From a640536e7495286f781acc852e70efc72189cf6d Mon Sep 17 00:00:00 2001 From: API version update Date: Fri, 17 Jan 2025 09:55:46 +0000 Subject: [PATCH 1/2] api version automatically generated --- beacon/conf/api_version.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/beacon/conf/api_version.yml b/beacon/conf/api_version.yml index 8b48abd..9ed481f 100644 --- a/beacon/conf/api_version.yml +++ b/beacon/conf/api_version.yml @@ -1 +1 @@ -api_version: v2.0-928e368 +api_version: v2.0-68abde0 From 23f161962cfdffa71b158d96123c1b46208cb359 Mon Sep 17 00:00:00 2001 From: costero-e Date: Fri, 17 Jan 2025 10:57:50 +0100 Subject: [PATCH 2/2] updating headers for ri-tools --- ri-tools/files/deref_schemas/cohorts.json | 369 +++++++++++++++- ri-tools/files/deref_schemas/individuals.json | 397 +++++++++++++++++- ri-tools/files/headers/cohorts.txt | 6 +- ri-tools/files/headers/individuals.txt | 2 +- 4 files changed, 766 insertions(+), 8 deletions(-) diff --git a/ri-tools/files/deref_schemas/cohorts.json b/ri-tools/files/deref_schemas/cohorts.json index cfd6061..00c2618 100644 --- a/ri-tools/files/deref_schemas/cohorts.json +++ b/ri-tools/files/deref_schemas/cohorts.json @@ -1 +1,368 @@ -{"cohortDataTypes": {"id": "", "label": ""}, "cohortDesign": {"id": "", "label": ""}, "cohortSize": 0, "cohortType": "", "collectionEvents": [{"eventAgeRange": {"availability": true, "availabilityCount": 0, "distribution": {}}, "eventDataTypes": {"availability": true, "availabilityCount": 0, "distribution": {}}, "eventDiseases": {"availability": true, "availabilityCount": 0, "distribution": {}}, "eventEthnicities": {"availability": true, "availabilityCount": 0, "distribution": {}}, "eventGenders": {"availability": true, "availabilityCount": 0, "distribution": {}}, "eventLocations": {"availability": true, "availabilityCount": 0, "distribution": {}}, "eventPhenotypes": {"availability": true, "availabilityCount": 0, "distribution": {}}, "eventTimeline": {"availability": true, "availabilityCount": 0, "distribution": {}}}], "exclusionCriteria": {"ageRange": {"end": {"iso8601duration": ""}, "start": {"iso8601duration": ""}}, "diseaseConditions": [{"ageOfOnset": [{"iso8601duration": ""}, {"end": {"iso8601duration": ""}, "start": {"iso8601duration": ""}}, {"days": 0, "weeks": 0}, "", {"end": "", "start": ""}, {"id": "", "label": ""}], "diseaseCode": {"id": "", "label": ""}, "familyHistory": true, "notes": "", "severity": {"id": "", "label": ""}, "stage": {"id": "", "label": ""}}], "ethnicities": [{"id": "", "label": ""}], "genders": [{"id": "", "label": ""}], "locations": [{"id": "", "label": ""}], "phenotypicConditions": [{"evidence": {"evidenceCode": {"id": "", "label": ""}, "reference": {"id": "", "notes": "", "reference": ""}}, "excluded": true, "featureType": {"id": "", "label": ""}, "modifiers": [{"id": "", "label": ""}], "notes": "", "onset": [{"iso8601duration": ""}, {"end": {"iso8601duration": ""}, "start": {"iso8601duration": ""}}, {"days": 0, "weeks": 0}, "", {"end": "", "start": ""}, {"id": "", "label": ""}], "resolution": [{"iso8601duration": ""}, {"end": {"iso8601duration": ""}, "start": {"iso8601duration": ""}}, {"days": 0, "weeks": 0}, "", {"end": "", "start": ""}, {"id": "", "label": ""}], "severity": {"id": "", "label": ""}}], "type": {"availability": true, "availabilityCount": 0, "distribution": {}}}, "id": "", "inclusionCriteria": {"ageRange": {"end": {"iso8601duration": ""}, "start": {"iso8601duration": ""}}, "diseaseConditions": [{"ageOfOnset": [{"iso8601duration": ""}, {"end": {"iso8601duration": ""}, "start": {"iso8601duration": ""}}, {"days": 0, "weeks": 0}, "", {"end": "", "start": ""}, {"id": "", "label": ""}], "diseaseCode": {"id": "", "label": ""}, "familyHistory": true, "notes": "", "severity": {"id": "", "label": ""}, "stage": {"id": "", "label": ""}}], "ethnicities": [{"id": "", "label": ""}], "genders": [{"id": "", "label": ""}], "locations": [{"id": "", "label": ""}], "phenotypicConditions": [{"evidence": {"evidenceCode": {"id": "", "label": ""}, "reference": {"id": "", "notes": "", "reference": ""}}, "excluded": true, "featureType": {"id": "", "label": ""}, "modifiers": [{"id": "", "label": ""}], "notes": "", "onset": [{"iso8601duration": ""}, {"end": {"iso8601duration": ""}, "start": {"iso8601duration": ""}}, {"days": 0, "weeks": 0}, "", {"end": "", "start": ""}, {"id": "", "label": ""}], "resolution": [{"iso8601duration": ""}, {"end": {"iso8601duration": ""}, "start": {"iso8601duration": ""}}, {"days": 0, "weeks": 0}, "", {"end": "", "start": ""}, {"id": "", "label": ""}], "severity": {"id": "", "label": ""}}], "type": {"availability": true, "availabilityCount": 0, "distribution": {}}}, "name": ""} \ No newline at end of file +{ + "cohortDataTypes": { + "id": "", + "label": "" + }, + "cohortDesign": { + "id": "", + "label": "" + }, + "cohortSize": 0, + "cohortType": "", + "collectionEvents": [ + { + "eventAgeRange": { + "availability": true, + "availabilityCount": 0, + "distribution": {} + }, + "eventDataTypes": { + "availability": true, + "availabilityCount": 0, + "distribution": {} + }, + "eventDiseases": { + "availability": true, + "availabilityCount": 0, + "distribution": {} + }, + "eventEthnicities": { + "availability": true, + "availabilityCount": 0, + "distribution": {} + }, + "eventGenders": { + "availability": true, + "availabilityCount": 0, + "distribution": {} + }, + "eventLocations": { + "availability": true, + "availabilityCount": 0, + "distribution": {} + }, + "eventPhenotypes": { + "availability": true, + "availabilityCount": 0, + "distribution": {} + }, + "eventTimeline": { + "availability": true, + "availabilityCount": 0, + "distribution": {} + } + } + ], + "exclusionCriteria": { + "ageRange": { + "end": { + "iso8601duration": "" + }, + "start": { + "iso8601duration": "" + } + }, + "diseaseConditions": [ + { + "ageOfOnset": [ + { + "iso8601duration": "" + }, + { + "end": { + "iso8601duration": "" + }, + "start": { + "iso8601duration": "" + } + }, + { + "days": 0, + "weeks": 0 + }, + "", + { + "end": "", + "start": "" + }, + { + "id": "", + "label": "" + } + ], + "diseaseCode": { + "id": "", + "label": "" + }, + "familyHistory": true, + "notes": "", + "severity": { + "id": "", + "label": "" + }, + "stage": { + "id": "", + "label": "" + } + } + ], + "ethnicities": [ + { + "id": "", + "label": "" + } + ], + "genders": [ + { + "id": "", + "label": "" + } + ], + "locations": [ + { + "id": "", + "label": "" + } + ], + "phenotypicConditions": [ + { + "evidence": { + "evidenceCode": { + "id": "", + "label": "" + }, + "reference": { + "id": "", + "notes": "", + "reference": "" + } + }, + "excluded": true, + "featureType": { + "id": "", + "label": "" + }, + "modifiers": [ + { + "id": "", + "label": "" + } + ], + "notes": "", + "onset": [ + { + "iso8601duration": "" + }, + { + "end": { + "iso8601duration": "" + }, + "start": { + "iso8601duration": "" + } + }, + { + "days": 0, + "weeks": 0 + }, + "", + { + "end": "", + "start": "" + }, + { + "id": "", + "label": "" + } + ], + "resolution": [ + { + "iso8601duration": "" + }, + { + "end": { + "iso8601duration": "" + }, + "start": { + "iso8601duration": "" + } + }, + { + "days": 0, + "weeks": 0 + }, + "", + { + "end": "", + "start": "" + }, + { + "id": "", + "label": "" + } + ], + "severity": { + "id": "", + "label": "" + } + } + ] + }, + "id": "", + "inclusionCriteria": { + "ageRange": { + "end": { + "iso8601duration": "" + }, + "start": { + "iso8601duration": "" + } + }, + "diseaseConditions": [ + { + "ageOfOnset": [ + { + "iso8601duration": "" + }, + { + "end": { + "iso8601duration": "" + }, + "start": { + "iso8601duration": "" + } + }, + { + "days": 0, + "weeks": 0 + }, + "", + { + "end": "", + "start": "" + }, + { + "id": "", + "label": "" + } + ], + "diseaseCode": { + "id": "", + "label": "" + }, + "familyHistory": true, + "notes": "", + "severity": { + "id": "", + "label": "" + }, + "stage": { + "id": "", + "label": "" + } + } + ], + "ethnicities": [ + { + "id": "", + "label": "" + } + ], + "genders": [ + { + "id": "", + "label": "" + } + ], + "locations": [ + { + "id": "", + "label": "" + } + ], + "phenotypicConditions": [ + { + "evidence": { + "evidenceCode": { + "id": "", + "label": "" + }, + "reference": { + "id": "", + "notes": "", + "reference": "" + } + }, + "excluded": true, + "featureType": { + "id": "", + "label": "" + }, + "modifiers": [ + { + "id": "", + "label": "" + } + ], + "notes": "", + "onset": [ + { + "iso8601duration": "" + }, + { + "end": { + "iso8601duration": "" + }, + "start": { + "iso8601duration": "" + } + }, + { + "days": 0, + "weeks": 0 + }, + "", + { + "end": "", + "start": "" + }, + { + "id": "", + "label": "" + } + ], + "resolution": [ + { + "iso8601duration": "" + }, + { + "end": { + "iso8601duration": "" + }, + "start": { + "iso8601duration": "" + } + }, + { + "days": 0, + "weeks": 0 + }, + "", + { + "end": "", + "start": "" + }, + { + "id": "", + "label": "" + } + ], + "severity": { + "id": "", + "label": "" + } + } + ] + }, + "name": "" +} \ No newline at end of file diff --git a/ri-tools/files/deref_schemas/individuals.json b/ri-tools/files/deref_schemas/individuals.json index c054aee..331fff9 100644 --- a/ri-tools/files/deref_schemas/individuals.json +++ b/ri-tools/files/deref_schemas/individuals.json @@ -1 +1,396 @@ -{"diseases": [{"ageOfOnset": [{"iso8601duration": ""}, {"end": {"iso8601duration": ""}, "start": {"iso8601duration": ""}}, {"days": 0, "weeks": 0}, "", {"end": "", "start": ""}, {"id": "", "label": ""}], "diseaseCode": {"id": "", "label": ""}, "familyHistory": true, "notes": "", "severity": {"id": "", "label": ""}, "stage": {"id": "", "label": ""}}], "ethnicity": {"id": "", "label": ""}, "exposures": [{"ageAtExposure": {"iso8601duration": ""}, "date": "", "duration": "", "exposureCode": {"id": "", "label": ""}, "unit": {"id": "", "label": ""}}], "geographicOrigin": {"id": "", "label": ""}, "id": "", "info": {}, "interventionsOrProcedures": [{"ageAtProcedure": [{"iso8601duration": ""}, {"end": {"iso8601duration": ""}, "start": {"iso8601duration": ""}}, {"days": 0, "weeks": 0}, "", {"end": "", "start": ""}, {"id": "", "label": ""}], "bodySite": {"id": "", "label": ""}, "dateOfProcedure": "", "procedureCode": {"id": "", "label": ""}}], "karyotypicSex": "", "measures": [{"assayCode": {"id": "", "label": ""}, "date": "", "measurementValue": [{"referenceRange": {"high": 0, "low": 0, "unit": {"id": "", "label": ""}}}, {"unit": {"id": "", "label": ""}, "value": 0, "id": "", "label": ""}, {"typedQuantities": {"quantity": {"referenceRange": {"high": 0, "low": 0, "unit": {"id": "", "label": ""}}, "unit": {"id": "", "label": ""}, "value": 0}}}], "notes": "", "observationMoment": [{"iso8601duration": ""}, {"end": {"iso8601duration": ""}, "start": {"iso8601duration": ""}}, {"days": 0, "weeks": 0}, "", {"end": "", "start": ""}, {"id": "", "label": ""}], "procedure": {"ageAtProcedure": [{"iso8601duration": ""}, {"end": {"iso8601duration": ""}, "start": {"iso8601duration": ""}}, {"days": 0, "weeks": 0}, "", {"end": "", "start": ""}, {"id": "", "label": ""}], "bodySite": {"id": "", "label": ""}, "dateOfProcedure": "", "procedureCode": {"id": "", "label": ""}}}], "pedigrees": [{"disease": {"ageOfOnset": [{"iso8601duration": ""}, {"end": {"iso8601duration": ""}, "start": {"iso8601duration": ""}}, {"days": 0, "weeks": 0}, "", {"end": "", "start": ""}, {"id": "", "label": ""}], "diseaseCode": {"id": "", "label": ""}, "familyHistory": true, "notes": "", "severity": {"id": "", "label": ""}, "stage": {"id": "", "label": ""}}, "id": "", "members": {"affected": true, "memberId": "", "role": {"id": "", "label": ""}}}], "phenotypicFeatures": [{"evidence": {"evidenceCode": {"id": "", "label": ""}, "reference": {"id": "", "notes": "", "reference": ""}}, "excluded": true, "featureType": {"id": "", "label": ""}, "modifiers": [{"id": "", "label": ""}], "notes": "", "onset": [{"iso8601duration": ""}, {"end": {"iso8601duration": ""}, "start": {"iso8601duration": ""}}, {"days": 0, "weeks": 0}, "", {"end": "", "start": ""}, {"id": "", "label": ""}], "resolution": [{"iso8601duration": ""}, {"end": {"iso8601duration": ""}, "start": {"iso8601duration": ""}}, {"days": 0, "weeks": 0}, "", {"end": "", "start": ""}, {"id": "", "label": ""}], "severity": {"id": "", "label": ""}}], "sex": {"id": "", "label": ""}, "treatments": [{"ageAtOnset": {"iso8601duration": ""}, "cumulativeDose": {"referenceRange": {"id": "", "label": ""}, "unit": {}}, "doseIntervals": [{"id": "", "label": ""}], "routeOfAdministration": {"id": "", "label": ""}, "treatmentCode": {"id": "", "label": ""}}]} \ No newline at end of file +{ + "diseases": [ + { + "ageOfOnset": [ + { + "iso8601duration": "" + }, + { + "end": { + "iso8601duration": "" + }, + "start": { + "iso8601duration": "" + } + }, + { + "days": 0, + "weeks": 0 + }, + "", + { + "end": "", + "start": "" + }, + { + "id": "", + "label": "" + } + ], + "diseaseCode": { + "id": "", + "label": "" + }, + "familyHistory": true, + "notes": "", + "severity": { + "id": "", + "label": "" + }, + "stage": { + "id": "", + "label": "" + } + } + ], + "ethnicity": { + "id": "", + "label": "" + }, + "exposures": [ + { + "ageAtExposure": { + "iso8601duration": "" + }, + "date": "", + "duration": "", + "exposureCode": { + "id": "", + "label": "" + }, + "unit": { + "id": "", + "label": "" + } + } + ], + "geographicOrigin": { + "id": "", + "label": "" + }, + "id": "", + "info": {}, + "interventionsOrProcedures": [ + { + "ageAtProcedure": [ + { + "iso8601duration": "" + }, + { + "end": { + "iso8601duration": "" + }, + "start": { + "iso8601duration": "" + } + }, + { + "days": 0, + "weeks": 0 + }, + "", + { + "end": "", + "start": "" + }, + { + "id": "", + "label": "" + } + ], + "bodySite": { + "id": "", + "label": "" + }, + "dateOfProcedure": "", + "procedureCode": { + "id": "", + "label": "" + } + } + ], + "karyotypicSex": "", + "measures": [ + { + "assayCode": { + "id": "", + "label": "" + }, + "date": "", + "measurementValue": [ + { + "referenceRange": { + "high": 0, + "low": 0, + "unit": { + "id": "", + "label": "" + } + } + }, + { + "unit": { + "id": "", + "label": "" + }, + "value": 0, + "id": "", + "label": "" + }, + { + "typedQuantities": { + "quantity": { + "referenceRange": { + "high": 0, + "low": 0, + "unit": { + "id": "", + "label": "" + } + }, + "unit": { + "id": "", + "label": "" + }, + "value": 0 + } + } + } + ], + "notes": "", + "observationMoment": [ + { + "iso8601duration": "" + }, + { + "end": { + "iso8601duration": "" + }, + "start": { + "iso8601duration": "" + } + }, + { + "days": 0, + "weeks": 0 + }, + "", + { + "end": "", + "start": "" + }, + { + "id": "", + "label": "" + } + ], + "procedure": { + "ageAtProcedure": [ + { + "iso8601duration": "" + }, + { + "end": { + "iso8601duration": "" + }, + "start": { + "iso8601duration": "" + } + }, + { + "days": 0, + "weeks": 0 + }, + "", + { + "end": "", + "start": "" + }, + { + "id": "", + "label": "" + } + ], + "bodySite": { + "id": "", + "label": "" + }, + "dateOfProcedure": "", + "procedureCode": { + "id": "", + "label": "" + } + } + } + ], + "pedigrees": [ + { + "disease": { + "ageOfOnset": [ + { + "iso8601duration": "" + }, + { + "end": { + "iso8601duration": "" + }, + "start": { + "iso8601duration": "" + } + }, + { + "days": 0, + "weeks": 0 + }, + "", + { + "end": "", + "start": "" + }, + { + "id": "", + "label": "" + } + ], + "diseaseCode": { + "id": "", + "label": "" + }, + "familyHistory": true, + "notes": "", + "severity": { + "id": "", + "label": "" + }, + "stage": { + "id": "", + "label": "" + } + }, + "id": "", + "members": { + "affected": true, + "memberId": "", + "role": { + "id": "", + "label": "" + } + } + } + ], + "phenotypicFeatures": [ + { + "evidence": { + "evidenceCode": { + "id": "", + "label": "" + }, + "reference": { + "id": "", + "notes": "", + "reference": "" + } + }, + "excluded": true, + "featureType": { + "id": "", + "label": "" + }, + "modifiers": [ + { + "id": "", + "label": "" + } + ], + "notes": "", + "onset": [ + { + "iso8601duration": "" + }, + { + "end": { + "iso8601duration": "" + }, + "start": { + "iso8601duration": "" + } + }, + { + "days": 0, + "weeks": 0 + }, + "", + { + "end": "", + "start": "" + }, + { + "id": "", + "label": "" + } + ], + "resolution": [ + { + "iso8601duration": "" + }, + { + "end": { + "iso8601duration": "" + }, + "start": { + "iso8601duration": "" + } + }, + { + "days": 0, + "weeks": 0 + }, + "", + { + "end": "", + "start": "" + }, + { + "id": "", + "label": "" + } + ], + "severity": { + "id": "", + "label": "" + } + } + ], + "sex": { + "id": "", + "label": "" + }, + "treatments": [ + { + "ageAtOnset": { + "iso8601duration": "" + }, + "cumulativeDose": { + "referenceRange": { + "id": "", + "label": "" + }, + "unit": {} + }, + "doseIntervals": [ + { + "id": "", + "label": "" + } + ], + "routeOfAdministration": { + "id": "", + "label": "" + }, + "treatmentCode": { + "id": "", + "label": "" + } + } + ] +} \ No newline at end of file diff --git a/ri-tools/files/headers/cohorts.txt b/ri-tools/files/headers/cohorts.txt index 086d690..ad3b1fd 100644 --- a/ri-tools/files/headers/cohorts.txt +++ b/ri-tools/files/headers/cohorts.txt @@ -57,8 +57,6 @@ exclusionCriteria|phenotypicConditions|onset exclusionCriteria|phenotypicConditions|resolution exclusionCriteria|phenotypicConditions|severity|id exclusionCriteria|phenotypicConditions|severity|label -exclusionCriteria|type|availability -exclusionCriteria|type|availabilityCount id inclusionCriteria|ageRange inclusionCriteria|ageRange|end|iso8601duration @@ -89,6 +87,4 @@ inclusionCriteria|phenotypicConditions|onset inclusionCriteria|phenotypicConditions|resolution inclusionCriteria|phenotypicConditions|severity|id inclusionCriteria|phenotypicConditions|severity|label -inclusionCriteria|type|availability -inclusionCriteria|type|availabilityCount -name +name \ No newline at end of file diff --git a/ri-tools/files/headers/individuals.txt b/ri-tools/files/headers/individuals.txt index 647acfd..6c8a4e7 100644 --- a/ri-tools/files/headers/individuals.txt +++ b/ri-tools/files/headers/individuals.txt @@ -137,4 +137,4 @@ treatments|doseIntervals|label treatments|routeOfAdministration|id treatments|routeOfAdministration|label treatments|treatmentCode|id -treatments|treatmentCode|label +treatments|treatmentCode|label \ No newline at end of file