <m.bernt@ufz.de>
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Yes, the quick tests are those that don't start galaxy. Full tests are in the nonredundant chunk (https://github.com/galaxyproject/planemo/actions/runs/3566510641/jobs/5993046612#step:8:62) |
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that's just a noisy way to fail on an empty file. |
jmchilton
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Nov 29, 2022
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Fixes a bunch of data manager tests that are failing the weekly iuc tests. I think this started failing after we stopped copying the whole tool directory to tmp.
The additional
--docker_extra_volumechange let's us mount the whole tool repo for tool tests, which would fix test using symlinks to scripts outside of the tool directory, and for the iwc we can just mount in the whole of cvmfs, which means we don't need to use--tool_data_path(which brings additional things in, like watching for changes, which I think is unnecessary in a CI context).