Unverified Commit 631e33f5 authored by John Chilton's avatar John Chilton Committed by GitHub
Browse files

Merge pull request #19716 from jmchilton/fix_citation_handling 

[24.2] Fix #19515 - invalid citation handling changed with 24.2.
parents 65d265fd 1c8fbbb9

lib/galaxy/tool_util/fetcher.py

+4 −2
Original line number Diff line number Diff line 
import os

from typing import (

    Dict,

    Type,
@@ -8,6 +9,7 @@ from galaxy.util import plugin_config 


if TYPE_CHECKING:

    from galaxy.tool_util.locations import ToolLocationResolver

    from galaxy.util.path import StrPath





class ToolLocationFetcher:
@@ -19,8 +21,8 @@ class ToolLocationFetcher: 


        return plugin_config.plugins_dict(galaxy.tool_util.locations, "scheme")



    def to_tool_path(self, path_or_uri_like: str, **kwds) -> str:

        if "://" not in path_or_uri_like:

    def to_tool_path(self, path_or_uri_like: "StrPath", **kwds) -> "StrPath":

        if isinstance(path_or_uri_like, os.PathLike) or "://" not in path_or_uri_like:

            path = path_or_uri_like

        else:

            uri_like = path_or_uri_like

lib/galaxy/tool_util/parser/factory.py

+1 −2
Original line number Diff line number Diff line
@@ -86,9 +86,8 @@ def get_tool_source( 
        tool_location_fetcher = ToolLocationFetcher()



    assert config_file

    config_file = str(config_file)



    config_file = tool_location_fetcher.to_tool_path(config_file)

    config_file = str(tool_location_fetcher.to_tool_path(config_file))

    if not enable_beta_formats:

        tree, macro_paths = load_tool_with_refereces(config_file)

        return XmlToolSource(tree, source_path=config_file, macro_paths=macro_paths)

lib/galaxy/tool_util/parser/xml.py

+7 −1
Original line number Diff line number Diff line
@@ -708,7 +708,13 @@ class XmlToolSource(ToolSource): 
            return citations



        for citation_elem in citations_elem:

            try:

                citation = parse_citation_elem(citation_elem)

            except Exception:

                if Version(self.parse_profile()) < Version("24.2"):

                    continue

                else:

                    raise

            if citation:

                citations.append(citation)

test/unit/tool_util/invalid_citation.xml

0 → 100644
+17 −0
Original line number Diff line number Diff line 
<tool id="invalid_citation" name="invalid_citation" version="1.0.0">

    <command>

        cat $input1 > $out_file1

    </command>

    <inputs>

        <param name="input1" type="data" label="Concatenate Dataset"/>

    </inputs>

    <outputs>

        <data name="out_file1" format="input" metadata_source="input1"/>

    </outputs>

    <!-- https://github.com/workflow4metabolomics/anova/blob/4bd408440b71359eac2c373917f5daff2ec9f69f/galaxy/stat_anova/abims_anova.xml -->

    <citations>

        <citation>Ronald A. Fisher in the 1930s</citation>

    </citations>

    <help>

    </help>

</tool>

test/unit/tool_util/invalid_citation_24.2.xml

0 → 100644
+17 −0
Original line number Diff line number Diff line 
<tool id="invalid_citation" name="invalid_citation" version="1.0.0" profile="24.2">

    <command>

        cat $input1 > $out_file1

    </command>

    <inputs>

        <param name="input1" type="data" label="Concatenate Dataset"/>

    </inputs>

    <outputs>

        <data name="out_file1" format="input" metadata_source="input1"/>

    </outputs>

    <!-- https://github.com/workflow4metabolomics/anova/blob/4bd408440b71359eac2c373917f5daff2ec9f69f/galaxy/stat_anova/abims_anova.xml -->

    <citations>

        <citation>Ronald A. Fisher in the 1930s</citation>

    </citations>

    <help>

    </help>

</tool>