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Jsonld context definition #5

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1690df1
automatic context from linkml, change the context fields based on the…
stefanches7 Dec 10, 2024
0f4793f
change name & version of the context, change id
stefanches7 Dec 10, 2024
d0917ed
do not add empty field to the context
stefanches7 Dec 10, 2024
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45 changes: 45 additions & 0 deletions src/collect_defined_fields_for_context.py
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import json
import csv

# Exported from https://docs.google.com/spreadsheets/d/1uoun-T-QcgBvUlz245RYuWvVB72vDzzQlMV8oprWEWg/edit?gid=0#gid=0
CONSENSUS_FIELDS_SHEET = "/home/ubuntu/src/ome-ld/static/OME-Core Semantic Fields - Fields.tsv"

context_ld_json_path = "/home/ubuntu/src/ome-ld/src/gen-linkml/context-manual.ld.json"

# Load the JSON-LD context file
with open(context_ld_json_path, 'r') as file:
context_data = json.load(file)

# Access the @context field
context = context_data.get('@context')

# consensus fields from tsv
second_column_values = []
with open(CONSENSUS_FIELDS_SHEET, 'r') as tsvfile:
reader = csv.reader(tsvfile, delimiter='\t')
for row in reader:
if len(row) > 1: # Ensure there are at least two columns
second_column_values.append(row[1])

for value in second_column_values:
ome_schema_prefix = "http://www.openmicroscopy.org/Schemas/OME/2016-06#"
tbd_prefix = "TBD#"
fieldName = ""
if value.startswith(ome_schema_prefix):
fieldName = value.split(ome_schema_prefix)[1]
elif value.startswith(tbd_prefix):
fieldName = value.split(tbd_prefix)[1]
else:
print("Field %s does not start with OME schema prefix or TBD prefix. Skipping." % value)

# Check if the field is already defined in the context
if fieldName == "":
continue
if fieldName in context:
print("Field %s is already defined in the context." % fieldName)
else:
context[fieldName] = ome_schema_prefix + fieldName

# Save the updated context
with open(context_ld_json_path, 'w') as file:
json.dump(context_data, file, indent=4)
102 changes: 102 additions & 0 deletions src/gen-linkml/context-manual.ld.json
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{
"@id": "https://raw.githubusercontent.com/joshmoore/ome-ld/refs/heads/main/src/gen-linkml/context-manual.ld.json",
"name": [
"OME JSON-LD context"
],
"version": "0.1.0",
"schemaVersion": {
"@id": "http://schema.org/version/5.0/"
},
"license": {
"@id": "https://creativecommons.org/publicdomain/zero/1.0/"
},
"comments": {
"schema:description": "Context for the creation of OME JSON-LD records",
"schema:creationDate": "2024-12-10T10:48:43",
"author": [
{
"name": "Josh Moore",
"email": "josh@openmicroscopy.org",
"@id": {
"@type": "ORCID",
"@id": "0000-0003-4028-811X"
},
"@type": "schema:Person"
},
{
"name": "Stefan Dvoretskii",
"email": "stefan.dvoretskii@dkfz-heidelberg.de",
"@id": {
"@type": "ORCID",
"@id": "0000-0001-7769-0167"
},
"@type": "schema:Person"
}
]
},
"@context": {
"schema": "http://schema.org/",
"skos": "http://www.w3.org/2004/02/skos/core#",
"name": "http://www.openmicroscopy.org/Schemas/OME/2016-06#name",
"description": "http://www.openmicroscopy.org/Schemas/OME/2016-06#description",
"manufacturer": "http://www.openmicroscopy.org/Schemas/OME/2016-06#manufacturer",
"model": "http://www.openmicroscopy.org/Schemas/OME/2016-06#model",
"serialNumber": "http://www.openmicroscopy.org/Schemas/OME/2016-06#serialNumber",
"microscopeType": "http://www.openmicroscopy.org/Schemas/OME/2016-06#microscopeType",
"version": "http://www.openmicroscopy.org/Schemas/OME/2016-06#version",
"voltage": "http://www.openmicroscopy.org/Schemas/OME/2016-06#voltage",
"gain": "http://www.openmicroscopy.org/Schemas/OME/2016-06#gain",
"offsetValue": "http://www.openmicroscopy.org/Schemas/OME/2016-06#offsetValue",
"zoom": "http://www.openmicroscopy.org/Schemas/OME/2016-06#zoom",
"amplificationGain": "http://www.openmicroscopy.org/Schemas/OME/2016-06#amplificationGain",
"detectorType": "http://www.openmicroscopy.org/Schemas/OME/2016-06#detectorType",
"nominalMagnification": "http://www.openmicroscopy.org/Schemas/OME/2016-06#nominalMagnification",
"calibratedMagnification": "http://www.openmicroscopy.org/Schemas/OME/2016-06#calibratedMagnification",
"lensNA": "http://www.openmicroscopy.org/Schemas/OME/2016-06#lensNA",
"immersion": "http://www.openmicroscopy.org/Schemas/OME/2016-06#immersion",
"correction": "http://www.openmicroscopy.org/Schemas/OME/2016-06#correction",
"workingDistance": "http://www.openmicroscopy.org/Schemas/OME/2016-06#workingDistance",
"iris": "http://www.openmicroscopy.org/Schemas/OME/2016-06#iris",
"lotNumber": "http://www.openmicroscopy.org/Schemas/OME/2016-06#lotNumber",
"dichroic": "http://www.openmicroscopy.org/Schemas/OME/2016-06#dichroic",
"Instrument": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Instrument",
"Microscope": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Microscope",
"Detector": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Detector",
"Objective": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Objective",
"FilterSet": "http://www.openmicroscopy.org/Schemas/OME/2016-06#FilterSet",
"": "http://www.openmicroscopy.org/Schemas/OME/2016-06#",
"Channel": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Channel",
"Experimenter": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Experimenter",
"ExperimenterGroup": "http://www.openmicroscopy.org/Schemas/OME/2016-06#ExperimenterGroup",
"MapAnnotation": "http://www.openmicroscopy.org/Schemas/OME/2016-06#MapAnnotation",
"Name": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Name",
"OMEImage": "http://www.openmicroscopy.org/Schemas/OME/2016-06#OMEImage",
"Pixels": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Pixels",
"TagAnnotation": "http://www.openmicroscopy.org/Schemas/OME/2016-06#TagAnnotation",
"canAnnotate": "http://www.openmicroscopy.org/Schemas/OME/2016-06#canAnnotate",
"canDelete": "http://www.openmicroscopy.org/Schemas/OME/2016-06#canDelete",
"canEdit": "http://www.openmicroscopy.org/Schemas/OME/2016-06#canEdit",
"canLink": "http://www.openmicroscopy.org/Schemas/OME/2016-06#canLink",
"isGroupAnnotate": "http://www.openmicroscopy.org/Schemas/OME/2016-06#isGroupAnnotate",
"isGroupRead": "http://www.openmicroscopy.org/Schemas/OME/2016-06#isGroupRead",
"isGroupWrite": "http://www.openmicroscopy.org/Schemas/OME/2016-06#isGroupWrite",
"isUserRead": "http://www.openmicroscopy.org/Schemas/OME/2016-06#isUserRead",
"isUserWrite": "http://www.openmicroscopy.org/Schemas/OME/2016-06#isUserWrite",
"isWorldRead": "http://www.openmicroscopy.org/Schemas/OME/2016-06#isWorldRead",
"isWorldWrite": "http://www.openmicroscopy.org/Schemas/OME/2016-06#isWorldWrite",
"perm": "http://www.openmicroscopy.org/Schemas/OME/2016-06#perm",
"AcquisitionMode": "http://www.openmicroscopy.org/Schemas/OME/2016-06#AcquisitionMode",
"ChecksumAlgorithm": "http://www.openmicroscopy.org/Schemas/OME/2016-06#ChecksumAlgorithm",
"ContrastMethod": "http://www.openmicroscopy.org/Schemas/OME/2016-06#ContrastMethod",
"Details": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Details",
"DimensionOrder": "http://www.openmicroscopy.org/Schemas/OME/2016-06#DimensionOrder",
"ExternalInfo": "http://www.openmicroscopy.org/Schemas/OME/2016-06#ExternalInfo",
"Format": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Format",
"Illumination": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Illumination",
"OriginalFile": "http://www.openmicroscopy.org/Schemas/OME/2016-06#OriginalFile",
"Permissions": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Permissions",
"PhotometricInterpretation": "http://www.openmicroscopy.org/Schemas/OME/2016-06#PhotometricInterpretation",
"PixelsType": "http://www.openmicroscopy.org/Schemas/OME/2016-06#PixelsType",
"LengthI": "http://www.openmicroscopy.org/Schemas/OME/2016-06#LengthI"
}
}
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