From f2a448ca689f25da4051318045da9997fba4dfd5 Mon Sep 17 00:00:00 2001
From: vkovtun <viktor.kovtun@id.ethz.ch>
Date: Mon, 6 Feb 2023 14:34:32 +0100
Subject: [PATCH] SSDM-13367 Fixing issues with non-ascii characters when
exporting.
---
.../exports-api/exportsApi.py | 42 ++++++++++---------
1 file changed, 22 insertions(+), 20 deletions(-)
diff --git a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/dss/reporting-plugins/exports-api/exportsApi.py b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/dss/reporting-plugins/exports-api/exportsApi.py
index 5c4fd14cc39..9565d715b0f 100644
--- a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/dss/reporting-plugins/exports-api/exportsApi.py
+++ b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/dss/reporting-plugins/exports-api/exportsApi.py
@@ -151,10 +151,12 @@ def validateDataSize(entitiesToExport, tr):
estimatedSizeInBytes += 12000; # AVG File Metadata size
estimatedSizeInMegabytes = estimatedSizeInBytes / 1000000;
operationLog.info(
- "Size Limit check - limitDataSizeInBytes: " + str(limitDataSizeInBytes) + " > " + " estimatedSizeInBytes: " + str(estimatedSizeInBytes));
+ u"Size Limit check - limitDataSizeInBytes: " + str(limitDataSizeInBytes).encode('utf-8') +
+ u" > estimatedSizeInBytes: " + str(estimatedSizeInBytes).encode('utf-8'));
if estimatedSizeInBytes > limitDataSizeInBytes:
- raise UserFailureException("The selected data is " + str(estimatedSizeInMegabytes) + " MB that is bigger than the configured limit of " + str(
- limitDataSizeInMegabytes) + " MB");
+ raise UserFailureException(u"The selected data is " + estimatedSizeInMegabytes +
+ u" MB that is bigger than the configured limit of " +
+ limitDataSizeInMegabytes + u" MB");
def findEntitiesToExport(params):
@@ -172,17 +174,17 @@ def findEntitiesToExport(params):
if entity.get("expand"):
entitiesToExpand.append(entityAsPythonMap);
- operationLog.info("Found %d entities to expand." % len(entitiesToExpand))
+ operationLog.info(u"Found %d entities to expand." % len(entitiesToExpand))
while entitiesToExpand:
entityToExpand = entitiesToExpand.popleft();
type = entityToExpand["type"];
permId = entityToExpand["permId"];
- operationLog.info("Expanding type: " + str(type) + " permId: " + str(permId));
+ operationLog.info(u"Expanding type: " + type.encode("utf-8") + u" permId: " + permId.encode("utf-8"));
if type == "ROOT":
criteria = SpaceSearchCriteria();
results = v3.searchSpaces(sessionToken, criteria, SpaceFetchOptions());
- operationLog.info("Found: " + str(results.getTotalCount()) + " spaces");
+ operationLog.info(u"Found: %d spaces" % results.getTotalCount());
for space in results.getObjects():
entityFound = {"type": "SPACE", "permId": space.getCode(), "registrationDate": space.getRegistrationDate()};
addToExportWithoutRepeating(entitiesToExport, entityFound);
@@ -191,7 +193,7 @@ def findEntitiesToExport(params):
criteria = ProjectSearchCriteria();
criteria.withSpace().withCode().thatEquals(permId);
results = v3.searchProjects(sessionToken, criteria, ProjectFetchOptions());
- operationLog.info("Found: " + str(results.getTotalCount()) + " projects");
+ operationLog.info(u"Found: %d projects" % results.getTotalCount());
for project in results.getObjects():
entityFound = {"type": "PROJECT", "permId": project.getPermId().getPermId(), "registrationDate": project.getRegistrationDate()};
addToExportWithoutRepeating(entitiesToExport, entityFound);
@@ -200,7 +202,7 @@ def findEntitiesToExport(params):
criteria = ExperimentSearchCriteria();
criteria.withProject().withPermId().thatEquals(permId);
results = v3.searchExperiments(sessionToken, criteria, ExperimentFetchOptions());
- operationLog.info("Found: " + str(results.getTotalCount()) + " experiments");
+ operationLog.info(u"Found: %d experiments" % results.getTotalCount());
for experiment in results.getObjects():
entityFound = {"type": "EXPERIMENT", "permId": experiment.getPermId().getPermId(),
"registrationDate": experiment.getRegistrationDate()};
@@ -210,7 +212,7 @@ def findEntitiesToExport(params):
criteria = SampleSearchCriteria();
criteria.withExperiment().withPermId().thatEquals(permId);
results = v3.searchSamples(sessionToken, criteria, SampleFetchOptions());
- operationLog.info("Found: " + str(results.getTotalCount()) + " samples");
+ operationLog.info(u"Found: %d samples" % results.getTotalCount());
dCriteria = DataSetSearchCriteria();
dCriteria.withExperiment().withPermId().thatEquals(permId);
@@ -218,13 +220,13 @@ def findEntitiesToExport(params):
fetchOptions = DataSetFetchOptions()
fetchOptions.withDataStore()
dResults = v3.searchDataSets(sessionToken, dCriteria, fetchOptions);
- operationLog.info("Found: " + str(dResults.getTotalCount()) + " datasets");
+ operationLog.info(u"Found: %d datasets" % dResults.getTotalCount());
for dataset in dResults.getObjects():
entityFound = {"type": "DATASET", "permId": dataset.getPermId().getPermId(), "registrationDate": dataset.getRegistrationDate()};
addToExportWithoutRepeating(entitiesToExport, entityFound);
entitiesToExpand.append(entityFound);
- operationLog.info("Found: " + str(results.getTotalCount()) + " samples");
+ operationLog.info(u"Found: %d samples" % results.getTotalCount());
for sample in results.getObjects():
entityFound = {"type": "SAMPLE", "permId": sample.getPermId().getPermId(), "registrationDate": sample.getRegistrationDate()};
addToExportWithoutRepeating(entitiesToExport, entityFound);
@@ -235,7 +237,7 @@ def findEntitiesToExport(params):
fetchOptions = DataSetFetchOptions()
fetchOptions.withDataStore()
results = v3.searchDataSets(sessionToken, criteria, fetchOptions);
- operationLog.info("Found: " + str(results.getTotalCount()) + " datasets");
+ operationLog.info(u"Found: %d datasets" % results.getTotalCount());
for dataset in results.getObjects():
entityFound = {"type": "DATASET", "permId": dataset.getPermId().getPermId(), "registrationDate": dataset.getRegistrationDate()};
addToExportWithoutRepeating(entitiesToExport, entityFound);
@@ -244,7 +246,7 @@ def findEntitiesToExport(params):
criteria = DataSetFileSearchCriteria();
criteria.withDataSet().withPermId().thatEquals(permId);
results = v3d.searchFiles(sessionToken, criteria, DataSetFileFetchOptions());
- operationLog.info("Found: " + str(results.getTotalCount()) + " files");
+ operationLog.info(u"Found: %d files" % results.getTotalCount());
for file in results.getObjects():
entityFound = {"type": "FILE", "permId": permId, "path": file.getPath(), "isDirectory": file.isDirectory(),
"length": file.getFileLength()};
@@ -282,7 +284,7 @@ def generateFilesInZip(zos, entities, includeRoot, sessionToken, tempDirPath, de
for entity in entities:
type = entity["type"];
permId = entity["permId"];
- operationLog.info("exporting type: " + str(type) + " permId: " + str(permId));
+ operationLog.info(u"exporting type: " + type.encode("utf-8") + u" permId: " + permId.encode("utf-8"));
entityObj = None;
entityFilePath = None;
@@ -383,8 +385,7 @@ def generateFilesInZip(zos, entities, includeRoot, sessionToken, tempDirPath, de
if entityObj is not None:
objectCache[permId] = entityObj;
- operationLog.info("--> Entity type: " + type + " permId: " + permId + " obj: " + str(entityObj is not None) + " path: " + str(
- entityFilePath) + " before files.");
+ operationLog.info(u"--> Entity type: %s permId: %s obj: %s path: %s before files." % (type, permId, str(entityObj is not None), entityFilePath));
if entityObj is not None and entityFilePath is not None:
# JSON
entityJson = String(objectMapper.writerWithDefaultPrettyPrinter().writeValueAsString(entityObj));
@@ -403,19 +404,20 @@ def generateFilesInZip(zos, entities, includeRoot, sessionToken, tempDirPath, de
entityHTML = getDOCX(entityObj, v3, sessionToken, True);
fileMetadatum = addFile(tempDirPath, entityFilePath, "html", entityHTML, zos, deflated=deflated);
fileMetadata.append(fileMetadatum)
- operationLog.info("--> Entity type: " + type + " permId: " + permId + " post html.");
+ operationLog.info(u"--> Entity type: " + type.encode("utf-8") + u" permId: " + permId.encode("utf-8") +
+ u" post html.");
if emptyZip:
- raise IOError('Nothing added to ZIP file.')
+ raise IOError("Nothing added to ZIP file.")
return fileMetadata
def generateDownloadUrl(sessionToken, tempZipFileName, tempZipFilePath):
# Store on workspace to be able to generate a download link
- operationLog.info("Zip file can be found on the temporal directory: " + tempZipFilePath);
+ operationLog.info(u"Zip file can be found on the temporal directory: " + tempZipFilePath.encode("utf-8"));
dssService = ServiceProvider.getApplicationContext().getBean("dss-service-rpc-generic")
dssService.putFileToSessionWorkspace(sessionToken, tempZipFileName, FileInputStream(File(tempZipFilePath)))
tempZipFileWorkspaceURL = DataStoreServer.getConfigParameters().getDownloadURL() + "/datastore_server/session_workspace_file_download?sessionID=" + sessionToken + "&filePath=" + tempZipFileName;
- operationLog.info("Zip file can be downloaded from the workspace: " + tempZipFileWorkspaceURL);
+ operationLog.info(u"Zip file can be downloaded from the workspace: " + tempZipFileWorkspaceURL.encode("utf-8"));
return tempZipFileWorkspaceURL
--
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