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Merge pull request #20158 from mvdbeek/yaml_parser_fixes

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Yaml parser fixes and improvements (part 1)
This commit is contained in:
Marius van den Beek
2025-05-06 09:25:58 +02:00
committed by GitHub
parent 7a3c08ca7d 386742d12e
commit 2266a09e68
15 changed files with 37 additions and 33 deletions
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client/src/components/Tool/ToolFooter.vue
+3 -3
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@@ -40,7 +40,7 @@
<span v-localize class="footer-section-name">References</span>
<div v-for="(xref, index) in xrefs" :key="index">
-
<template v-if="xref.reftype == 'bio.tools'">
<template v-if="xref.type == 'bio.tools'">
bio.tools: {{ xref.value }} (<a :href="`https://bio.tools/${xref.value}`" target="_blank"
>bio.tools
<FontAwesomeIcon
@@ -55,13 +55,13 @@
icon="external-link-alt" /> </a
>)
</template>
<template v-else-if="xref.reftype == 'bioconductor'">
<template v-else-if="xref.type == 'bioconductor'">
Bioconductor Package:
<a :href="`https://bioconductor.org/packages/${xref.value}/`" target="_blank"
>{{ xref.value }} (doi:10.18129/B9.bioc.{{ xref.value }})</a
>
</template>
<template v-else> {{ xref.reftype }}: {{ xref.value }} </template>
<template v-else> {{ xref.type }}: {{ xref.value }} </template>
</div>
</div>
<div v-if="hasCreators" class="mb-1">
lib/galaxy/tool_util/linters/general.py
+1 -1
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@@ -237,7 +237,7 @@ class BioToolsValid(Linter):
_, tool_node = _tool_xml_and_root(tool_source)
xrefs = tool_source.parse_xrefs()
for xref in xrefs:
if xref["reftype"] != "bio.tools":
if xref["type"] != "bio.tools":
continue
metadata_source = ApiBiotoolsMetadataSource()
if not metadata_source.get_biotools_metadata(xref["value"]):
lib/galaxy/tool_util/ontologies/ontology_data.py
+3 -3
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@@ -53,7 +53,7 @@ class OntologyData(NamedTuple):
def biotools_reference(xrefs):
for xref in xrefs:
if xref["reftype"] == "bio.tools":
if xref["type"] == "bio.tools":
return xref["value"]
return None
@@ -69,11 +69,11 @@ def expand_ontology_data(
tool_source: ToolSource, all_ids: List[str], biotools_metadata_source: Optional[BiotoolsMetadataSource]
) -> OntologyData:
xrefs = tool_source.parse_xrefs()
has_biotools_reference = any(x["reftype"] == "bio.tools" for x in xrefs)
has_biotools_reference = any(x["type"] == "bio.tools" for x in xrefs)
if not has_biotools_reference:
for legacy_biotools_ref in legacy_biotools_external_reference(all_ids):
if legacy_biotools_ref is not None:
xrefs.append({"value": legacy_biotools_ref, "reftype": "bio.tools"})
xrefs.append({"value": legacy_biotools_ref, "type": "bio.tools"})
edam_operations = tool_source.parse_edam_operations()
edam_topics = tool_source.parse_edam_topics()
lib/galaxy/tool_util/parser/cwl.py
+1 -1
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@@ -159,7 +159,7 @@ class CwlToolSource(ToolSource):
output.format = "expression.json"
output.change_format = []
output.format_source = None
output.metadata_source = ""
output.metadata_source = None
output.parent = None
output.label = None
output.count = None
lib/galaxy/tool_util/parser/output_collection_def.py
+1 -1
View File
@@ -58,7 +58,7 @@ def dataset_collector_descriptions_from_elem(elem, legacy=True):
def dataset_collector_descriptions_from_output_dict(as_dict):
discover_datasets_dicts = as_dict.get("discover_datasets", [])
discover_datasets_dicts = as_dict.get("discover_datasets") or []
if is_dict(discover_datasets_dicts):
discover_datasets_dicts = [discover_datasets_dicts]
dataset_collector_descriptions = dataset_collector_descriptions_from_list(discover_datasets_dicts)
lib/galaxy/tool_util/parser/output_objects.py
+10 -9
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@@ -175,24 +175,25 @@ class ToolOutput(ToolOutputBase):
hidden=self.hidden,
format=self.format,
format_source=self.format_source,
metadata_source=self.metadata_source or None, # model is decorated as Optional
metadata_source=self.metadata_source,
discover_datasets=[d.to_model() for d in self.dataset_collector_descriptions],
from_work_dir=self.from_work_dir,
)
@staticmethod
def from_dict(name: str, output_dict: Dict[str, Any], app: Optional[ToolOutputActionApp] = None) -> "ToolOutput":
output = ToolOutput(name)
output.format = output_dict.get("format", "data")
output.format = output_dict.get("format") or "data"
output.change_format = []
output.format_source = output_dict.get("format_source", None)
output.default_identifier_source = output_dict.get("default_identifier_source", None)
output.metadata_source = output_dict.get("metadata_source", "")
output.parent = output_dict.get("parent", None)
output.label = output_dict.get("label", None)
output.format_source = output_dict.get("format_source")
output.default_identifier_source = output_dict.get("default_identifier_source")
output.metadata_source = output_dict.get("metadata_source")
output.parent = output_dict.get("parent")
output.label = output_dict.get("label")
output.count = output_dict.get("count", 1)
output.filters = []
output.from_work_dir = output_dict.get("from_work_dir", None)
output.hidden = output_dict.get("hidden", False)
output.from_work_dir = output_dict.get("from_work_dir")
output.hidden = output_dict.get("hidden") or False
# TODO: implement tool output action group fixes
if app is not None:
output.actions = ToolOutputActionGroup(app, None)
lib/galaxy/tool_util/parser/xml.py
+3 -3
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@@ -224,7 +224,7 @@ class XmlToolSource(ToolSource):
if xrefs is None:
return []
return [
XrefDict(value=xref.text.strip(), reftype=str(xref.attrib["type"]))
XrefDict(value=xref.text.strip(), type=str(xref.attrib["type"]))
for xref in xrefs.findall("xref")
if xref.get("type") and xref.text
]
@@ -489,7 +489,7 @@ class XmlToolSource(ToolSource):
inherit_format = string_as_bool(collection_elem.get("inherit_format", None))
inherit_metadata = string_as_bool(collection_elem.get("inherit_metadata", None))
default_format_source = collection_elem.get("format_source", None)
default_metadata_source = collection_elem.get("metadata_source", "")
default_metadata_source = collection_elem.get("metadata_source", None)
filters = collection_elem.findall("filter")
dataset_collector_descriptions = None
@@ -560,7 +560,7 @@ class XmlToolSource(ToolSource):
app: Optional[ToolOutputActionApp] = None,
default_format="data",
default_format_source=None,
default_metadata_source="",
default_metadata_source=None,
expression_type=None,
):
from_expression = data_elem.get("from")
lib/galaxy/tool_util/parser/yaml.py
+2 -2
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@@ -86,7 +86,7 @@ class YamlToolSource(ToolSource):
def parse_xrefs(self) -> List[XrefDict]:
xrefs = self.root_dict.get("xrefs", [])
return [XrefDict(value=xref["value"], reftype=xref["type"]) for xref in xrefs if xref["type"]]
return [XrefDict(value=xref["value"], type=xref["type"]) for xref in xrefs if xref["type"]]
def parse_sanitize(self):
return self.root_dict.get("sanitize", True)
@@ -192,7 +192,7 @@ class YamlToolSource(ToolSource):
inherit_format = output_dict.get("inherit_format", None)
inherit_metadata = output_dict.get("inherit_metadata", None)
default_format_source = output_dict.get("format_source", None)
default_metadata_source = output_dict.get("metadata_source", "")
default_metadata_source = output_dict.get("metadata_source", None)
filters = []
dataset_collector_descriptions = dataset_collector_descriptions_from_output_dict(output_dict)
lib/galaxy/tool_util_models/tool_outputs.py
+1
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@@ -33,6 +33,7 @@ class ToolOutputDataset(ToolOutputBaseModel):
format_source: Optional[str]
metadata_source: Optional[str]
discover_datasets: Optional[List["DatasetCollectionDescriptionT"]]
from_work_dir: Optional[str] = None
class ToolOutputCollectionStructure(BaseModel):
lib/galaxy/tool_util_models/tool_source.py
+1 -1
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@@ -15,7 +15,7 @@ from typing_extensions import (
class XrefDict(TypedDict):
value: str
reftype: str
type: str
class Citation(BaseModel):
lib/galaxy_test/api/test_tools.py
+1 -1
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@@ -257,7 +257,7 @@ class TestToolsApi(ApiTestCase, TestsTools):
assert "xrefs" in get_json
assert len(get_json["xrefs"]) == 1
xref = get_json["xrefs"][0]
assert xref["reftype"] == "bio.tools"
assert xref["type"] == "bio.tools"
assert xref["value"] == "bwa"
@skip_without_tool("test_data_source")
lib/tool_shed/webapp/frontend/src/components/pages/ToolVersionPage.vue
+3 -3
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@@ -156,11 +156,11 @@ const linkedFromOlderRevision = computed(() => {
<q-list bordered separator>
<q-item v-for="xref in xrefs" :key="xref.value">
<q-item-section>
<q-item-label overline>REFERENCE {{ xref.reftype }}</q-item-label>
<q-item-label v-if="xref.reftype == 'bio.tools'">
<q-item-label overline>REFERENCE {{ xref.type }}</q-item-label>
<q-item-label v-if="xref.type == 'bio.tools'">
<bio-tools-link :id="xref.value" />
</q-item-label>
<q-item-label v-else-if="xref.reftype == 'bioconductor'">
<q-item-label v-else-if="xref.type == 'bioconductor'">
<bioconductor-link :id="xref.value" />
</q-item-label>
<q-item-label v-else>
lib/tool_shed/webapp/frontend/src/schema/schema.ts
+4 -2
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@@ -2727,6 +2727,8 @@ export interface components {
format: string
/** Format Source */
format_source: string | null
/** From Work Dir */
from_work_dir?: string | null
/** Hidden */
hidden: boolean
/** Label */
@@ -3006,8 +3008,8 @@ export interface components {
}
/** XrefDict */
XrefDict: {
/** Reftype */
reftype: string
/** Type */
type: string
/** Value */
value: string
}
test/unit/tool_util/test_ontologies.py
+1 -1
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@@ -87,7 +87,7 @@ def test_parse_edam_mapping_operations_legacy():
def test_parse_biotools_default_mapping():
test_source = get_test_tool_source(source_file_name="testtool.yml", source_contents=TOOL_YAML_NO_EXPLICIT_XREFS)
ontology_data = expand_ontology_data(test_source, ["cheetah_problem_unbound_var_input"], None)
assert ontology_data.xrefs[0]["reftype"] == "bio.tools"
assert ontology_data.xrefs[0]["type"] == "bio.tools"
assert ontology_data.xrefs[0]["value"] == "bwa"
test_source = get_test_tool_source(source_file_name="testtool.yml", source_contents=TOOL_YAML_NO_EXPLICIT_XREFS)
test/unit/tool_util/test_parsing.py
+2 -2
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@@ -416,7 +416,7 @@ class TestXmlLoader(BaseLoaderTestCase):
def test_xrefs(self):
xrefs = self._tool_source.parse_xrefs()
assert xrefs == [{"value": "bwa", "reftype": "bio.tools"}]
assert xrefs == [{"value": "bwa", "type": "bio.tools"}]
def test_exit_code(self):
tool_source = self._get_tool_source(
@@ -622,7 +622,7 @@ class TestYamlLoader(BaseLoaderTestCase):
def test_xrefs(self):
xrefs = self._tool_source.parse_xrefs()
assert xrefs == [{"value": "bwa", "reftype": "bio.tools"}]
assert xrefs == [{"value": "bwa", "type": "bio.tools"}]
def test_sanitize(self):
assert self._tool_source.parse_sanitize() is True