Unverified Commit 2891489c authored by Martin Cech's avatar Martin Cech Committed by GitHub
Browse files

Merge pull request #18389 from mvdbeek/ensure_data_extension_if_no_extension_specified 

[24.0] Assign default ``data`` extension on discovered collection output
parents f5610e77 6551f316

lib/galaxy/model/store/discover.py

+13 −7
Original line number Diff line number Diff line
@@ -38,6 +38,10 @@ from galaxy.util import ( 
from galaxy.util.hash_util import HASH_NAME_MAP



if TYPE_CHECKING:

    from galaxy.job_execution.output_collect import (

        DatasetCollector,

        ToolMetadataDatasetCollector,

    )

    from galaxy.model.store import ModelExportStore



log = logging.getLogger(__name__)
@@ -50,7 +54,7 @@ class MaxDiscoveredFilesExceededError(ValueError): 
    pass





CollectorT = Any  # TODO: setup an interface for these file collectors data classes.

CollectorT = Union["DatasetCollector", "ToolMetadataDatasetCollector"]





class ModelPersistenceContext(metaclass=abc.ABCMeta):
@@ -1056,19 +1060,21 @@ class JsonCollectedDatasetMatch: 
        return self.as_dict.get("name")



    @property

    def dbkey(self):

        return self.as_dict.get("dbkey", getattr(self.collector, "default_dbkey", "?"))

    def dbkey(self) -> str:

        return self.as_dict.get("dbkey", self.collector and self.collector.default_dbkey or "?")



    @property

    def ext(self):

        return self.as_dict.get("ext", getattr(self.collector, "default_ext", "data"))

    def ext(self) -> str:

        return self.as_dict.get("ext", self.collector and self.collector.default_ext or "data")



    @property

    def visible(self):

    def visible(self) -> bool:

        try:

            return self.as_dict["visible"].lower() == "visible"

        except KeyError:

            return getattr(self.collector, "default_visible", True)

            if self.collector and self.collector.default_visible is not None:

                return self.collector.default_visible

            return True



    @property

    def link_data(self):

lib/galaxy/tool_util/parser/output_collection_def.py

+7 −1
Original line number Diff line number Diff line
@@ -34,7 +34,13 @@ def dataset_collector_descriptions_from_elem(elem, legacy=True): 
    if num_discover_dataset_blocks == 0 and legacy:

        collectors = [DEFAULT_DATASET_COLLECTOR_DESCRIPTION]

    else:

        collectors = [dataset_collection_description(**e.attrib) for e in primary_dataset_elems]

        default_format = elem.attrib.get("format")

        collectors = []

        for e in primary_dataset_elems:

            description_attributes = e.attrib

            if default_format and "format" not in description_attributes and "ext" not in description_attributes:

                description_attributes["format"] = default_format

            collectors.append(dataset_collection_description(**description_attributes))



    return _validate_collectors(collectors)

lib/galaxy/tool_util/xsd/galaxy.xsd

+6 −4
Original line number Diff line number Diff line
@@ -5360,11 +5360,13 @@ The default is ``galaxy.json``. 
  <xs:attributeGroup name="OutputCommon">

    <xs:attribute name="format" type="xs:string">

      <xs:annotation>

        <xs:documentation xml:lang="en">The short name for the output datatype.

The valid values for format can be found in

        <xs:documentation xml:lang="en"><![CDATA[

The short name for the output datatype. The valid values for format can be found in

[/config/datatypes_conf.xml.sample](https://github.com/galaxyproject/galaxy/blob/dev/config/datatypes_conf.xml.sample)

(e.g. ``format="pdf"`` or ``format="fastqsanger"``). For collections this is the default format for all included

elements. Note that the format specified here is ignored for discovered data sets.</xs:documentation>

(e.g. ``format="pdf"`` or ``format="fastqsanger"``). For collections this is the default

format for all included elements. Note that the format specified here is ignored for

discovered data sets on Galaxy versions prior to 24.0 and should be specified using the ``<discovered_data>`` tag set.

        ]]></xs:documentation>

      </xs:annotation>

    </xs:attribute>

    <xs:attribute name="format_source" type="xs:string">

test/functional/tools/discover_default_ext.xml

0 → 100644
+52 −0
Original line number Diff line number Diff line 
<tool id="discover_default_ext" name="discover_default_ext" version="0.1.0">

    <command><![CDATA[

echo 1 > 1.txt;

]]></command>

    <inputs />

    <outputs>

        <collection name="collection_with_default_ext" type="list" label="with default format" format="fasta">

            <discover_datasets pattern="__name_and_ext__" />

        </collection>

        <collection name="collection_default_ext_and_explicit_format" type="list" label="with default format and static element format" format="fasta">

            <discover_datasets pattern="__name__" format="txt" />

        </collection>

        <collection name="collection_default_ext_used" type="list" label="with default format and no override" format="fasta">

            <discover_datasets pattern="__name__" />

        </collection>

        <collection name="collection_without_default_ext" type="list" label="wihtout default ext, should be data">

            <discover_datasets pattern="__name__" />

        </collection>

    </outputs>

    <tests>

        <test expect_num_outputs="4">

            <output_collection name="collection_with_default_ext" type="list" count="1">

                <element name="1" ftype="txt">

                    <assert_contents>

                        <has_text text="1" />

                    </assert_contents>

                </element>

            </output_collection>

            <output_collection name="collection_default_ext_and_explicit_format" type="list" count="1">

                <element name="1.txt" ftype="txt">

                    <assert_contents>

                        <has_text text="1" />

                    </assert_contents>

                </element>

            </output_collection>

            <output_collection name="collection_default_ext_used" type="list" count="1">

                <element name="1.txt" ftype="fasta">

                    <assert_contents>

                        <has_text text="1" />

                    </assert_contents>

                </element>

            </output_collection>

            <output_collection name="collection_without_default_ext" type="list" count="1">

                <element name="1.txt" ftype="data">

                    <assert_contents>

                        <has_text text="1" />

                    </assert_contents>

                </element>

            </output_collection>

        </test>

    </tests>

</tool>

test/functional/tools/sample_tool_conf.xml

+1 −0
Original line number Diff line number Diff line
@@ -206,6 +206,7 @@ 
  <tool file="collection_cat_group_tag.xml" />

  <tool file="collection_cat_group_tag_multiple.xml" />

  <tool file="discover_sort_by.xml" />

  <tool file="discover_default_ext.xml" />

  <tool file="expression_forty_two.xml" />

  <tool file="expression_pick_larger_file.xml" />

  <tool file="expression_parse_int.xml" />