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Merged
manulera merged 1 commit into from
Oct 20, 2025
Merged

Make input default to empty list by editing python files with a script #62

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2 changes: 2 additions & 0 deletions Makefile
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Original file line number Diff line number Diff line change
Expand Up @@ -114,6 +114,8 @@ gen-project: $(PYMODEL)
# Format with black
$(RUN) black $(PYMODEL)/_models.py
$(RUN) black $(DEST)/*/*.py
# Use default_factory=list for input field
$(RUN) python modify_input_default.py


test: test-schema test-python test-examples
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18 changes: 18 additions & 0 deletions modify_input_default.py
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@@ -0,0 +1,18 @@
import re

with open("src/opencloning_linkml/datamodel/_models.py", "r") as f:
content = f.read()

new_content = []
change_next_line = False
for line in content.split("\n"):
new_line = line
if re.match(r"^\s+input:", line):
change_next_line = True
elif change_next_line:
new_line = new_line.replace("default=None", "default_factory=list")
change_next_line = False
new_content.append(new_line)

with open("src/opencloning_linkml/datamodel/_models.py", "w") as f:
f.write("\n".join(new_content))
Binary file modified project/excel/opencloning_linkml.xlsx
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2 changes: 1 addition & 1 deletion project/jsonld/opencloning_linkml.context.jsonld
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@@ -1,7 +1,7 @@
{
"comments": {
"description": "Auto generated by LinkML jsonld context generator",
"generation_date": "2025-10-03T14:02:10",
"generation_date": "2025-10-20T16:29:26",
"source": "opencloning_linkml.yaml"
},
"@context": {
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4 changes: 2 additions & 2 deletions project/jsonld/opencloning_linkml.jsonld
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Expand Up @@ -3542,9 +3542,9 @@
],
"metamodel_version": "1.7.0",
"source_file": "opencloning_linkml.yaml",
"source_file_date": "2025-10-03T13:59:29",
"source_file_date": "2025-10-20T16:11:45",
"source_file_size": 26051,
"generation_date": "2025-10-03T14:02:11",
"generation_date": "2025-10-20T16:29:26",
"@type": "SchemaDefinition",
"@context": [
"project/jsonld/opencloning_linkml.context.jsonld",
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998 changes: 499 additions & 499 deletions project/owl/opencloning_linkml.owl.ttl
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2 changes: 1 addition & 1 deletion project/python/opencloning_linkml.py
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@@ -1,5 +1,5 @@
# Auto generated from opencloning_linkml.yaml by pythongen.py version: 0.0.1
# Generation date: 2025-10-03T14:02:12
# Generation date: 2025-10-20T16:29:27
# Schema: OpenCloning_LinkML
#
# id: https://opencloning.github.io/OpenCloning_LinkML
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1,610 changes: 805 additions & 805 deletions project/shacl/opencloning_linkml.shacl.ttl
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66 changes: 33 additions & 33 deletions src/opencloning_linkml/datamodel/_models.py
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Original file line number Diff line number Diff line change
Expand Up @@ -590,7 +590,7 @@ class Source(NamedThing):
},
)
input: Optional[list[Union[SourceInput, AssemblyFragment]]] = Field(
default=None,
default_factory=list,
description="""The inputs to this source. If the source represents external import of a sequence, it's empty.""",
json_schema_extra={"linkml_meta": {"alias": "input", "domain_of": ["Source"], "slot_uri": "schema:object"}},
)
Expand Down Expand Up @@ -650,7 +650,7 @@ class DatabaseSource(Source):
json_schema_extra={"linkml_meta": {"alias": "output_name", "domain_of": ["Source"]}},
)
input: Optional[list[Union[SourceInput, AssemblyFragment]]] = Field(
default=None,
default_factory=list,
description="""The inputs to this source. If the source represents external import of a sequence, it's empty.""",
json_schema_extra={"linkml_meta": {"alias": "input", "domain_of": ["Source"], "slot_uri": "schema:object"}},
)
Expand Down Expand Up @@ -735,7 +735,7 @@ class CollectionSource(Source):
},
)
input: Optional[list[Union[SourceInput, AssemblyFragment]]] = Field(
default=None,
default_factory=list,
description="""The inputs to this source. If the source represents external import of a sequence, it's empty.""",
json_schema_extra={"linkml_meta": {"alias": "input", "domain_of": ["Source"], "slot_uri": "schema:object"}},
)
Expand Down Expand Up @@ -964,7 +964,7 @@ class ManuallyTypedSource(Source):
},
)
input: Optional[list[Union[SourceInput, AssemblyFragment]]] = Field(
default=None,
default_factory=list,
description="""The inputs to this source. If the source represents external import of a sequence, it's empty.""",
json_schema_extra={"linkml_meta": {"alias": "input", "domain_of": ["Source"], "slot_uri": "schema:object"}},
)
Expand Down Expand Up @@ -1066,7 +1066,7 @@ class UploadedFileSource(Source):
},
)
input: Optional[list[Union[SourceInput, AssemblyFragment]]] = Field(
default=None,
default_factory=list,
description="""The inputs to this source. If the source represents external import of a sequence, it's empty.""",
json_schema_extra={"linkml_meta": {"alias": "input", "domain_of": ["Source"], "slot_uri": "schema:object"}},
)
Expand Down Expand Up @@ -1130,7 +1130,7 @@ class RepositoryIdSource(Source):
},
)
input: Optional[list[Union[SourceInput, AssemblyFragment]]] = Field(
default=None,
default_factory=list,
description="""The inputs to this source. If the source represents external import of a sequence, it's empty.""",
json_schema_extra={"linkml_meta": {"alias": "input", "domain_of": ["Source"], "slot_uri": "schema:object"}},
)
Expand Down Expand Up @@ -1214,7 +1214,7 @@ class AddgeneIdSource(RepositoryIdSource):
},
)
input: Optional[list[Union[SourceInput, AssemblyFragment]]] = Field(
default=None,
default_factory=list,
description="""The inputs to this source. If the source represents external import of a sequence, it's empty.""",
json_schema_extra={"linkml_meta": {"alias": "input", "domain_of": ["Source"], "slot_uri": "schema:object"}},
)
Expand Down Expand Up @@ -1320,7 +1320,7 @@ class WekWikGeneIdSource(RepositoryIdSource):
},
)
input: Optional[list[Union[SourceInput, AssemblyFragment]]] = Field(
default=None,
default_factory=list,
description="""The inputs to this source. If the source represents external import of a sequence, it's empty.""",
json_schema_extra={"linkml_meta": {"alias": "input", "domain_of": ["Source"], "slot_uri": "schema:object"}},
)
Expand Down Expand Up @@ -1448,7 +1448,7 @@ class SEVASource(RepositoryIdSource):
},
)
input: Optional[list[Union[SourceInput, AssemblyFragment]]] = Field(
default=None,
default_factory=list,
description="""The inputs to this source. If the source represents external import of a sequence, it's empty.""",
json_schema_extra={"linkml_meta": {"alias": "input", "domain_of": ["Source"], "slot_uri": "schema:object"}},
)
Expand Down Expand Up @@ -1551,7 +1551,7 @@ class BenchlingUrlSource(RepositoryIdSource):
},
)
input: Optional[list[Union[SourceInput, AssemblyFragment]]] = Field(
default=None,
default_factory=list,
description="""The inputs to this source. If the source represents external import of a sequence, it's empty.""",
json_schema_extra={"linkml_meta": {"alias": "input", "domain_of": ["Source"], "slot_uri": "schema:object"}},
)
Expand Down Expand Up @@ -1648,7 +1648,7 @@ class SnapGenePlasmidSource(RepositoryIdSource):
},
)
input: Optional[list[Union[SourceInput, AssemblyFragment]]] = Field(
default=None,
default_factory=list,
description="""The inputs to this source. If the source represents external import of a sequence, it's empty.""",
json_schema_extra={"linkml_meta": {"alias": "input", "domain_of": ["Source"], "slot_uri": "schema:object"}},
)
Expand Down Expand Up @@ -1736,7 +1736,7 @@ class EuroscarfSource(RepositoryIdSource):
},
)
input: Optional[list[Union[SourceInput, AssemblyFragment]]] = Field(
default=None,
default_factory=list,
description="""The inputs to this source. If the source represents external import of a sequence, it's empty.""",
json_schema_extra={"linkml_meta": {"alias": "input", "domain_of": ["Source"], "slot_uri": "schema:object"}},
)
Expand Down Expand Up @@ -1847,7 +1847,7 @@ class IGEMSource(RepositoryIdSource):
},
)
input: Optional[list[Union[SourceInput, AssemblyFragment]]] = Field(
default=None,
default_factory=list,
description="""The inputs to this source. If the source represents external import of a sequence, it's empty.""",
json_schema_extra={"linkml_meta": {"alias": "input", "domain_of": ["Source"], "slot_uri": "schema:object"}},
)
Expand Down Expand Up @@ -1952,7 +1952,7 @@ class OpenDNACollectionsSource(RepositoryIdSource):
},
)
input: Optional[list[Union[SourceInput, AssemblyFragment]]] = Field(
default=None,
default_factory=list,
description="""The inputs to this source. If the source represents external import of a sequence, it's empty.""",
json_schema_extra={"linkml_meta": {"alias": "input", "domain_of": ["Source"], "slot_uri": "schema:object"}},
)
Expand Down Expand Up @@ -2059,7 +2059,7 @@ class GenomeCoordinatesSource(Source):
},
)
input: Optional[list[Union[SourceInput, AssemblyFragment]]] = Field(
default=None,
default_factory=list,
description="""The inputs to this source. If the source represents external import of a sequence, it's empty.""",
json_schema_extra={"linkml_meta": {"alias": "input", "domain_of": ["Source"], "slot_uri": "schema:object"}},
)
Expand Down Expand Up @@ -2132,7 +2132,7 @@ class SequenceCutSource(Source):
},
)
input: Optional[list[Union[SourceInput, AssemblyFragment]]] = Field(
default=None,
default_factory=list,
description="""The inputs to this source. If the source represents external import of a sequence, it's empty.""",
json_schema_extra={"linkml_meta": {"alias": "input", "domain_of": ["Source"], "slot_uri": "schema:object"}},
)
Expand Down Expand Up @@ -2205,7 +2205,7 @@ class RestrictionEnzymeDigestionSource(SequenceCutSource):
},
)
input: Optional[list[Union[SourceInput, AssemblyFragment]]] = Field(
default=None,
default_factory=list,
description="""The inputs to this source. If the source represents external import of a sequence, it's empty.""",
json_schema_extra={"linkml_meta": {"alias": "input", "domain_of": ["Source"], "slot_uri": "schema:object"}},
)
Expand Down Expand Up @@ -2315,7 +2315,7 @@ class AssemblySource(Source):
},
)
input: Optional[list[Union[SourceInput, AssemblyFragment]]] = Field(
default=None,
default_factory=list,
description="""The inputs to this source. If the source represents external import of a sequence, it's empty.""",
json_schema_extra={"linkml_meta": {"alias": "input", "domain_of": ["Source"], "slot_uri": "schema:object"}},
)
Expand Down Expand Up @@ -2387,7 +2387,7 @@ class PCRSource(AssemblySource):
},
)
input: Optional[list[Union[SourceInput, AssemblyFragment]]] = Field(
default=None,
default_factory=list,
description="""The inputs to this source. If the source represents external import of a sequence, it's empty.""",
json_schema_extra={"linkml_meta": {"alias": "input", "domain_of": ["Source"], "slot_uri": "schema:object"}},
)
Expand Down Expand Up @@ -2452,7 +2452,7 @@ class LigationSource(AssemblySource):
},
)
input: Optional[list[Union[SourceInput, AssemblyFragment]]] = Field(
default=None,
default_factory=list,
description="""The inputs to this source. If the source represents external import of a sequence, it's empty.""",
json_schema_extra={"linkml_meta": {"alias": "input", "domain_of": ["Source"], "slot_uri": "schema:object"}},
)
Expand Down Expand Up @@ -2517,7 +2517,7 @@ class HomologousRecombinationSource(AssemblySource):
},
)
input: Optional[list[Union[SourceInput, AssemblyFragment]]] = Field(
default=None,
default_factory=list,
description="""The inputs to this source. If the source represents external import of a sequence, it's empty.""",
json_schema_extra={"linkml_meta": {"alias": "input", "domain_of": ["Source"], "slot_uri": "schema:object"}},
)
Expand Down Expand Up @@ -2582,7 +2582,7 @@ class GibsonAssemblySource(AssemblySource):
},
)
input: Optional[list[Union[SourceInput, AssemblyFragment]]] = Field(
default=None,
default_factory=list,
description="""The inputs to this source. If the source represents external import of a sequence, it's empty.""",
json_schema_extra={"linkml_meta": {"alias": "input", "domain_of": ["Source"], "slot_uri": "schema:object"}},
)
Expand Down Expand Up @@ -2647,7 +2647,7 @@ class InFusionSource(AssemblySource):
},
)
input: Optional[list[Union[SourceInput, AssemblyFragment]]] = Field(
default=None,
default_factory=list,
description="""The inputs to this source. If the source represents external import of a sequence, it's empty.""",
json_schema_extra={"linkml_meta": {"alias": "input", "domain_of": ["Source"], "slot_uri": "schema:object"}},
)
Expand Down Expand Up @@ -2712,7 +2712,7 @@ class OverlapExtensionPCRLigationSource(AssemblySource):
},
)
input: Optional[list[Union[SourceInput, AssemblyFragment]]] = Field(
default=None,
default_factory=list,
description="""The inputs to this source. If the source represents external import of a sequence, it's empty.""",
json_schema_extra={"linkml_meta": {"alias": "input", "domain_of": ["Source"], "slot_uri": "schema:object"}},
)
Expand Down Expand Up @@ -2777,7 +2777,7 @@ class InVivoAssemblySource(AssemblySource):
},
)
input: Optional[list[Union[SourceInput, AssemblyFragment]]] = Field(
default=None,
default_factory=list,
description="""The inputs to this source. If the source represents external import of a sequence, it's empty.""",
json_schema_extra={"linkml_meta": {"alias": "input", "domain_of": ["Source"], "slot_uri": "schema:object"}},
)
Expand Down Expand Up @@ -2857,7 +2857,7 @@ class RestrictionAndLigationSource(AssemblySource):
},
)
input: Optional[list[Union[SourceInput, AssemblyFragment]]] = Field(
default=None,
default_factory=list,
description="""The inputs to this source. If the source represents external import of a sequence, it's empty.""",
json_schema_extra={"linkml_meta": {"alias": "input", "domain_of": ["Source"], "slot_uri": "schema:object"}},
)
Expand Down Expand Up @@ -2932,7 +2932,7 @@ class GatewaySource(AssemblySource):
},
)
input: Optional[list[Union[SourceInput, AssemblyFragment]]] = Field(
default=None,
default_factory=list,
description="""The inputs to this source. If the source represents external import of a sequence, it's empty.""",
json_schema_extra={"linkml_meta": {"alias": "input", "domain_of": ["Source"], "slot_uri": "schema:object"}},
)
Expand Down Expand Up @@ -2997,7 +2997,7 @@ class CreLoxRecombinationSource(AssemblySource):
},
)
input: Optional[list[Union[SourceInput, AssemblyFragment]]] = Field(
default=None,
default_factory=list,
description="""The inputs to this source. If the source represents external import of a sequence, it's empty.""",
json_schema_extra={"linkml_meta": {"alias": "input", "domain_of": ["Source"], "slot_uri": "schema:object"}},
)
Expand Down Expand Up @@ -3062,7 +3062,7 @@ class CRISPRSource(HomologousRecombinationSource):
},
)
input: Optional[list[Union[SourceInput, AssemblyFragment]]] = Field(
default=None,
default_factory=list,
description="""The inputs to this source. If the source represents external import of a sequence, it's empty.""",
json_schema_extra={"linkml_meta": {"alias": "input", "domain_of": ["Source"], "slot_uri": "schema:object"}},
)
Expand Down Expand Up @@ -3127,7 +3127,7 @@ class OligoHybridizationSource(Source):
},
)
input: Optional[list[Union[SourceInput, AssemblyFragment]]] = Field(
default=None,
default_factory=list,
description="""The inputs to this source. If the source represents external import of a sequence, it's empty.""",
json_schema_extra={"linkml_meta": {"alias": "input", "domain_of": ["Source"], "slot_uri": "schema:object"}},
)
Expand Down Expand Up @@ -3182,7 +3182,7 @@ class PolymeraseExtensionSource(Source):
},
)
input: Optional[list[Union[SourceInput, AssemblyFragment]]] = Field(
default=None,
default_factory=list,
description="""The inputs to this source. If the source represents external import of a sequence, it's empty.""",
json_schema_extra={"linkml_meta": {"alias": "input", "domain_of": ["Source"], "slot_uri": "schema:object"}},
)
Expand Down Expand Up @@ -3458,7 +3458,7 @@ class AnnotationSource(Source):
},
)
input: Optional[list[Union[SourceInput, AssemblyFragment]]] = Field(
default=None,
default_factory=list,
description="""The inputs to this source. If the source represents external import of a sequence, it's empty.""",
json_schema_extra={"linkml_meta": {"alias": "input", "domain_of": ["Source"], "slot_uri": "schema:object"}},
)
Expand Down Expand Up @@ -3513,7 +3513,7 @@ class ReverseComplementSource(Source):
},
)
input: Optional[list[Union[SourceInput, AssemblyFragment]]] = Field(
default=None,
default_factory=list,
description="""The inputs to this source. If the source represents external import of a sequence, it's empty.""",
json_schema_extra={"linkml_meta": {"alias": "input", "domain_of": ["Source"], "slot_uri": "schema:object"}},
)
Expand Down