feat: update flat model and demo data (#4169)

backend/molgenis-emx2-typescript/src/test/resources/expected-catalogue-types.ts

@@ -1,4 +1,4 @@
-// Generated (on: 2024-08-22T10:48:44.823278) from Generator.java for schema: catalogue
+// Generated (on: 2024-09-02) from Generator.java for schema: catalogue
 
 export interface IFile {
     id?: string;
@@ -329,8 +329,6 @@ export interface ICollections {
     recordTrigger?: string;
     subcohorts?: ICollectionSubcohorts[];
     collectionEvents?: ICollectionEvents[];
-    datasets?: ICollectionDatasets[];
-    samplesets?: ICollectionSamplesets[];
     collections?: ICollections[];
     partOfCollections?: ICollections[];
     numberOfParticipants?: number;
@@ -356,6 +354,8 @@ export interface ICollections {
     peopleInvolved?: ICollectionContacts[];
     organisationsInvolved?: ICollectionOrganisations[];
     networksInvolved?: ICollections[];
+    datasets?: ICollectionDatasets[];
+    samplesets?: ICollectionSamplesets[];
     areasOfInformation?: IOntologyNode[];
     areasOfInformationRwd?: IOntologyNode[];
     qualityOfLifeOther?: string;
@@ -377,9 +377,8 @@ export interface ICollections {
     hasIdentifier?: boolean;
     identifierDescription?: string;
     prelinked?: boolean;
-    linkageDescription?: string;
+    linkageOptions?: string;
     linkagePossibility?: boolean;
-    linkagePossibilityDescription?: string;
     linkedCollections?: ICollectionLinkages[];
     informedConsentType?: IOntologyNode;
     informedConsentRequired?: IOntologyNode;

data/_demodata/applications/datacatalogue/Catalogues.csv

@@ -1,9 +1,9 @@
-network,type,description
-LifeCycle,project,a description about the project
-ATHLETE,project,a description about the project
-IPEC,theme,a description about the project
-EUChildNetwork,project,a description about the project
-OOM,project,a description about the project
-LongITools,project,a description about the project
-testNetwork1,theme,a description about the project
-testNetworkofNetworks,project,a description about the project
+network,type,publisher,name,description
+LifeCycle,project,,LifeCycle,to be filled out
+ATHLETE,project,,ATHLETE,to be filled out
+IPEC,theme,,IPEC,to be filled out
+EUChildNetwork,project,,EUChildNetwork,to be filled out
+OOM,project,,OOM,to be filled out
+LongITools,project,,LongITools,to be filled out
+testNetwork1,theme,,testNetwork1,to be filled out
+testNetworkofNetworks,project,,testNetworkofNetworks,to be filled out

data/_demodata/applications/datacatalogue/Contacts.csv → data/_demodata/applications/datacatalogue/Collection contacts.csv

@@ -1,4 +1,4 @@
-resource,role,role description,first name,last name,prefix,initials,title,organisation,email,orcid,homepage,photo,photo_filename,expertise
+collection,role,role description,first name,last name,prefix,initials,title,organisation,email,orcid,homepage,photo,photo_filename,expertise
 ABCD,Primary contact,,Bob,Ross,,BR,dr.,,[email protected],0000-0033-1119-366,https://en.wikipedia.org/wiki/Bob_Ross,,,Painting
 ALSPAC,Principal Investigator,,Bob,Ross,,BR,dr.,,[email protected],0000-0033-1119-366,https://en.wikipedia.org/wiki/Bob_Ross,,,Painting
 ALSPAC,Primary contact,,Jack,Ross,,JR,prof.,,[email protected],0000-0033-1119-366,https://en.wikipedia.org/wiki/Bob_Ross,,,Carpenting

data/_demodata/applications/datacatalogue/Collection counts.csv

@@ -0,0 +1 @@
+collection,age group,population size,active size,no individuals with samples,mean observation years,mean years active,median age,proportion female

data/_demodata/applications/datacatalogue/Datasets.csv → data/_demodata/applications/datacatalogue/Collection datasets.csv

@@ -1,7 +1,7 @@
-resource,name,label,unit of observation,keywords,description,number of rows,since version,until version
+collection,name,label,unit of observation,keywords,description,number of rows,since version,until version
 testCohort3,test dataset for testCohort3,,,,,,,
 testCohort4,test dataset for testCohort4,,,,,,,
-testNetwork1_CDM,cdm_1,,,,,,,
+testNetwork1,cdm_1,,,,,,,
 G21,child,child,person,,,,1,
 G21,blood_pressure,blood pressure,,,blood pressure of the child measured during G21 cohort follow-ups,,1.0.0,
 ENVIRONAGE,measurements after birth,,,,,,,
@@ -39,28 +39,28 @@ SPA,SPA,,,,,,1.0,
 SPECIALISTICA,SPECIALISTICA,,,,,,1.0,
 SPF,SPF,,,,,,1.0,
 VCN,VCN,,,,,,1.0,
-OOM_CDM,VISIT_OCCURRENCE,,,,,,2.2,
-OOM_CDM,EVENTS,,,,,,2.2,
-OOM_CDM,MEDICINES,,,,,,2.2,
-OOM_CDM,PROCEDURES,,,,,,2.2,
-OOM_CDM,VACCINES,,,,,,2.2,
-OOM_CDM,MEDICAL_OBSERVATIONS,,,,,,2.2,
-OOM_CDM,EUROCAT,,,,,,2.2,
-OOM_CDM,SURVEY_ID,,,,,,2.2,
-OOM_CDM,SURVEY_OBSERVATIONS,,,,,,2.2,
-OOM_CDM,PERSONS,,,,,,2.2,
-OOM_CDM,OBSERVATION_PERIODS,,,,,,2.2,
-OOM_CDM,PERSON_RELATIONSHIPS,,,,,,2.2,
-OOM_CDM,PRODUCTS,,,,,,2.2,
-OOM_CDM,METADATA,,,,,,2.2,
-OOM_CDM,CDM_SOURCE,,,,,,2.2,
-OOM_CDM,INSTANCE,,,,,,2.2,
-ATHLETE_CDM,outcome_ath,Outcome (ATHLETE),,,,,1.1.0,
-ATHLETE_CDM,chemicals_ath,Chemicals (ATHLETE),,,,,1.1.0,
-LifeCycle_CDM,core,,Patient,,,,1.0.0,
-LifeCycle_CDM,outcomes,,,,,,1.0.0,
-LifeCycle_CDM,outcome,,,,,,1.0.0,
-LongITools_CDM,wave_01,Wave 1 variables,,,Table of wave 1 variables for LongITools,,1.0.0,
+OOM,VISIT_OCCURRENCE,,,,,,2.2,
+OOM,EVENTS,,,,,,2.2,
+OOM,MEDICINES,,,,,,2.2,
+OOM,PROCEDURES,,,,,,2.2,
+OOM,VACCINES,,,,,,2.2,
+OOM,MEDICAL_OBSERVATIONS,,,,,,2.2,
+OOM,EUROCAT,,,,,,2.2,
+OOM,SURVEY_ID,,,,,,2.2,
+OOM,SURVEY_OBSERVATIONS,,,,,,2.2,
+OOM,PERSONS,,,,,,2.2,
+OOM,OBSERVATION_PERIODS,,,,,,2.2,
+OOM,PERSON_RELATIONSHIPS,,,,,,2.2,
+OOM,PRODUCTS,,,,,,2.2,
+OOM,METADATA,,,,,,2.2,
+OOM,CDM_SOURCE,,,,,,2.2,
+OOM,INSTANCE,,,,,,2.2,
+ATHLETE,outcome_ath,Outcome (ATHLETE),,,,,1.1.0,
+ATHLETE,chemicals_ath,Chemicals (ATHLETE),,,,,1.1.0,
+LifeCycle,core,,Patient,,,,1.0.0,
+LifeCycle,outcomes,,,,,,1.0.0,
+LifeCycle,outcome,,,,,,1.0.0,
+LongITools,wave_01,Wave 1 variables,,,Table of wave 1 variables for LongITools,,1.0.0,
 NFBC1966,core,,,,,,1.0.0,
 NFBC1966,wave_01,wave 1 variables,,,Wave 1 variables for NFBC1966,,1.0.0,
 PELAGIE,pelagie_q2,Questionnaire at 2 years old of the child,Patient,,Questionnaire at 2 years old of the child,,1.0.0,

data/_demodata/applications/datacatalogue/Documentation.csv → data/_demodata/applications/datacatalogue/Collection documentation.csv

@@ -1,4 +1,4 @@
-resource,name,type,description,url,file,file_filename
+collection,name,type,description,url,file,file_filename
 testCohort1,test documentation for cohort 1,Informed consent,test description of informed consent for cohort 1,https://umcgonline.sharepoint.com/:w:/r/sites/SGCohortcatalogues/Gedeelde%20documenten/Test%20activities%20Feb%2024/Test%20data/Test%20document%20for%20cohort%201%20informed%20consent.docx?d=w2aef48c74311495daab95ea93b432327&csf=1&web=1&e=TsEg9O,,
 testCohort2,test signed code of conduct for cohort 2,Signed code of conduct,description of test signed code of conduct for cohort 2,https://umcgonline.sharepoint.com/:w:/r/sites/SGCohortcatalogues/Gedeelde%20documenten/Test%20activities%20Feb%2024/Test%20data/Test%20document%20for%20cohort%202%20signed%20code%20of%20conduct.docx?d=w0cd34e6d7fb04918a25ca9fec2337f3f&csf=1&web=1&e=ORGQHI,,
 testCohort1,test doc 2 for test cohort 1,Procedure of data extraction,test description of the data extraction procedure for test doc 2 for test cohort 1,https://umcgonline.sharepoint.com/:w:/r/sites/SGCohortcatalogues/Gedeelde%20documenten/Test%20activities%20Feb%2024/Test%20data/Test%20doc%202%20for%20cohort%201%20procedure%20data%20extraction.docx?d=wbfb6619cf48a4fd8b33defd5c0359d38&csf=1&web=1&e=2Zivun,,