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Refactor code for improved readability and consistency #49

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160 changes: 89 additions & 71 deletions biii-import/biseEU_LD_export.py
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Original file line number Diff line number Diff line change
Expand Up @@ -412,7 +412,7 @@ def rdfize_bioschema_tool(json_entry):

for item in entry["field_has_function"]:
if "target_uuid" in item.keys():
if not "featureList" in out.keys():
if "featureList" not in out.keys():
out["featureList"] = [{"@id": item["target_uuid"]}]
else:
out["featureList"].append({"@id": item["target_uuid"]})
Expand All @@ -424,29 +424,29 @@ def rdfize_bioschema_tool(json_entry):

for item in entry["field_has_topic"]:
if "target_uuid" in item.keys():
if not "hasTopic" in out.keys():
if "hasTopic" not in out.keys():
out["hasTopic"] = [{"@id": item["target_uuid"]}]
# print(f"Added first topic {item['target_uuid']}")
else:
out["hasTopic"].append({"@id": item["target_uuid"]})
# print(f"Added another topic {item['target_uuid']}")

for item in entry["field_has_reference_publication"]:
if not "citation" in out.keys():
if "citation" not in out.keys():
out["citation"] = []
if item["uri"]:
out["citation"].append({"@id": item["uri"].strip()})
if item["title"]:
out["citation"].append(item["title"])

for item in entry["field_has_license"]:
if not "license" in out.keys():
if "license" not in out.keys():
out["license"] = []
if item["value"]:
out["license"].append(item["value"])

for item in entry["field_has_author"]:
if not "publisher" in out.keys():
if "publisher" not in out.keys():
out["publisher"] = []
if item["value"]:
out["publisher"].append(item["value"])
Expand All @@ -462,12 +462,12 @@ def rdfize_bioschema_tool(json_entry):
out["dateModified"] = str(date.isoformat())

for item in entry["field_is_dependent_of"]:
if not "softwareRequirements" in out.keys():
if "softwareRequirements" not in out.keys():
out["softwareRequirements"] = []
if item["target_id"]:
out["softwareRequirements"].append({
"@id": "http://biii.eu/node/" + str(item["target_id"]).strip()
})
out["softwareRequirements"].append(
{"@id": "http://biii.eu/node/" + str(item["target_id"]).strip()}
)

out.update(ctx)

Expand Down Expand Up @@ -536,13 +536,13 @@ def rdfize(json_entry):
entry["hasTitle"] = entry["title"][0]["value"]

for item in entry["field_image"]:
if not "hasIllustration" in entry.keys():
if "hasIllustration" not in entry.keys():
entry["hasIllustration"] = [item["url"]]
else:
entry["hasIllustration"].append(item["url"])

for item in entry["field_has_author"]:
if not "hasAuthor" in entry.keys():
if "hasAuthor" not in entry.keys():
entry["hasAuthor"] = []
if item["value"]:
entry["hasAuthor"].append(item["value"])
Expand All @@ -553,190 +553,208 @@ def rdfize(json_entry):
for item in entry["field_has_function"]:
# print(item)
if "target_uuid" in item.keys():
if not "hasFunction" in entry.keys():
if "hasFunction" not in entry.keys():
entry["hasFunction"] = [{"@id": item["target_uuid"]}]
else:
entry["hasFunction"].append({"@id": item["target_uuid"]})

for item in entry["field_has_topic"]:
# print(item)
if "target_uuid" in item.keys():
if not "hasTopic" in entry.keys():
if "hasTopic" not in entry.keys():
entry["hasTopic"] = [{"@id": item["target_uuid"]}]
else:
entry["hasTopic"].append({"@id": item["target_uuid"]})

for item in entry["field_is_dependent_of"]:
# print(item)
if "target_id" in item.keys():
if not "requires" in entry.keys():
if "requires" not in entry.keys():
entry["requires"] = [
{"@id": "http://biii.eu/node/" + str(item["target_id"])}
]
else:
entry["requires"].append({
"@id": "http://biii.eu/node/" + str(item["target_id"])
})
entry["requires"].append(
{"@id": "http://biii.eu/node/" + str(item["target_id"])}
)

for item in entry["field_has_reference_publication"]:
if not "citation" in entry.keys():
if "citation" not in entry.keys():
entry["citation"] = []
if item["uri"]:
entry["citation"].append({
"@id": urllib.parse.quote(item["uri"], safe=":/")
})
entry["citation"].append(
{"@id": urllib.parse.quote(item["uri"], safe=":/")}
)
if item["title"]:
entry["citation"].append(item["title"])

for item in entry["field_has_location"]:
if not "location" in entry.keys():
if "location" not in entry.keys():
entry["location"] = []
if item["uri"]:
entry["location"].append({
"@id": urllib.parse.quote(item["uri"], safe=":/")
})
entry["location"].append(
{"@id": urllib.parse.quote(item["uri"], safe=":/")}
)
if item["title"]:
entry["location"].append(item["title"])

for item in entry["field_has_license"]:
if not "license" in entry.keys():
if "license" not in entry.keys():
entry["license"] = []
if item["value"]:
entry["license"].append(item["value"])

for item in entry["field_license_openness"]:
if "target_id" in item.keys():
if not "openess" in entry.keys():
if "openess" not in entry.keys():
entry["openess"] = [
{
"@id": "http://biii.eu/taxonomy/term/"
+ str(item["target_id"])
}
]
else:
entry["openess"].append({
"@id": "http://biii.eu/taxonomy/term/" + str(item["target_id"])
})
entry["openess"].append(
{
"@id": "http://biii.eu/taxonomy/term/"
+ str(item["target_id"])
}
)

for item in entry["field_has_implementation"]:
# print(item)
if "target_id" in item.keys():
if not "hasImplementation" in entry.keys():
if "hasImplementation" not in entry.keys():
entry["hasImplementation"] = [
{
"@id": "http://biii.eu/taxonomy/term/"
+ str(item["target_id"])
}
]
else:
entry["hasImplementation"].append({
"@id": "http://biii.eu/taxonomy/term/" + str(item["target_id"])
})
entry["hasImplementation"].append(
{
"@id": "http://biii.eu/taxonomy/term/"
+ str(item["target_id"])
}
)

for item in entry["field_type"]:
if "target_id" in item.keys():
if not "hasType" in entry.keys():
if "hasType" not in entry.keys():
entry["hasType"] = [
{
"@id": "http://biii.eu/taxonomy/term/"
+ str(item["target_id"])
}
]
else:
entry["hasType"].append({
"@id": "http://biii.eu/taxonomy/term/" + str(item["target_id"])
})
entry["hasType"].append(
{
"@id": "http://biii.eu/taxonomy/term/"
+ str(item["target_id"])
}
)

for item in entry["field_has_programming_language"]:
if "target_id" in item.keys():
if not "hasProgrammingLanguage" in entry.keys():
if "hasProgrammingLanguage" not in entry.keys():
entry["hasProgrammingLanguage"] = [
{
"@id": "http://biii.eu/taxonomy/term/"
+ str(item["target_id"])
}
]
else:
entry["hasProgrammingLanguage"].append({
"@id": "http://biii.eu/taxonomy/term/" + str(item["target_id"])
})
entry["hasProgrammingLanguage"].append(
{
"@id": "http://biii.eu/taxonomy/term/"
+ str(item["target_id"])
}
)

for item in entry["field_platform"]:
if "target_id" in item.keys():
if not "hasPlatform" in entry.keys():
if "hasPlatform" not in entry.keys():
entry["hasPlatform"] = [
{
"@id": "http://biii.eu/taxonomy/term/"
+ str(item["target_id"])
}
]
else:
entry["hasPlatform"].append({
"@id": "http://biii.eu/taxonomy/term/" + str(item["target_id"])
})
entry["hasPlatform"].append(
{
"@id": "http://biii.eu/taxonomy/term/"
+ str(item["target_id"])
}
)

for item in entry["field_supported_image_dimension"]:
if "target_id" in item.keys():
if not "hasSupportedImageDimension" in entry.keys():
if "hasSupportedImageDimension" not in entry.keys():
entry["hasSupportedImageDimension"] = [
{
"@id": "http://biii.eu/taxonomy/term/"
+ str(item["target_id"])
}
]
else:
entry["hasSupportedImageDimension"].append({
"@id": "http://biii.eu/taxonomy/term/" + str(item["target_id"])
})
entry["hasSupportedImageDimension"].append(
{
"@id": "http://biii.eu/taxonomy/term/"
+ str(item["target_id"])
}
)

for item in entry["field_is_covered_by_training_mat"]:
if "target_id" in item.keys():
if not "hasTrainingMaterial" in entry.keys():
if "hasTrainingMaterial" not in entry.keys():
entry["hasTrainingMaterial"] = [
{"@id": "http://biii.eu/node/" + str(item["target_id"])}
]
else:
entry["hasTrainingMaterial"].append({
"@id": "http://biii.eu/node/" + str(item["target_id"])
})
entry["hasTrainingMaterial"].append(
{"@id": "http://biii.eu/node/" + str(item["target_id"])}
)

for item in entry["field_has_documentation"]:
if not "uri" in entry.keys():
if "uri" not in entry.keys():
entry["hasDocumentation"] = []
if item["uri"]:
entry["hasDocumentation"].append({
"@id": urllib.parse.quote(item["uri"], safe=":/")
})
entry["hasDocumentation"].append(
{"@id": urllib.parse.quote(item["uri"], safe=":/")}
)
if item["title"]:
entry["hasDocumentation"].append(item["title"])

for item in entry["field_has_comparison"]:
if not "uri" in entry.keys():
if "uri" not in entry.keys():
entry["hasComparison"] = []
if item["uri"]:
entry["hasComparison"].append({
"@id": urllib.parse.quote(item["uri"], safe=":/")
})
entry["hasComparison"].append(
{"@id": urllib.parse.quote(item["uri"], safe=":/")}
)
if item["title"]:
entry["hasComparison"].append(item["title"])

for item in entry["field_has_usage_example"]:
if not "uri" in entry.keys():
if "uri" not in entry.keys():
entry["hasUsageExample"] = []
if item["uri"]:
entry["hasUsageExample"].append({
"@id": urllib.parse.quote(item["uri"], safe=":/")
})
entry["hasUsageExample"].append(
{"@id": urllib.parse.quote(item["uri"], safe=":/")}
)
if item["title"]:
entry["hasUsageExample"].append(item["title"])

for item in entry["field_has_doi"]:
if not "uri" in entry.keys():
if "uri" not in entry.keys():
entry["hasDOI"] = []
if item["uri"]:
entry["hasDOI"].append({
"@id": urllib.parse.quote(item["uri"], safe=":/")
})
entry["hasDOI"].append(
{"@id": urllib.parse.quote(item["uri"], safe=":/")}
)
if item["title"]:
entry["hasDOI"].append(item["title"])

Expand Down Expand Up @@ -796,7 +814,7 @@ def get_software_list(connection):
except urllib3.exceptions.HTTPError as e:
print("Connection error")
print(e)
except json.decoder.JSONDecodeError as e:
except json.decoder.JSONDecodeError:
print(f"Contents are not propertly formatted in {req.geturl()}")
print("Response contents:", req.data)
return None
Expand Down
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