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OpenBisClient.java
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OpenBisClient.java
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package life.qbic.openbis.openbisclient;
import static life.qbic.openbis.openbisclient.helper.OpenBisClientHelper.fetchDataSetsCompletely;
import static life.qbic.openbis.openbisclient.helper.OpenBisClientHelper.fetchExperimentTypesCompletely;
import static life.qbic.openbis.openbisclient.helper.OpenBisClientHelper.fetchExperimentsCompletely;
import static life.qbic.openbis.openbisclient.helper.OpenBisClientHelper.fetchProjectsCompletely;
import static life.qbic.openbis.openbisclient.helper.OpenBisClientHelper.fetchSampleTypesCompletely;
import static life.qbic.openbis.openbisclient.helper.OpenBisClientHelper.fetchSamplesCompletely;
import ch.ethz.sis.openbis.generic.asapi.v3.IApplicationServerApi;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.attachment.Attachment;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.common.interfaces.IEntityType;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.common.search.SearchResult;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.dataset.DataSet;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.dataset.DataSetType;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.dataset.fetchoptions.DataSetTypeFetchOptions;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.dataset.search.DataSetSearchCriteria;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.dataset.search.DataSetTypeSearchCriteria;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.experiment.Experiment;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.experiment.ExperimentType;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.experiment.fetchoptions.ExperimentFetchOptions;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.experiment.fetchoptions.ExperimentTypeFetchOptions;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.experiment.id.ExperimentIdentifier;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.experiment.id.IExperimentId;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.experiment.search.ExperimentSearchCriteria;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.experiment.search.ExperimentTypeSearchCriteria;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.person.Person;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.person.fetchoptions.PersonFetchOptions;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.person.search.PersonSearchCriteria;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.project.Project;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.project.fetchoptions.ProjectFetchOptions;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.project.id.IProjectId;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.project.id.ProjectIdentifier;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.project.search.ProjectSearchCriteria;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.property.PropertyType;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.property.fetchoptions.PropertyAssignmentFetchOptions;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.roleassignment.Role;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.roleassignment.RoleAssignment;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.sample.Sample;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.sample.SampleType;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.sample.fetchoptions.SampleFetchOptions;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.sample.fetchoptions.SampleTypeFetchOptions;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.sample.id.SampleIdentifier;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.sample.search.SampleSearchCriteria;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.sample.search.SampleTypeSearchCriteria;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.space.Space;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.space.fetchoptions.SpaceFetchOptions;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.space.search.SpaceSearchCriteria;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.vocabulary.Vocabulary;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.vocabulary.VocabularyTerm;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.vocabulary.fetchoptions.VocabularyTermFetchOptions;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.vocabulary.search.VocabularyTermSearchCriteria;
import ch.ethz.sis.openbis.generic.asapi.v3.exceptions.NotFetchedException;
import ch.ethz.sis.openbis.generic.dssapi.v3.IDataStoreServerApi;
import ch.systemsx.cisd.common.exceptions.NotImplementedException;
import ch.systemsx.cisd.common.exceptions.UserFailureException;
import ch.systemsx.cisd.common.spring.HttpInvokerUtils;
import ch.systemsx.cisd.openbis.common.api.client.ServiceFinder;
import ch.systemsx.cisd.openbis.plugin.query.shared.api.v1.IQueryApiServer;
import life.qbic.openbis.openbisclient.helper.OpenBisClientHelper;
import java.io.InputStream;
import java.net.MalformedURLException;
import java.net.URL;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.HashMap;
import java.util.HashSet;
import java.util.List;
import java.util.Map;
import java.util.Set;
import org.apache.commons.lang.WordUtils;
import org.apache.commons.lang3.StringUtils;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
/**
* The type Open bis client.
*/
public class OpenBisClient implements IOpenBisClient {
private final int TIMEOUT = 100000;
private String userId, password, sessionToken, serviceURL, url;
private IApplicationServerApi v3;
private IDataStoreServerApi dss3;
private static final Logger logger = LogManager.getLogger(OpenBisClient.class);
/**
* Instantiates a new Open bis client.
*
* @param userId the user id
* @param password the password
* @param apiURL the api url
*/
public OpenBisClient(String userId, String password, String apiURL) {
this.userId = userId;
this.password = password;
this.serviceURL = apiURL + IApplicationServerApi.SERVICE_URL;
this.url = apiURL;
// get a reference to AS API
v3 = HttpInvokerUtils.createServiceStub(IApplicationServerApi.class, serviceURL, TIMEOUT);
dss3 = HttpInvokerUtils.createServiceStub(IDataStoreServerApi.class, serviceURL, TIMEOUT);
sessionToken = null;
}
/**
* Function map an integer value to a char
*
* @param i the integer value which should be mapped
* @return the resulting char value
*/
public static char mapToChar(int i) {
i += 48;
if (i > 57) {
i += 7;
}
return (char) i;
}
/**
* Function to generate the checksum for the given barcode string
*
* @param s the barcode string
* @return the checksum for the given barcode
*/
public static char checksum(String s) {
int i = 1;
int sum = 0;
for (int idx = 0; idx <= s.length() - 1; idx++) {
sum += (((int) s.charAt(idx))) * i;
i += 1;
}
return mapToChar(sum % 34);
}
/**
* Gets v 3.
*
* @return the v 3
*/
// TODO Added for testing reasons...
public IApplicationServerApi getV3() {
return v3;
}
/**
* Checks if we are logged in
*/
@Override
public boolean loggedin() {
try {
return v3.isSessionActive(sessionToken);
} catch (Exception e) {
return false;
}
}
/**
* logs out of the OpenBIS server
*/
@Override
public void logout() {
if (loggedin()) {
v3.logout(sessionToken);
// TODO Set sessionToken to null
sessionToken = null;
} else {
}
}
/**
* logs in to the OpenBIS server with the system userid after calling this function, the user has
* to provide the password
*/
@Override
public void login() {
if (loggedin()) {
logout();
}
// login to obtain a session token
sessionToken = v3.login(userId, password);
}
public void loginAsUser(String user) {
if (loggedin()) {
logout();
}
// login to obtain a session token
sessionToken = v3.loginAs(userId, password, user);
}
/**
* Get session token of current openBIS session
*
* @return session token as string
*/
@Override
public String getSessionToken() {
return sessionToken;
}
/**
* Checks if logged in, reconnects if not
*/
@Override
public void ensureLoggedIn() {
if (!this.loggedin()) {
this.login();
}
}
/**
* Function to get a list of all space identifiers which are registered in this openBIS instance
*
* @return list with the identifiers of all available spaces
*/
@Override
public List<String> listSpaces() {
ensureLoggedIn();
SearchResult<Space> spaces =
v3.searchSpaces(sessionToken, new SpaceSearchCriteria(), new SpaceFetchOptions());
List<String> spaceIdentifiers = new ArrayList<>();
for (Space space : spaces.getObjects()) {
spaceIdentifiers.add(space.getCode());
}
return spaceIdentifiers;
}
/**
* Function to get all projects which are registered in this openBIS instance
*
* @return list with all projects which are registered in this openBIS instance
*/
@Override
public List<Project> listProjects() {
ensureLoggedIn();
SearchResult<Project> projects =
v3.searchProjects(sessionToken, new ProjectSearchCriteria(), fetchProjectsCompletely());
return projects.getObjects();
}
/**
* Function to list all Experiments which are registered in the openBIS instance.
*
* @return list with all experiments registered in this openBIS instance
*/
@Override
public List<Experiment> listExperiments() {
ensureLoggedIn();
SearchResult<Experiment> experiments = v3.searchExperiments(sessionToken,
new ExperimentSearchCriteria(), fetchExperimentsCompletely());
return experiments.getObjects();
}
/**
* Function to retrieve all samples of a given experiment Note: seems to throw a
* ch.systemsx.cisd.common.exceptions.UserFailureException if wrong identifier given TODO Should
* we catch it and throw an illegalargumentexception instead? would be a lot clearer in my opinion
*
* @param experimentIdentifier identifier/code (both should work) of the openBIS experiment
* @return list with all samples of the given experiment
*/
@Override
public List<Sample> getSamplesofExperiment(String experimentIdentifier) {
ensureLoggedIn();
SampleSearchCriteria sampleSearchCriteria = new SampleSearchCriteria();
sampleSearchCriteria.withExperiment().withCode().thatEquals(experimentIdentifier);
SearchResult<Sample> samplesOfExperiment =
v3.searchSamples(sessionToken, sampleSearchCriteria, fetchSamplesCompletely());
return samplesOfExperiment.getObjects();
}
/**
* Function to retrieve all samples of a given space
*
* @param spaceIdentifier identifier of the openBIS space
* @return list with all samples of the given space
*/
@Override
public List<Sample> getSamplesofSpace(String spaceIdentifier) {
ensureLoggedIn();
SampleSearchCriteria sampleSearchCriteria = new SampleSearchCriteria();
sampleSearchCriteria.withSpace().withCode().thatEquals(spaceIdentifier);
SearchResult<Sample> samplesOfExperiment =
v3.searchSamples(sessionToken, sampleSearchCriteria, fetchSamplesCompletely());
return samplesOfExperiment.getObjects();
}
@Override
public Sample getSampleByIdentifier(String sampleIdentifier) {
ensureLoggedIn();
SampleSearchCriteria sampleSearchCriteria = new SampleSearchCriteria();
sampleSearchCriteria.withId().thatEquals(new SampleIdentifier(sampleIdentifier));
SearchResult<Sample> samples =
v3.searchSamples(sessionToken, sampleSearchCriteria, fetchSamplesCompletely());
if (samples.getObjects().isEmpty()) {
return null;
} else {
return samples.getObjects().get(0);
}
}
@Override
public List<PropertyType> getPropertiesOfExperimentType(ExperimentType type) {
ensureLoggedIn();
ExperimentTypeSearchCriteria criteria = new ExperimentTypeSearchCriteria();
criteria.withCode().thatEquals(type.getCode());
ExperimentTypeFetchOptions options = new ExperimentTypeFetchOptions();
PropertyAssignmentFetchOptions paFetchOptions = new PropertyAssignmentFetchOptions();
paFetchOptions.withPropertyType();
options.withPropertyAssignmentsUsing(paFetchOptions);
List<IEntityType> res = new ArrayList<>();
res.addAll(v3.searchExperimentTypes(sessionToken, criteria, options).getObjects());
if (res.isEmpty()) {
throw new NotFetchedException("Experiment type could not be found: " + type.getCode());
}
if (res.size() > 1) {
throw new NotFetchedException("More than one entity type found for: " + type.getCode());
}
IEntityType typeWithProperties = res.get(0);
return OpenBisClientHelper.getPropertiesOfEntityType(typeWithProperties);
}
@Override
public List<PropertyType> getPropertiesOfSampleType(SampleType type) {
ensureLoggedIn();
SampleTypeSearchCriteria criteria = new SampleTypeSearchCriteria();
criteria.withCode().thatEquals(type.getCode());
SampleTypeFetchOptions options = new SampleTypeFetchOptions();
PropertyAssignmentFetchOptions paFetchOptions = new PropertyAssignmentFetchOptions();
paFetchOptions.withPropertyType();
options.withPropertyAssignmentsUsing(paFetchOptions);
List<IEntityType> res = new ArrayList<>();
res.addAll(v3.searchSampleTypes(sessionToken, criteria, options).getObjects());
if (res.isEmpty()) {
throw new NotFetchedException("Sample type could not be found: " + type.getCode());
}
if (res.size() > 1) {
throw new NotFetchedException("More than one entity type found for: " + type.getCode());
}
IEntityType typeWithProperties = res.get(0);
return OpenBisClientHelper.getPropertiesOfEntityType(typeWithProperties);
}
@Override
public List<PropertyType> getPropertiesOfDataSetType(DataSetType type) {
ensureLoggedIn();
DataSetTypeSearchCriteria criteria = new DataSetTypeSearchCriteria();
criteria.withCode().thatEquals(type.getCode());
DataSetTypeFetchOptions options = new DataSetTypeFetchOptions();
PropertyAssignmentFetchOptions paFetchOptions = new PropertyAssignmentFetchOptions();
paFetchOptions.withPropertyType();
options.withPropertyAssignmentsUsing(paFetchOptions);
List<IEntityType> res = new ArrayList<>();
res.addAll(v3.searchDataSetTypes(sessionToken, criteria, options).getObjects());
if (res.isEmpty()) {
throw new NotFetchedException("DataSet type could not be found: " + type.getCode());
}
if (res.size() > 1) {
throw new NotFetchedException("More than one entity type found for: " + type.getCode());
}
IEntityType typeWithProperties = res.get(0);
return OpenBisClientHelper.getPropertiesOfEntityType(typeWithProperties);
}
@Override
public List<Sample> getSamplesOfProject(String projIdentifier) {
ensureLoggedIn();
SampleSearchCriteria sampleSearchCriteria = new SampleSearchCriteria();
sampleSearchCriteria.withOrOperator();
sampleSearchCriteria.withExperiment().withProject().withCode().thatEquals(projIdentifier);
sampleSearchCriteria.withExperiment().withProject().withId()
.thatEquals(new ProjectIdentifier(projIdentifier));
SearchResult<Sample> samples =
v3.searchSamples(sessionToken, sampleSearchCriteria, fetchSamplesCompletely());
return samples.getObjects();
}
/**
* Function to get a sample with its parents and children
*
* @param sampCode code of the openBIS sample
* @return sample
*/
@Override
public List<Sample> getSamplesWithParentsAndChildren(String sampCode) {
// TODO unclear if parents and children should be fetched or directly included into the list
ensureLoggedIn();
SampleSearchCriteria sampleSearchCriteria = new SampleSearchCriteria();
sampleSearchCriteria.withCode().thatEquals(sampCode);
SearchResult<Sample> samples =
v3.searchSamples(sessionToken, sampleSearchCriteria, fetchSamplesCompletely());
return samples.getObjects();
}
@Override
public List<Experiment> getExperimentsOfProjectByIdentifier(String projectIdentifier) {
ensureLoggedIn();
ExperimentSearchCriteria sc = new ExperimentSearchCriteria();
sc.withOrOperator();
sc.withProject().withId().thatEquals(new ProjectIdentifier(projectIdentifier));
sc.withProject().withCode().thatEquals(projectIdentifier);
SearchResult<Experiment> experiments =
v3.searchExperiments(sessionToken, sc, fetchExperimentsCompletely());
return experiments.getObjects();
}
/**
* Function to list all Experiments for a specific project which are registered in the openBIS
* instance. av: 19353 ms
*
* @param project the project for which the experiments should be listed
* @return list with all experiments registered in this openBIS instance
*/
@Override
public List<Experiment> getExperimentsForProject(Project project) {
ensureLoggedIn();
ExperimentSearchCriteria sc = new ExperimentSearchCriteria();
sc.withProject().withCode().thatEquals(project.getCode());
SearchResult<Experiment> experiments =
v3.searchExperiments(sessionToken, sc, fetchExperimentsCompletely());
return experiments.getObjects();
}
/**
* Function to list all Experiments for a specific project which are registered in the openBIS
* instance.
*
* @param projectIdentifier project identifer as defined by openbis, for which the experiments
* should be listed
* @return list with all experiments registered in this openBIS instance
*/
@Override
public List<Experiment> getExperimentsForProject(String projectIdentifier) {
// TODO equal to getExperimentsOfProjectByIdentifier
ensureLoggedIn();
return getExperimentsOfProjectByIdentifier(projectIdentifier);
}
@Override
public List<Experiment> getExperimentsOfProjectByCode(String projectCode) {
// TODO Could be combined with getExperimentsOfProjectByIdentifier
ensureLoggedIn();
ExperimentSearchCriteria sc = new ExperimentSearchCriteria();
sc.withProject().withCode().thatEquals(projectCode);
SearchResult<Experiment> experiments =
v3.searchExperiments(sessionToken, sc, fetchExperimentsCompletely());
return experiments.getObjects();
}
@Override
public Map<String, List<Experiment>> getProjectExperimentMapping(String spaceIdentifier) {
Map<String, List<Experiment>> projectExperimentMapping = new HashMap<>();
List<Project> projects = getProjectsOfSpace(spaceIdentifier);
for (Project project : projects) {
String code = project.getCode();
projectExperimentMapping.put(code, getExperimentsOfProjectByCode(code));
}
return projectExperimentMapping;
}
@Override
public List<Experiment> getExperimentsOfSpace(String spaceIdentifier) {
ensureLoggedIn();
ExperimentSearchCriteria sc = new ExperimentSearchCriteria();
sc.withProject().withSpace().withCode().thatEquals(spaceIdentifier);
SearchResult<Experiment> experiments =
v3.searchExperiments(sessionToken, sc, fetchExperimentsCompletely());
return experiments.getObjects();
}
@Override
public List<Experiment> getExperimentsOfType(String type) {
ensureLoggedIn();
ExperimentSearchCriteria sc = new ExperimentSearchCriteria();
sc.withType().withCode().thatEquals(type);
SearchResult<Experiment> experiments =
v3.searchExperiments(sessionToken, sc, fetchExperimentsCompletely());
return experiments.getObjects();
}
@Override
public List<Sample> getSamplesOfType(String type) {
ensureLoggedIn();
SampleSearchCriteria sampleSearchCriteria = new SampleSearchCriteria();
sampleSearchCriteria.withType().withCode().thatEquals(type);
SearchResult<Sample> samples =
v3.searchSamples(sessionToken, sampleSearchCriteria, fetchSamplesCompletely());
return samples.getObjects();
}
@Override
public List<Project> getProjectsOfSpace(String space) {
ensureLoggedIn();
ProjectSearchCriteria sc = new ProjectSearchCriteria();
sc.withSpace().withCode().thatEquals(space);
SearchResult<Project> projects = v3.searchProjects(sessionToken, sc, fetchProjectsCompletely());
return projects.getObjects();
}
/**
* Returns Space names a given user should be able to see
*
* @param userID Username found in openBIS
* @return List of space names with projects this user has access to
*/
@Override
public List<String> getUserSpaces(String userID) {
// this sets the user sessionToken
loginAsUser(userID);
List<String> spaceIdentifiers = new ArrayList<>();
// we are not using external functions to make sure this user is actually used
try {
SearchResult<Space> spaces =
v3.searchSpaces(sessionToken, new SpaceSearchCriteria(), new SpaceFetchOptions());
if (spaces != null) {
for (Space space : spaces.getObjects()) {
spaceIdentifiers.add(space.getCode());
}
}
} catch (UserFailureException u) {
logger.error("Could not fetch spaces for user " + userID
+ ", because they could not be logged in. Is user " + this.userId + " an admin user?");
logger.warn("No spaces were returned.");
}
logout();
login();
return spaceIdentifiers;
}
/**
* Returns wether a user is instance admin in openBIS
*
* @return true, if user is instance admin, false otherwise
*/
@Override
public boolean isUserAdmin(String userID) {
ensureLoggedIn();
PersonSearchCriteria criteria = new PersonSearchCriteria();
criteria.withUserId().thatEquals(userID);
PersonFetchOptions options = new PersonFetchOptions();
options.withRoleAssignments();
SearchResult<Person> res = v3.searchPersons(sessionToken, criteria, options);
for (Person p : res.getObjects()) {
for (RoleAssignment r : p.getRoleAssignments()) {
if (r.getRole().equals(Role.ADMIN)) {
return true;
}
}
}
return false;
}
@Override
public Project getProjectByIdentifier(String projectIdentifier) {
ensureLoggedIn();
ProjectSearchCriteria sc = new ProjectSearchCriteria();
sc.withOrOperator();
sc.withId().thatEquals(new ProjectIdentifier(projectIdentifier));
sc.withCode().thatEquals(projectIdentifier);
SearchResult<Project> projects = v3.searchProjects(sessionToken, sc, fetchProjectsCompletely());
if (projects.getObjects().isEmpty()) {
return null;
} else {
return projects.getObjects().get(0);
}
}
@Override
public Project getProjectByCode(String projectCode) {
ensureLoggedIn();
ProjectSearchCriteria sc = new ProjectSearchCriteria();
sc.withOrOperator();
sc.withId().thatEquals(new ProjectIdentifier(projectCode));
sc.withCode().thatEquals(projectCode);
SearchResult<Project> projects = v3.searchProjects(sessionToken, sc, fetchProjectsCompletely());
if (projects.getObjects().isEmpty()) {
return null;
} else {
return projects.getObjects().get(0);
}
}
@Override
public Experiment getExperimentByCode(String experimentCode) {
ensureLoggedIn();
ExperimentSearchCriteria sc = new ExperimentSearchCriteria();
sc.withCode().thatEquals(experimentCode);
SearchResult<Experiment> experiments =
v3.searchExperiments(sessionToken, sc, fetchExperimentsCompletely());
if (experiments.getObjects().isEmpty()) {
return null;
} else {
return experiments.getObjects().get(0);
}
}
@Override
public Experiment getExperimentById(String experimentId) {
ensureLoggedIn();
ExperimentSearchCriteria sc = new ExperimentSearchCriteria();
sc.withOrOperator();
sc.withId().thatEquals(new ExperimentIdentifier(experimentId));
SearchResult<Experiment> experiment =
v3.searchExperiments(sessionToken, sc, fetchExperimentsCompletely());
if (experiment.getObjects().isEmpty()) {
return null;
}
return experiment.getObjects().get(0);
}
@Override
public Project getProjectOfExperimentByIdentifier(String experimentIdentifier) {
ensureLoggedIn();
ExperimentSearchCriteria sc = new ExperimentSearchCriteria();
sc.withId().thatEquals(new ExperimentIdentifier(experimentIdentifier));
SearchResult<Experiment> experiments =
v3.searchExperiments(sessionToken, sc, fetchExperimentsCompletely());
if (experiments.getObjects().isEmpty()) {
return null;
} else {
return experiments.getObjects().get(0).getProject();
}
}
/**
* Function to list all datasets of a specific sample (watch out there are different dataset
* classes)
*
* @param sampleIdentifier identifier of the openBIS sample
* @return list with all datasets of the given sample
*/
@Override
public List<DataSet> getDataSetsOfSampleByIdentifier(String sampleIdentifier) {
DataSetSearchCriteria sc = new DataSetSearchCriteria();
sc.withOrOperator();
sc.withSample().withId().thatEquals(new SampleIdentifier(sampleIdentifier));
SearchResult<DataSet> dataSets = v3.searchDataSets(sessionToken, sc, fetchDataSetsCompletely());
return dataSets.getObjects();
}
/**
* Function to list all datasets of a specific sample (watch out there are different dataset
* classes)
*
* @param sampleCode code or identifier of the openBIS sample
* @return list with all datasets of the given sample
*/
@Override
public List<DataSet> getDataSetsOfSample(String sampleCode) {
DataSetSearchCriteria sc = new DataSetSearchCriteria();
sc.withSample().withCode().thatEquals(sampleCode);
SearchResult<DataSet> dataSets = v3.searchDataSets(sessionToken, sc, fetchDataSetsCompletely());
return dataSets.getObjects();
}
/**
* Function to list all datasets of a specific experiment (watch out there are different dataset
* classes)
*
* @param experimentPermID permId of the openBIS experiment
* @return list with all datasets of the given experiment
*/
@Override
public List<DataSet> getDataSetsOfExperiment(String experimentPermID) {
DataSetSearchCriteria sc = new DataSetSearchCriteria();
sc.withExperiment().withPermId().thatEquals(experimentPermID);
SearchResult<DataSet> dataSets = v3.searchDataSets(sessionToken, sc, fetchDataSetsCompletely());
return dataSets.getObjects();
}
/**
* Returns all datasets of a given experiment. The new version should run smoother
*
* @param experimentIdentifier identifier or code of the openbis experiment
* @return list of all datasets of the given experiment
*/
@Override
public List<DataSet> getDataSetsOfExperimentByIdentifier(String experimentIdentifier) {
DataSetSearchCriteria sc = new DataSetSearchCriteria();
sc.withExperiment().withId().thatEquals(new ExperimentIdentifier(experimentIdentifier));
SearchResult<DataSet> dataSets = v3.searchDataSets(sessionToken, sc, fetchDataSetsCompletely());
return dataSets.getObjects();
}
/**
* Function to list all datasets of a specific openBIS space
*
* @param spaceIdentifier identifier of the openBIS space
* @return list with all datasets of the given space
*/
@Override
public List<DataSet> getDataSetsOfSpaceByIdentifier(String spaceIdentifier) {
DataSetSearchCriteria sc = new DataSetSearchCriteria();
sc.withSample().withSpace().withCode().thatEquals(spaceIdentifier);
SearchResult<DataSet> dataSets = v3.searchDataSets(sessionToken, sc, fetchDataSetsCompletely());
return dataSets.getObjects();
}
/**
* Function to list all datasets of a specific openBIS project
*
* @param projectIdentifier identifier of the openBIS project
* @return list with all datasets of the given project
*/
@Override
public List<DataSet> getDataSetsOfProjectByIdentifier(String projectIdentifier) {
// TODO does not work yet
throw new NotImplementedException();
}
/**
* Function to list all datasets of a specific openBIS project
*
* @param projectIdentifier identifier of the openBIS project
* @return list with all datasets of the given project
*/
@Override
public List<DataSet> getDataSetsOfProjects(List<Project> projectIdentifier) {
// TODO does not work yet
throw new NotImplementedException();
}
@Override
public List<DataSet> getDataSetsByType(String type) {
ensureLoggedIn();
DataSetSearchCriteria sc = new DataSetSearchCriteria();
sc.withType().withCode().thatEquals(type);
SearchResult<DataSet> dataSets = v3.searchDataSets(sessionToken, sc, fetchDataSetsCompletely());
return dataSets.getObjects();
}
@Override
public List<Attachment> listAttachmentsForSampleByIdentifier(String sampleIdentifier) {
ensureLoggedIn();
return getSampleByIdentifier(sampleIdentifier).getAttachments();
}
@Override
public List<Attachment> listAttachmentsForProjectByIdentifier(String projectIdentifier) {
ensureLoggedIn();
return getProjectByIdentifier(projectIdentifier).getAttachments();
}
/**
* Returns all users of a Space.
*
* @param spaceCode code of the openBIS space
* @return set of user names as string
*/
@Override
public Set<String> getSpaceMembers(String spaceCode) {
// TODO cannot find an opportunity to do that
return null;
}
/**
* Function to list the vocabulary codes for a given property which has been added to openBIS. The
* property has to be a Controlled Vocabulary Property. Use
*
* @param property the property type
* @return list of the vocabulary terms of the given property
*/
@Override
public List<String> listVocabularyTermsForProperty(PropertyType property) {
throw new NotImplementedException();
}
/**
* Function to get the label of a CV item for some property
*
* @param propertyType the property type
* @param propertyValue the property value
* @return Label of CV item
*/
@Override
public String getCVLabelForProperty(PropertyType propertyType, String propertyValue) {
throw new NotImplementedException();
}
@Override
public SampleType getSampleTypeByString(String sampleType) {
SampleTypeSearchCriteria sc = new SampleTypeSearchCriteria();
sc.withCode().thatEquals(sampleType);
SearchResult<SampleType> sampleTypes =
v3.searchSampleTypes(sessionToken, sc, fetchSampleTypesCompletely());
if (sampleTypes.getObjects().isEmpty()) {
return null;
} else {
return sampleTypes.getObjects().get(0);
}
}
/**
* Function to retrieve a map with sample type code as key and the sample type object as value
*
* @return map with sample types
*/
@Override
public Map<String, SampleType> getSampleTypes() {
SearchResult<SampleType> sampleTypes = v3.searchSampleTypes(sessionToken,
new SampleTypeSearchCriteria(), fetchSampleTypesCompletely());
Map<String, SampleType> types = new HashMap<>();
for (SampleType t : sampleTypes.getObjects()) {
types.put(t.getCode(), t);
}
return types;
}
/**
* Function to get a ExperimentType object of a experiment type
*
* @param experimentType the experiment type as string
* @return the ExperimentType object of the corresponding experiment type
*/
@Override
public ExperimentType getExperimentTypeByString(String experimentType) {
ExperimentTypeSearchCriteria sc = new ExperimentTypeSearchCriteria();
sc.withCode().thatContains(experimentType);
SearchResult<ExperimentType> experimentTypes =
v3.searchExperimentTypes(sessionToken, sc, fetchExperimentTypesCompletely());
if (experimentTypes.getObjects().isEmpty()) {
return null;
} else {
return experimentTypes.getObjects().get(0);
}
}
/**
* Function to trigger ingestion services registered in openBIS
*
* @param serviceName name of the ingestion service which should be triggered
* @param parameters map with needed information for registration process
* @return object name of the QueryTableModel which is returned by the aggregation service
*/
@Override
public String triggerIngestionService(String serviceName, Map<String, Object> parameters) {
return null;
}
@Override
public String generateBarcode(String proj, int number_of_samples_offset) {
Project project = getProjectByIdentifier(proj);
int numberOfSamples = getSamplesOfProject(project.getCode()).size();
String barcode = project.getCode() + String.format("%03d", (numberOfSamples + 1)) + "S";
barcode += checksum(barcode);
return barcode;
}
/**
* Function to transform openBIS entity type to human readable text. Performs String replacement
* and does not query openBIS!
*
* @param entityCode the entity code as string
* @return entity code as string in human readable text
*/
@Override
public String openBIScodeToString(String entityCode) {
entityCode = WordUtils.capitalizeFully(entityCode.replace("_", " ").toLowerCase());
String edit_string = entityCode.replace("Ngs", "NGS").replace("Hla", "HLA")
.replace("Rna", "RNA").replace("Dna", "DNA").replace("Ms", "MS");
if (edit_string.startsWith("Q ")) {
edit_string = edit_string.replace("Q ", "");
}
return edit_string;
}
/**
* Function to get the download url for a file stored in the openBIS datastore server. Note that
* this method does no checks, whether datasetcode or openbisFilename do exist. Deprecated: Use
* getUrlForDataset() instead
*
* @param dataSetCode code of the openBIS dataset
* @param openbisFilename name of the file stored in the given dataset
* @return URL object of the download url for the given file
* @throws MalformedURLException Returns an download url for the openbis dataset with the given
* code and dataset_type. Throughs MalformedURLException if a url can not be created from
* the given parameters. NOTE: datastoreURL differs from serverURL only by the port ->
* quick hack used
*/
@Override
public URL getDataStoreDownloadURL(String dataSetCode, String openbisFilename)
throws MalformedURLException {
String base = this.serviceURL.split(".de")[0] + ".de";
String downloadURL = base + ":444";
downloadURL += "/datastore_server/";
downloadURL += dataSetCode;
downloadURL += "/original/";
downloadURL += openbisFilename;
downloadURL += "?mode=simpleHtml&sessionID=";
downloadURL += this.getSessionToken();
return new URL(downloadURL);
}
@Override
public URL getDataStoreDownloadURLLessGeneric(String dataSetCode, String openbisFilename)
throws MalformedURLException {
String base = this.serviceURL.split(".de")[0] + ".de";
String downloadURL = base + ":444";
downloadURL += "/datastore_server/";
downloadURL += dataSetCode;
downloadURL += "/";
downloadURL += openbisFilename;
downloadURL += "?mode=simpleHtml&sessionID=";
downloadURL += this.getSessionToken();
return new URL(downloadURL);
}
@Override
public Map<Sample, List<Sample>> getParentMap(List<Sample> samples) {
Map<Sample, List<Sample>> parentMap = new HashMap<>();
for (Sample sample : samples) {
List<Sample> parents = new ArrayList<>();
try {
parents = sample.getParents();
} catch (Exception e) {
logger.warn("Parents of sample were not available, contacting openBIS to fetch them.");
List<Sample> samplesWithParents = getSamplesWithParentsAndChildren(sample.getCode());
for (Sample s : samplesWithParents) {
parents.addAll(s.getParents());
}
}
parentMap.put(sample, parents);
}
return parentMap;
}