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Refactor adding EDAM ontologies and allowing detect more patterns (e.g., versions.yml) #3519

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Merged
merged 7 commits into from
Mar 28, 2025
Merged

Refactor adding EDAM ontologies and allowing detect more patterns (e.g., versions.yml) #3519

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36b80e4
update pending work
toniher Mar 26, 2025
2397ca9
Merge branch 'dev' of github.com:nf-core/tools into further-check-ont…
toniher Mar 27, 2025
5eff207
handling more pattern cases and likely solving https://github.com/nf-…
toniher Mar 27, 2025
cb39617
Refactor input and output in add_edam_ontology function
toniher Mar 27, 2025
2ace110
Fix for warnings
toniher Mar 27, 2025
989bf7e
[automated] Update CHANGELOG.md
nf-core-bot Mar 27, 2025
e8769c0
Update nf_core/modules/lint/__init__.py
toniher Mar 28, 2025
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Original file line number Diff line number Diff line change
Expand Up @@ -53,6 +53,7 @@
- Bugfix - add back logo to the README ([#3504](https://github.com/nf-core/tools/pull/3504))
- Update dead link ([#3505](https://github.com/nf-core/tools/pull/3505))
- Changing retrieval of file extension from EDAM ([#3512](https://github.com/nf-core/tools/pull/3512))
- Refactor adding EDAM ontologies and allowing detect more patterns (e.g., versions.yml) ([#3519](https://github.com/nf-core/tools/pull/3519))

## [v3.2.0 - Pewter Pangolin](https://github.com/nf-core/tools/releases/tag/3.2.0) - [2025-01-27]

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88 changes: 38 additions & 50 deletions nf_core/modules/lint/__init__.py
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Original file line number Diff line number Diff line change
Expand Up @@ -372,68 +372,56 @@ def update_meta_yml_file(self, mod):
)
break

def add_edam_ontologies(section, edam_formats, desc):
expected_ontologies = []
current_ontologies = []
if "pattern" in section:
pattern = section["pattern"]
# Check pattern detection and process for different cases
if re.search(r"{", pattern):
for extension in re.split(r",|{|}", pattern):
if extension in edam_formats:
expected_ontologies.append((edam_formats[extension][0], extension))
else:
if re.search(r"\.\w+$", pattern):
extension = pattern.split(".")[-1]
if extension in edam_formats:
expected_ontologies.append((edam_formats[extension][0], extension))
if "ontologies" in section:
for ontology in section["ontologies"]:
current_ontologies.append(ontology["edam"])
elif section["type"] == "file":
section["ontologies"] = []
log.debug(f"expected ontologies for {desc}: {expected_ontologies}")
log.debug(f"current ontologies for {desc}: {current_ontologies}")
for ontology, ext in expected_ontologies:
if ontology not in current_ontologies:
try:
section["ontologies"].append(ruamel.yaml.comments.CommentedMap({"edam": ontology}))
section["ontologies"][-1].yaml_add_eol_comment(f"{edam_formats[ext][1]}", "edam")
except KeyError:
log.warning(f"Could not add ontologies in {desc}")

# EDAM ontologies
edam_formats = nf_core.modules.modules_utils.load_edam()
if "input" in meta_yml:
for i, channel in enumerate(corrected_meta_yml["input"]):
for j, element in enumerate(channel):
element_name = list(element.keys())[0]
expected_ontologies_i = []
current_ontologies_i = []
if "pattern" in corrected_meta_yml["input"][i][j][element_name]:
pattern = corrected_meta_yml["input"][i][j][element_name]["pattern"]
for extension in re.split(r",|{|}", pattern):
if extension in edam_formats:
expected_ontologies_i.append((edam_formats[extension][0], extension))
if "ontologies" in corrected_meta_yml["input"][i][j][element_name]:
for ontology in corrected_meta_yml["input"][i][j][element_name]["ontologies"]:
current_ontologies_i.append(ontology["edam"])
elif corrected_meta_yml["input"][i][j][element_name]["type"] == "file":
corrected_meta_yml["input"][i][j][element_name]["ontologies"] = []
log.debug(f"expected ontologies for input: {expected_ontologies_i}")
log.debug(f"current ontologies for input: {current_ontologies_i}")
for ontology, ext in expected_ontologies_i:
if ontology not in current_ontologies_i:
try:
corrected_meta_yml["input"][i][j][element_name]["ontologies"].append(
ruamel.yaml.comments.CommentedMap({"edam": ontology})
)
corrected_meta_yml["input"][i][j][element_name]["ontologies"][-1].yaml_add_eol_comment(
f"{edam_formats[ext][1]}", "edam"
)
except KeyError:
log.warning(f"Could not add ontologies in input: {element_name}")
add_edam_ontologies(
corrected_meta_yml["input"][i][j][element_name], edam_formats, f"input - {element_name}"
)

if "output" in meta_yml:
for i, channel in enumerate(corrected_meta_yml["output"]):
ch_name = list(channel.keys())[0]
for j, element in enumerate(channel[ch_name]):
element_name = list(element.keys())[0]
expected_ontologies_o = []
current_ontologies_o = []
if "pattern" in corrected_meta_yml["output"][i][ch_name][j][element_name]:
pattern = corrected_meta_yml["output"][i][ch_name][j][element_name]["pattern"]
for extension in re.split(r",|{|}", pattern):
if extension in edam_formats:
expected_ontologies_o.append((edam_formats[extension][0], extension))
if "ontologies" in corrected_meta_yml["output"][i][ch_name][j][element_name]:
for ontology in corrected_meta_yml["output"][i][ch_name][j][element_name]["ontologies"]:
current_ontologies_o.append(ontology["edam"])
elif corrected_meta_yml["output"][i][ch_name][j][element_name]["type"] == "file":
corrected_meta_yml["output"][i][ch_name][j][element_name]["ontologies"] = []
log.debug(f"expected ontologies for output: {expected_ontologies_o}")
log.debug(f"current ontologies for output: {current_ontologies_o}")
for ontology, ext in expected_ontologies_o:
if ontology not in current_ontologies_o:
try:
corrected_meta_yml["output"][i][ch_name][j][element_name]["ontologies"].append(
ruamel.yaml.comments.CommentedMap({"edam": ontology})
)
corrected_meta_yml["output"][i][ch_name][j][element_name]["ontologies"][
-1
].yaml_add_eol_comment(f"{edam_formats[ext][1]}", key="edam")
except KeyError:
log.warning(f"Could not add ontologies in ouput: {ch_name} - {element_name}")
add_edam_ontologies(
corrected_meta_yml["output"][i][ch_name][j][element_name],
edam_formats,
f"output - {ch_name} - {element_name}",
)

# Add bio.tools identifier
for i, tool in enumerate(corrected_meta_yml["tools"]):
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