fix(directory): Add services to staging area template (#4555)

* Fix description of QualityInfoServices table

* Add Services table to data model

And refback from Biobanks

* Remove duplicate attribute

* Add demo data for Services

* Fix reference to Person id

* Remove capabilities from Biobanks (replaced by services)

* Update number of demo data files

* Remove capabilities from demo data as well

* Add ID validation

backend/molgenis-emx2-datamodels/src/test/java/org/molgenis/emx2/datamodels/TestLoaders.java

@@ -135,7 +135,7 @@ void test14DCATLoader() {
   void test15DirectoryStagingLoader() {
     Schema directoryStaging = database.createSchema(DIRECTORY_STAGING);
     DataModels.Regular.BIOBANK_DIRECTORY_STAGING.getImportTask(directoryStaging, false).run();
-    assertEquals(7, directoryStaging.getTableNames().size());
+    assertEquals(8, directoryStaging.getTableNames().size());
   }
 
   @Test

data/biobank-directory/molgenis.csv

@@ -164,9 +164,9 @@ Persons,,biobanks,Biobanks,refback,,false,true,Biobanks the person is connected
 Persons,,collections,Collections,refback,,false,true,Collections the person is connected to.,,Collections,contact,${name},,,,,
 Persons,,networks,Networks,refback,,false,true,Networks the person is connected to.,,Networks,contact,${name},,,,,
 Persons,,national_node,National Node,ref,,true,,The person originates from this national node.,,NationalNodes,,${description},,,,,
-QualityInfoServices,,,,,,,,Collection Quality Information,,,,,,,,,
+QualityInfoServices,,,,,,,,Service Quality Information,,,,,,,,,
 QualityInfoServices,,id,ID,auto_id,1,true,true,,,,,,,,,QIS-${mg_autoid},
-QualityInfoServices,,service,Collection,ref,,true,,,,Services,,${name},,,,,
+QualityInfoServices,,service,Service,ref,,true,,,,Services,,${name},,,,,
 QualityInfoServices,,qualityStandard,Quality Standard,ontology,,true,,,DirectoryOntologies,QualityStandards,,${label},,,,,
 QualityInfoServices,,assessmentLevel,Assessment Level,ontology,,true,,,DirectoryOntologies,AssessmentLevels,,${label},,,,,
 QualityInfoServices,,certificationNumber,Certification Number,string,,false,,,,,,,,,,,
@@ -185,7 +185,6 @@ Services,,tRL,Technology Readiness Level,ontology,,false,,Technology Readiness L
 Services,,accessDescription,Access Description,string,,true,,Description of the access policy of the service.,,,,,,,,,
 Services,,accessDescriptionUrl,Access Description URL,hyperlink,,false,,URL of the service access policy if available..,,,,,,,,,
 Services,,unitOfAccess,Unit of Access,string,,false,,Information about a standard unit used in calculations of costs of service provision.,,,,,,,,,
-Services,,accessDescription,Access Description,string,,true,,Description of the access policy of the service,,,,,,,,,
 Services,,unitCost,Unit Cost,string,,false,,Cost per unit.,,,,,,,,,
 Services,,qualityStandards,Quality Standards,refback,,false,true,The standards and/or technical specifications that the service is certified or accredited for.,,QualityInfoServices,service,${qualityStandard.label},,,,,
 Services,,contactInformation,Contact Information,ref,,false,,Contact information for the contact person or responsible person of the service,,Persons,,,,,,,

data/biobank-directory/stagingArea/demo/Biobanks.csv

@@ -1,3 +1,3 @@
-id,name,acronym,description,url,location,country,latitude,longitude,head,contact,juridical_person,network,also_known,capabilities,collaboration_commercial,collaboration_non_for_profit,withdrawn
-bbmri-eric:ID:DE_biobank1,Biobank1,bb1,The description of biobank1,,Berlin,DE,,,bbmri-eric:contactID:DE_head_bb1,bbmri-eric:contactID:DE_contact_bb1,A university,bbmri-eric:networkID:DE_network1,bbmri-eric:akiID:DE_00001,"covid19,nucleic-acid-extraction",true,false,false
-bbmri-eric:ID:NL_biobank2,Biobank2,bb2,The description of biobank2,,Amsterdam,NL,,,bbmri-eric:contactID:NL_person1,bbmri-eric:contactID:NL_person1,An institute,bbmri-eric:networkID:EU_network,bbmri-eric:akiID:NL_00001,"cell-culture,pathology-archive-access,Testing_Facility_Animal",false,true,false
+id,name,acronym,description,url,location,country,latitude,longitude,head,contact,juridical_person,network,also_known,collaboration_commercial,collaboration_non_for_profit,withdrawn
+bbmri-eric:ID:DE_biobank1,Biobank1,bb1,The description of biobank1,,Berlin,DE,,,bbmri-eric:contactID:DE_head_bb1,bbmri-eric:contactID:DE_contact_bb1,A university,bbmri-eric:networkID:DE_network1,bbmri-eric:akiID:DE_00001,true,false,false
+bbmri-eric:ID:NL_biobank2,Biobank2,bb2,The description of biobank2,,Amsterdam,NL,,,bbmri-eric:contactID:NL_person1,bbmri-eric:contactID:NL_person1,An institute,bbmri-eric:networkID:EU_network,bbmri-eric:akiID:NL_00001,false,true,false

data/biobank-directory/stagingArea/demo/Services.csv

@@ -0,0 +1,3 @@
+id,name,serviceTypes,acronym,description,descriptionUrl,device,deviceSystem,tRL,accessDescriptionUrl,unitOfAccess,accessDescription,unitCost,contactInformation,biobank
+bbmri-eric:serviceID:DE_1234,Biobank Service,"microbiome-analysis, sample-storage",,Service provided by this biobank,,,,TRL-4,,,https://myservice-access.de,,bbmri-eric:contactID:DE_contact_bb1,bbmri-eric:ID:DE_biobank1
+bbmri-eric:serviceID:NL_541,Dutch Biobank Service,"PET-Scans, TrainingResourceLabProtocols",,Services provided by Biobank2,,,,TRL-2,,,https://biobank2-service-access.nl,,,bbmri-eric:ID:NL_biobank2

data/biobank-directory/stagingArea/molgenis.csv

@@ -20,7 +20,7 @@ Biobanks,,juridical_person,Juridical Person,string,,true,,Juristic person of a b
 Biobanks,,network,Networks,ref_array,,false,,"Reference to a biobank network ID, to which the biobank belongs; this attribute can also be used for biobank network, where it refers to the superior biobank network.",,Networks,,${name},,,,,
 Biobanks,,also_known,Also Known In,ref_array,,false,,The biobank also exists in …,,AlsoKnownIn,,${name_system},,,,,
 Biobanks,,collections,Collections,refback,,false,,Collections belonging to the biobank.,,Collections,biobank,,,,,,
-Biobanks,,capabilities,Capabilities Provided,ontology_array,,false,,Capabilities that the biobank organisation can offer to a researcher.,DirectoryOntologies,Capabilities,,${label},,,,,
+Biobanks,,services,Services,refback,,false,,Capabilities and services that the biobank organisation can offer to a researcher.,,Services,biobank,${name},,,,,
 Biobanks,,collaboration_commercial,Commercial Collaboration,bool,,false,,The biobank can be used for collaboration with commercial partners.,,,,,,,,,
 Biobanks,,collaboration_non_for_profit,Non-for-profit Collaboration,bool,,false,,The biobank can be used for collaboration with non-for-profit partners.,,,,,,,,,
 Biobanks,,withdrawn,Withdrawn,bool,,true,,This biobank is withdrawn from the Directory.,,,,,false,,,,
@@ -129,4 +129,20 @@ Studies,,age_high,Age High,int,,false,,Age of oldest sample donor at time of sam
 Studies,,age_unit,Age Unit,ontology,,false,,"Unit defining Age Low and Age High. Can be one of the following values: YEAR, MONTH, WEEK, DAY - MIABIS-2.0-08.",DirectoryOntologies,AgeUnits,,${label},,,,,
 Studies,,number_of_subjects,Number of subjects,int,,false,,"The number of subjects that participated to the study",,,,,,,,,
 Studies,,also_known,Also Known In,ref_array,,false,,The study also exists in …,,AlsoKnownIn,,${name_system},,,,,
-Studies,,collections,Collections,refback,,false,true,,,Collections,studies,,,,,,
+Studies,,collections,Collections,refback,,false,true,,,Collections,studies,,,,,,
+Services,,,,,,,,Biobank Capabilities and Services,,,,,,,,,
+Services,,id,ID,string,1,true,,"Unique ID of the service, prefixed with bbmri-eric:serviceID:",,,,,,if(!/^bbmri-eric:serviceID:[\\w]+_[\\w-:]+$/.test(id))'ID should start with bbmri-eric:serviceID:{NationalNodeCode}_',,,
+Services,,name,Service Name,string,2,true,,Name of the service (preferably in English).,,,,,,,,,
+Services,,serviceTypes,Service Types,ref_array,,true,,Related service types,DirectoryOntologies,ServiceTypes,,${label},,,,,
+Services,,acronym,Acronym,string,,false,,Short name in use for the service. If applicable.,,,,,,,,,
+Services,,description,Description,string,,true,,Full description of the service (in English),,,,,,,,,
+Services,,descriptionUrl,Description URL,hyperlink,,false,,URL address of the service description if available.,,,,,,,,,
+Services,,device,Device,string,,false,,Name of the device(s) if the service is provided with the use of them.,,,,,,,,,
+Services,,deviceSystem,Device System,string,,false,,Name of a software system or platform if important for the device characteristics.,,,,,,,,,
+Services,,tRL,Technology Readiness Level,ontology,,false,,Technology Readiness Level - a concept for self-assessment of the service maturity,DirectoryOntologies,TRLs,,${label},,,,,
+Services,,accessDescription,Access Description,string,,true,,Description of the access policy of the service.,,,,,,,,,
+Services,,accessDescriptionUrl,Access Description URL,hyperlink,,false,,URL of the service access policy if available..,,,,,,,,,
+Services,,unitOfAccess,Unit of Access,string,,false,,Information about a standard unit used in calculations of costs of service provision.,,,,,,,,,
+Services,,unitCost,Unit Cost,string,,false,,Cost per unit.,,,,,,,,,
+Services,,contactInformation,Contact Information,ref,,false,,Contact information for the contact person or responsible person of the service,,Persons,,,,,,,
+Services,,biobank,Biobank,ref,,true,,"Reference to a biobank ID, to which the service belongs.",,Biobanks,,${name},,,,,