diff --git a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/dss/reporting-plugins/exports-api/exports-api.py b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/dss/reporting-plugins/exports-api/exports-api.py
index 131b8f43235399e3741ed27de1c8db64213819a3..dd849b5fd28bd06642acba68e2f970c500be6331 100644
--- a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/dss/reporting-plugins/exports-api/exports-api.py
+++ b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/dss/reporting-plugins/exports-api/exports-api.py
@@ -32,21 +32,31 @@ from java.util.zip import ZipEntry;
from java.util.zip import ZipOutputStream;
#To obtain the openBIS URL
-from ch.systemsx.cisd.openbis.dss.generic.server import DataStoreServer
-OPENBISURL = DataStoreServer.getConfigParameters().getServerURL() + "/openbis/openbis"
+from ch.systemsx.cisd.openbis.dss.generic.server import DataStoreServer;
+OPENBISURL = DataStoreServer.getConfigParameters().getServerURL() + "/openbis/openbis";
+V3_DSS_BEAN = "data-store-server_INTERNAL";
-#V3 API
+#V3 API - Metadata
from ch.systemsx.cisd.common.spring import HttpInvokerUtils;
-from ch.ethz.sis.openbis.generic.asapi.v3 import IApplicationServerApi
+from ch.ethz.sis.openbis.generic.asapi.v3 import IApplicationServerApi;
-from ch.ethz.sis.openbis.generic.asapi.v3.dto.project.search import ProjectSearchCriteria
-from ch.ethz.sis.openbis.generic.asapi.v3.dto.experiment.search import ExperimentSearchCriteria
-from ch.ethz.sis.openbis.generic.asapi.v3.dto.sample.search import SampleSearchCriteria
-from ch.ethz.sis.openbis.generic.asapi.v3.dto.dataset.search import DataSetSearchCriteria
-from ch.ethz.sis.openbis.generic.asapi.v3.dto.project.fetchoptions import ProjectFetchOptions
-from ch.ethz.sis.openbis.generic.asapi.v3.dto.experiment.fetchoptions import ExperimentFetchOptions
-from ch.ethz.sis.openbis.generic.asapi.v3.dto.sample.fetchoptions import SampleFetchOptions
-from ch.ethz.sis.openbis.generic.asapi.v3.dto.dataset.fetchoptions import DataSetFetchOptions
+from ch.ethz.sis.openbis.generic.asapi.v3.dto.project.search import ProjectSearchCriteria;
+from ch.ethz.sis.openbis.generic.asapi.v3.dto.experiment.search import ExperimentSearchCriteria;
+from ch.ethz.sis.openbis.generic.asapi.v3.dto.sample.search import SampleSearchCriteria;
+from ch.ethz.sis.openbis.generic.asapi.v3.dto.dataset.search import DataSetSearchCriteria;
+from ch.ethz.sis.openbis.generic.asapi.v3.dto.project.fetchoptions import ProjectFetchOptions;
+from ch.ethz.sis.openbis.generic.asapi.v3.dto.experiment.fetchoptions import ExperimentFetchOptions;
+from ch.ethz.sis.openbis.generic.asapi.v3.dto.sample.fetchoptions import SampleFetchOptions;
+from ch.ethz.sis.openbis.generic.asapi.v3.dto.dataset.fetchoptions import DataSetFetchOptions;
+
+#V3 API - Files
+from ch.ethz.sis.openbis.generic.dssapi.v3 import IDataStoreServerApi;
+from ch.ethz.sis.openbis.generic.dssapi.v3.dto.datasetfile.search import DataSetFileSearchCriteria;
+from ch.ethz.sis.openbis.generic.dssapi.v3.dto.datasetfile.fetchoptions import DataSetFileFetchOptions;
+from ch.systemsx.cisd.openbis.dss.generic.shared import ServiceProvider;
+from ch.ethz.sis.openbis.generic.dssapi.v3.dto.datasetfile.id import DataSetFilePermId;
+from ch.ethz.sis.openbis.generic.asapi.v3.dto.dataset.id import DataSetPermId;
+from ch.ethz.sis.openbis.generic.dssapi.v3.dto.datasetfile.download import DataSetFileDownloadOptions;
#JSON
from ch.ethz.sis.openbis.generic.server.sharedapi.v3.json import GenericObjectMapper;
@@ -82,6 +92,8 @@ def process(tr, params, tableBuilder):
def exportAll(tr, params):
sessionToken = params.get("sessionToken");
v3 = HttpInvokerUtils.createServiceStub(IApplicationServerApi, OPENBISURL + IApplicationServerApi.SERVICE_URL, 30 * 1000);
+ v3d = ServiceProvider.getApplicationContext().getBean(V3_DSS_BEAN);
+
entity = params.get("entity");
entityAsPythonMap = { "type" : entity.get("type"), "permId" : entity.get("permId") };
entitiesToExport = [entityAsPythonMap];
@@ -99,33 +111,45 @@ def exportAll(tr, params):
results = v3.searchProjects(sessionToken, criteria, ProjectFetchOptions());
print "Found: " + str(results.getTotalCount()) + " projects";
for project in results.getObjects():
- entitiesToExport.append({ "type" : "PROJECT", "permId" : project.getPermId().getPermId() });
- entitiesToExpand.append({ "type" : "PROJECT", "permId" : project.getPermId().getPermId() });
+ entityFound = { "type" : "PROJECT", "permId" : project.getPermId().getPermId() };
+ entitiesToExport.append(entityFound);
+ entitiesToExpand.append(entityFound);
if type == "PROJECT":
criteria = ExperimentSearchCriteria();
criteria.withProject().withPermId().thatEquals(permId);
results = v3.searchExperiments(sessionToken, criteria, ExperimentFetchOptions());
print "Found: " + str(results.getTotalCount()) + " experiments";
for experiment in results.getObjects():
- entitiesToExport.append({ "type" : "EXPERIMENT", "permId" : experiment.getPermId().getPermId() });
- entitiesToExpand.append({ "type" : "EXPERIMENT", "permId" : experiment.getPermId().getPermId() });
+ entityFound = { "type" : "EXPERIMENT", "permId" : experiment.getPermId().getPermId() };
+ entitiesToExport.append(entityFound);
+ entitiesToExpand.append(entityFound);
if type == "EXPERIMENT":
criteria = SampleSearchCriteria();
criteria.withExperiment().withPermId().thatEquals(permId);
results = v3.searchSamples(sessionToken, criteria, SampleFetchOptions());
print "Found: " + str(results.getTotalCount()) + " samples";
for sample in results.getObjects():
- entitiesToExport.append({ "type" : "SAMPLE", "permId" : sample.getPermId().getPermId() });
- entitiesToExpand.append({ "type" : "SAMPLE", "permId" : sample.getPermId().getPermId() });
+ entityFound = { "type" : "SAMPLE", "permId" : sample.getPermId().getPermId() };
+ entitiesToExport.append(entityFound);
+ entitiesToExpand.append(entityFound);
if type == "SAMPLE":
criteria = DataSetSearchCriteria();
criteria.withSample().withPermId().thatEquals(permId);
results = v3.searchDataSets(sessionToken, criteria, DataSetFetchOptions());
print "Found: " + str(results.getTotalCount()) + " datasets";
for dataset in results.getObjects():
- entitiesToExport.append({ "type" : "DATASET", "permId" : dataset.getPermId().getPermId() });
- entitiesToExpand.append({ "type" : "DATASET", "permId" : dataset.getPermId().getPermId() });
-
+ entityFound = { "type" : "DATASET", "permId" : dataset.getPermId().getPermId() };
+ entitiesToExport.append(entityFound);
+ entitiesToExpand.append(entityFound);
+ if type == "DATASET":
+ criteria = DataSetFileSearchCriteria();
+ criteria.withDataSet().withPermId().thatEquals(permId);
+ results = v3d.searchFiles(sessionToken, criteria, DataSetFileFetchOptions());
+ print "Found: " + str(results.getTotalCount()) + " files";
+ for file in results.getObjects():
+ entityFound = { "type" : "FILE", "permId" : permId, "path" : file.getPath(), "isDirectory" : file.isDirectory() };
+ entitiesToExport.append(entityFound);
+ entitiesToExpand.append(entityFound);
print "Found " + str(len(entitiesToExport)) + " entities to export.";
params.put("entities", entitiesToExport);
return export(tr, params);
@@ -161,6 +185,8 @@ def addToZipFile(path, file, zos):
def export(tr, params):
sessionToken = params.get("sessionToken");
v3 = HttpInvokerUtils.createServiceStub(IApplicationServerApi, OPENBISURL + IApplicationServerApi.SERVICE_URL, 30 * 1000);
+ v3d = ServiceProvider.getApplicationContext().getBean(V3_DSS_BEAN);
+ objectCache = {};
objectMapper = GenericObjectMapper();
objectMapper.enable(SerializationFeature.INDENT_OUTPUT);
@@ -232,7 +258,19 @@ def export(tr, params):
fetchOps.withChildren();
entityObj = v3.searchDataSets(sessionToken, criteria, fetchOps).getObjects().get(0);
entityFilePath = getFileName(entityObj.getSample().getExperiment().getProject().getSpace().getCode(), entityObj.getSample().getExperiment().getProject().getCode(), entityObj.getSample().getExperiment().getCode(), entityObj.getSample().getCode(), entityObj.getCode());
+ if type == "FILE" and not entity["isDirectory"]:
+ datasetEntityObj = objectCache[entity["permId"]];
+ datasetEntityFilePath = getFileName(datasetEntityObj.getSample().getExperiment().getProject().getSpace().getCode(), datasetEntityObj.getSample().getExperiment().getProject().getCode(), datasetEntityObj.getSample().getExperiment().getCode(), datasetEntityObj.getSample().getCode(), datasetEntityObj.getCode());
+ filePath = datasetEntityFilePath + "/" + entity["path"];
+ rawFileInputStream = v3d.downloadFiles(sessionToken, [DataSetFilePermId(DataSetPermId(permId), entity["path"])], DataSetFileDownloadOptions());
+ rawFile = File(rootDir + filePath + ".json");
+ rawFile.getParentFile().mkdirs();
+ IOUtils.copyLarge(rawFileInputStream, FileOutputStream(rawFile));
+ addToZipFile(filePath, rawFile, zos);
+ if entityObj is not None:
+ objectCache[permId] = entityObj;
+
if entityObj is not None and entityFilePath is not None:
entityJson = String(objectMapper.writeValueAsString(entityObj));
jsonEntityFile = File(rootDir + entityFilePath + ".json");