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Issue 1147 fix cv duplication in template json import #2104

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merged 11 commits into from
Jan 8, 2025
+550 −292
Merged

Issue 1147 fix cv duplication in template json import #2104

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f9c9254
Add user authentication
kdp-cloud Jan 7, 2025
052e661
remove unnecessary guard clause
kdp-cloud Jan 7, 2025
251d8c7
Make the uploaded template reuse the controlled vocabulary
kdp-cloud Jan 7, 2025
0584b67
Make it work for ontologies as well
kdp-cloud Jan 7, 2025
fe7fb86
Make it work for CV Lists
kdp-cloud Jan 8, 2025
299583b
Fix tests
kdp-cloud Jan 8, 2025
1b2813a
Add possibility to control define whether a CV allows free text
kdp-cloud Jan 8, 2025
e8787e5
Reformat
kdp-cloud Jan 8, 2025
14764da
Testing
kdp-cloud Jan 8, 2025
b9a3252
Better error handling when failing to fetch terms from OLS
kdp-cloud Jan 8, 2025
21f1e53
Fix failing job test
kdp-cloud Jan 8, 2025
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2 changes: 1 addition & 1 deletion app/controllers/templates_controller.rb
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Original file line number Diff line number Diff line change
Expand Up @@ -107,7 +107,7 @@ def populate_template

begin
running!
PopulateTemplatesJob.new.queue_job
PopulateTemplatesJob.perform_later(@current_user)
rescue StandardError
done!
end
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4 changes: 2 additions & 2 deletions app/jobs/populate_templates_job.rb
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Original file line number Diff line number Diff line change
Expand Up @@ -2,9 +2,9 @@
class PopulateTemplatesJob < ApplicationJob
queue_with_priority 1
queue_as QueueNames::TEMPLATES
def perform
def perform(user)
return unless Seek::Config.isa_json_compliance_enabled

Seek::IsaTemplates::TemplateExtractor.extract_templates
Seek::IsaTemplates::TemplateExtractor.extract_templates(user)
end
end
248 changes: 138 additions & 110 deletions lib/seek/isa_templates/template_attributes_schema.json
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Original file line number Diff line number Diff line change
@@ -1,112 +1,140 @@
{
"$schema": "http://json-schema.org/draft-04/schema",
"title": "ISA tempalte attribute schema",
"description": "JSON-schema representing an ISA template attribute in DataHub",
"type": "object",
"properties": {
"iri": {
"anyOf": [
{
"type": "string",
"format": "uri"
},
{
"type": "null"
}
]
},
"name": { "type": "string" },
"description": { "type": "string" },
"required": {
"anyOf": [
{
"type": "boolean"
},
{
"type": "null"
}
]
},
"ontology": {
"anyOf": [
{
"type": "object",
"properties": {
"name": { "type": "string" },
"version": {
"anyOf": [{ "type": "string" }, { "type": "number" }]
},
"description": { "type": "string" },
"rootTermURI": { "type": "string", "format": "uri" }
}
},
{
"type": "null"
}
]
},
"dataType": {
"type": "string",
"enum": [
"Date time",
"Date",
"Real number",
"Integer",
"Web link",
"Email address",
"Text",
"String",
"Boolean",
"Registered Sample",
"Registered Sample List",
"Controlled Vocabulary",
"URI",
"Registered Data file",
"ENA custom date"
]
},
"CVList": {
"anyOf": [
{
"type": "array"
},
{
"type": "null"
}
]
},
"isaTag": {
"anyOf": [
{
"type": "string",
"enum": [
"source",
"sample",
"protocol",
"source_characteristic",
"sample_characteristic",
"other_material",
"other_material_characteristic",
"data_file",
"data_file_comment",
"parameter_value"
]
},
{
"type": "null"
}
]
},
"title": {
"anyOf": [
{
"type": "boolean"
},
{
"type": "null"
}
]
}
},
"additionalProperties": false
"$schema": "http://json-schema.org/draft-04/schema",
"title": "ISA tempalte attribute schema",
"description": "JSON-schema representing an ISA template attribute in DataHub",
"type": "object",
"properties": {
"iri": {
"anyOf": [
{
"type": "string",
"format": "uri"
},
{
"type": "null"
}
]
},
"name": {
"type": "string"
},
"description": {
"type": "string"
},
"required": {
"anyOf": [
{
"type": "boolean"
},
{
"type": "null"
}
]
},
"ontology": {
"anyOf": [
{
"type": "object",
"properties": {
"name": {
"type": "string"
},
"version": {
"anyOf": [
{
"type": "string"
},
{
"type": "number"
}
]
},
"description": {
"type": "string"
},
"rootTermURI": {
"type": "string",
"format": "uri"
}
}
},
{
"type": "null"
}
]
},
"dataType": {
"type": "string",
"enum": [
"Date time",
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"Date",
"Real number",
"Integer",
"Web link",
"Email address",
"Text",
"String",
"Boolean",
"Registered Sample",
"Registered Sample List",
"Controlled Vocabulary",
"URI",
"Registered Data file",
"ENA custom date"
]
},
"allowCVFreeText": {
"anyOf": [
{
"type": "boolean"
},
{
"type": "null"
}
]
},
"CVList": {
"anyOf": [
{
"type": "array"
},
{
"type": "null"
}
]
},
"isaTag": {
"anyOf": [
{
"type": "string",
"enum": [
"source",
"sample",
"protocol",
"source_characteristic",
"sample_characteristic",
"other_material",
"other_material_characteristic",
"data_file",
"data_file_comment",
"parameter_value"
]
},
{
"type": "null"
}
]
},
"title": {
"anyOf": [
{
"type": "boolean"
},
{
"type": "null"
}
]
}
},
"additionalProperties": false
}
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