B C D E F G H I L M R S T U V

B

BbmriEricId - Class in de.samply.directory_sync.directory.model

This class represents a BBMRI-ERIC identifier which has the following form: bbmri-eric:ID:<country-code>_<suffix>

bbmriEricId(Organization) - Static method in class de.samply.directory_sync.fhir.FhirApi

Returns the BBMRI-ERIC identifier of collection if some valid one could be found.

Biobank - Class in de.samply.directory_sync.directory.model

Biobank() - Constructor for class de.samply.directory_sync.directory.model.Biobank

C

Collection - Class in de.samply.directory_sync.directory.model

Collection() - Constructor for class de.samply.directory_sync.directory.model.Collection

CollectionBundle - Class in de.samply.directory_sync.directory.model

CollectionBundle() - Constructor for class de.samply.directory_sync.directory.model.CollectionBundle

createResource(IBaseResource) - Method in class de.samply.directory_sync.fhir.FhirApi

createWithLogin(CloseableHttpClient, String, String, String) - Static method in class de.samply.directory_sync.directory.DirectoryApi

createWithToken(CloseableHttpClient, String, String) - Static method in class de.samply.directory_sync.directory.DirectoryApi

D

de.samply.directory_sync - package de.samply.directory_sync

de.samply.directory_sync.directory - package de.samply.directory_sync.directory

de.samply.directory_sync.directory.model - package de.samply.directory_sync.directory.model

de.samply.directory_sync.fhir - package de.samply.directory_sync.fhir

DirectoryApi - Class in de.samply.directory_sync.directory

DirectoryService - Class in de.samply.directory_sync.directory

DirectoryService(DirectoryApi) - Constructor for class de.samply.directory_sync.directory.DirectoryService

E

equals(Object) - Method in class de.samply.directory_sync.directory.model.BbmriEricId

F

fetchBiobank(BbmriEricId) - Method in class de.samply.directory_sync.directory.DirectoryApi

Fetches the Biobank with the given id.

fetchCollectionSizes() - Method in class de.samply.directory_sync.fhir.FhirReporting

Returns collection sample counts indexed by BBMRI-ERIC identifier.

FhirApi - Class in de.samply.directory_sync.fhir

Provides convenience methods for selected FHIR operations.

FhirApi(IGenericClient) - Constructor for class de.samply.directory_sync.fhir.FhirApi

FhirReporting - Class in de.samply.directory_sync.fhir

Provides functionality related to FHIR MeasureReports.

FhirReporting(FhirContext, FhirApi) - Constructor for class de.samply.directory_sync.fhir.FhirReporting

G

getAcronym() - Method in class de.samply.directory_sync.directory.model.Biobank

getAlso_known() - Method in class de.samply.directory_sync.directory.model.Biobank

getCountryCode() - Method in class de.samply.directory_sync.directory.model.BbmriEricId

Returns the two-letter upper-case country code of this identifier.

getDescription() - Method in class de.samply.directory_sync.directory.model.Biobank

getHead_firstname() - Method in class de.samply.directory_sync.directory.model.Biobank

getHead_lastname() - Method in class de.samply.directory_sync.directory.model.Biobank

getHead_role() - Method in class de.samply.directory_sync.directory.model.Biobank

getId() - Method in class de.samply.directory_sync.directory.model.Biobank

getIt_staff_site() - Method in class de.samply.directory_sync.directory.model.Biobank

getJuridical_person() - Method in class de.samply.directory_sync.directory.model.Biobank

getLatitude() - Method in class de.samply.directory_sync.directory.model.Biobank

getLongitude() - Method in class de.samply.directory_sync.directory.model.Biobank

getName() - Method in class de.samply.directory_sync.directory.model.Biobank

getUrl() - Method in class de.samply.directory_sync.directory.model.Biobank

H

hashCode() - Method in class de.samply.directory_sync.directory.model.BbmriEricId

I

initLibrary() - Method in class de.samply.directory_sync.fhir.FhirReporting

Tries to create Library and Measure resources if not present on the FHIR server.

initMeasure() - Method in class de.samply.directory_sync.fhir.FhirReporting

isCollaboration_commercial() - Method in class de.samply.directory_sync.directory.model.Biobank

isCollaboration_non_for_profit() - Method in class de.samply.directory_sync.directory.model.Biobank

isIs_available() - Method in class de.samply.directory_sync.directory.model.Biobank

isIt_support_available() - Method in class de.samply.directory_sync.directory.model.Biobank

isPartner_charter_signed() - Method in class de.samply.directory_sync.directory.model.Biobank

L

listAllBiobanks() - Method in class de.samply.directory_sync.fhir.FhirApi

Lists all Organization resources with the biobank profile.

listAllCollectionIds(String) - Method in class de.samply.directory_sync.directory.DirectoryApi

Make a call to the Directory to get all Collection IDs for the supplied countryCode.

listAllCollections() - Method in class de.samply.directory_sync.fhir.FhirApi

Lists all Organization resources with the collection profile.

M

Main - Class in de.samply.directory_sync

Main() - Constructor for class de.samply.directory_sync.Main

main(String[]) - Static method in class de.samply.directory_sync.Main

main(String[]) - Static method in class de.samply.directory_sync.Sync

mapOf() - Static method in class de.samply.directory_sync.Util

mapOf(K, V) - Static method in class de.samply.directory_sync.Util

R

resourceExists(Class<? extends IBaseResource>, String) - Method in class de.samply.directory_sync.fhir.FhirApi

Checks whether a resource of type and canonical uri exists.

S

setAcronym(String) - Method in class de.samply.directory_sync.directory.model.Biobank

setAlso_known(String[]) - Method in class de.samply.directory_sync.directory.model.Biobank

setCollaboration_commercial(boolean) - Method in class de.samply.directory_sync.directory.model.Biobank

setCollaboration_non_for_profit(boolean) - Method in class de.samply.directory_sync.directory.model.Biobank

setDescription(String) - Method in class de.samply.directory_sync.directory.model.Biobank

setHead_firstname(String) - Method in class de.samply.directory_sync.directory.model.Biobank

setHead_lastname(String) - Method in class de.samply.directory_sync.directory.model.Biobank

setHead_role(String) - Method in class de.samply.directory_sync.directory.model.Biobank

setId(BbmriEricId) - Method in class de.samply.directory_sync.directory.model.Biobank

setIs_available(boolean) - Method in class de.samply.directory_sync.directory.model.Biobank

setIt_staff_site(int) - Method in class de.samply.directory_sync.directory.model.Biobank

setIt_support_available(boolean) - Method in class de.samply.directory_sync.directory.model.Biobank

setJuridical_person(String) - Method in class de.samply.directory_sync.directory.model.Biobank

setLatitude(String) - Method in class de.samply.directory_sync.directory.model.Biobank

setLongitude(String) - Method in class de.samply.directory_sync.directory.model.Biobank

setName(String) - Method in class de.samply.directory_sync.directory.model.Biobank

setPartner_charter_signed(boolean) - Method in class de.samply.directory_sync.directory.model.Biobank

setUrl(String) - Method in class de.samply.directory_sync.directory.model.Biobank

Sync - Class in de.samply.directory_sync

Provides functionality to synchronize MOLGENIS directory and FHIR server in both directions.

Sync(FhirApi, FhirReporting, DirectoryApi, DirectoryService) - Constructor for class de.samply.directory_sync.Sync

syncCollectionSizesToDirectory() - Method in class de.samply.directory_sync.Sync

Updates collection sample count information for all collections that exist with the same BBMRI-ERIC identifier on the FHIR server and in the directory.

T

toString() - Method in class de.samply.directory_sync.directory.model.BbmriEricId

toString() - Method in class de.samply.directory_sync.directory.model.Biobank

U

updateAllBiobanksOnFhirServerIfNecessary() - Method in class de.samply.directory_sync.Sync

Updates all biobanks from the FHIR server with information from the Directory.

updateCollectionSizes(String, List<DirectoryApi.CollectionSizeDto>) - Method in class de.samply.directory_sync.directory.DirectoryApi

Send the collection sizes to the Directory.

updateCollectionSizes(Map<BbmriEricId, Integer>) - Method in class de.samply.directory_sync.directory.DirectoryService

updateCollectionSizes(String, List<Map.Entry<BbmriEricId, Integer>>) - Method in class de.samply.directory_sync.directory.DirectoryService

updateResource(IBaseResource) - Method in class de.samply.directory_sync.fhir.FhirApi

Util - Class in de.samply.directory_sync

Util() - Constructor for class de.samply.directory_sync.Util

V

valueOf(String) - Static method in class de.samply.directory_sync.directory.model.BbmriEricId

Tries to create a BBMRI-ERIC identifier from string.

B C D E F G H I L M R S T U V