From f4e5b52bb189219fec82d9f51a002152ecd5c926 Mon Sep 17 00:00:00 2001
From: Viktor Kovtun <viktor.kovtun@id.ethz.ch>
Date: Mon, 5 Aug 2019 15:58:51 +0200
Subject: [PATCH] SSDM-8405 Research Collection Integration.
---
.../eln-lims/1/as/master-data/data-model.xls | Bin 71168 -> 73728 bytes
.../publication-api/plugin.properties | 2 +
.../publication-api/publication-api.py | 93 +++++
.../html/img/research-collection-icon.png | Bin 0 -> 9943 bytes
.../1/as/webapps/eln-lims/html/index.html | 4 +
.../html/js/controllers/MainController.js | 15 +-
.../eln-lims/html/js/server/ServerFacade.js | 106 ++++-
.../webapps/eln-lims/html/js/util/FormUtil.js | 27 +-
.../html/js/views/Export/ExportTreeView.js | 2 +-
.../ResearchCollectionExportController.js | 127 ++++++
.../ResearchCollectionExportModel.js | 23 ++
.../ResearchCollectionExportView.js | 75 ++++
.../js/views/SideMenu/SideMenuWidgetView.js | 10 +-
.../{exports-api.py => exportsApi.py} | 343 ++++++++--------
.../exports-api/generalExports.py | 87 ++++
.../exports-api/plugin.properties | 2 +-
.../rc-exports-api/exportsApi.py | 1 +
.../rc-exports-api/plugin.properties | 8 +
.../rc-exports-api/rcExports.py | 384 ++++++++++++++++++
19 files changed, 1095 insertions(+), 214 deletions(-)
create mode 100644 openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/services/publication-api/plugin.properties
create mode 100644 openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/services/publication-api/publication-api.py
create mode 100644 openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/img/research-collection-icon.png
create mode 100644 openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/ResearchCollectionExport/ResearchCollectionExportController.js
create mode 100644 openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/ResearchCollectionExport/ResearchCollectionExportModel.js
create mode 100644 openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/ResearchCollectionExport/ResearchCollectionExportView.js
rename openbis_standard_technologies/dist/core-plugins/eln-lims/1/dss/reporting-plugins/exports-api/{exports-api.py => exportsApi.py} (80%)
create mode 100644 openbis_standard_technologies/dist/core-plugins/eln-lims/1/dss/reporting-plugins/exports-api/generalExports.py
create mode 120000 openbis_standard_technologies/dist/core-plugins/eln-lims/1/dss/reporting-plugins/rc-exports-api/exportsApi.py
create mode 100644 openbis_standard_technologies/dist/core-plugins/eln-lims/1/dss/reporting-plugins/rc-exports-api/plugin.properties
create mode 100644 openbis_standard_technologies/dist/core-plugins/eln-lims/1/dss/reporting-plugins/rc-exports-api/rcExports.py
diff --git a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/master-data/data-model.xls b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/master-data/data-model.xls
index 9f7724cae233674fc63335ad063636d9b015b00e..8d7784125bad3226f67a0cf35266de503b5a48cb 100644
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diff --git a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/services/publication-api/plugin.properties b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/services/publication-api/plugin.properties
new file mode 100644
index 00000000000..76d5aa52bab
--- /dev/null
+++ b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/services/publication-api/plugin.properties
@@ -0,0 +1,2 @@
+class = ch.ethz.sis.openbis.generic.server.asapi.v3.helper.service.JythonBasedCustomASServiceExecutor
+script-path = publication-api.py
\ No newline at end of file
diff --git a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/services/publication-api/publication-api.py b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/services/publication-api/publication-api.py
new file mode 100644
index 00000000000..cc5c7e99fe2
--- /dev/null
+++ b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/services/publication-api/publication-api.py
@@ -0,0 +1,93 @@
+import traceback
+
+from ch.ethz.sis.openbis.generic.asapi.v3.dto.dataset import DataSetKind
+from ch.ethz.sis.openbis.generic.asapi.v3.dto.dataset.create import DataSetCreation
+from ch.ethz.sis.openbis.generic.asapi.v3.dto.dataset.fetchoptions import DataSetFetchOptions
+from ch.ethz.sis.openbis.generic.asapi.v3.dto.dataset.id import DataSetPermId
+from ch.ethz.sis.openbis.generic.asapi.v3.dto.datastore.id import DataStorePermId
+from ch.ethz.sis.openbis.generic.asapi.v3.dto.entitytype import EntityKind
+from ch.ethz.sis.openbis.generic.asapi.v3.dto.entitytype.id import EntityTypePermId
+from ch.ethz.sis.openbis.generic.asapi.v3.dto.experiment.id import ExperimentIdentifier
+from ch.ethz.sis.openbis.generic.asapi.v3.dto.sample.create import SampleCreation
+from ch.ethz.sis.openbis.generic.asapi.v3.dto.space.id import SpacePermId
+from ch.systemsx.cisd.common.logging import LogCategory
+from ch.systemsx.cisd.openbis.generic.client.web.client.exception import UserFailureException
+from java.util import ArrayList
+from org.apache.log4j import Logger
+
+operationLog = Logger.getLogger(str(LogCategory.OPERATION) + '.publication-api.py')
+
+
+def process(context, parameters):
+ method = parameters.get('method')
+
+ try:
+ if method == 'insertPublication':
+ result = insertPublication(context, parameters)
+ else:
+ raise UserFailureException('Unknown method: "%s"' % str(method if method is not None else 'None'))
+ except Exception as e:
+ operationLog.error('Exception at: ' + traceback.format_exc())
+ operationLog.error('Exception: ' + str(e))
+ result = {
+ 'status': 'FAILED',
+ 'error': str(e)
+ }
+ return result
+
+
+def insertPublication(context, parameters):
+ transaction = context.applicationService
+ sessionToken = transaction.loginAsSystem()
+
+ v3 = context.applicationService
+
+ name = parameters.get('name')
+ if name is None:
+ raise UserFailureException('name parameter missing')
+
+ sampleId = createPublicationSample(parameters, sessionToken, v3).get(0)
+ createDataSet(parameters, sessionToken, v3, sampleId)
+
+ return {
+ 'status': 'OK',
+ }
+
+
+def createDataSet(parameters, sessionToken, v3, sampleId):
+ openBISRelatedIdentifiers = parameters.get('openBISRelatedIdentifiers').split(',')
+ identifiers = ArrayList(len(openBISRelatedIdentifiers))
+ for identifier in openBISRelatedIdentifiers:
+ identifiers.add(DataSetPermId(identifier))
+
+ dataSetIds = v3.getDataSets(sessionToken, identifiers, DataSetFetchOptions()).keys()
+ operationLog.debug('Found %d data sets.' % len(dataSetIds))
+
+ dataSetCreation = DataSetCreation()
+ dataSetCreation.setAutoGeneratedCode(True)
+ dataSetCreation.setTypeId(EntityTypePermId('PUBLICATION_DATA', EntityKind.DATA_SET))
+ dataSetCreation.setSampleId(sampleId)
+ dataSetCreation.setDataSetKind(DataSetKind.CONTAINER)
+ dataSetCreation.setComponentIds(dataSetIds)
+ dataSetCreation.setDataStoreId(DataStorePermId('STANDARD'))
+ v3.createDataSets(sessionToken, [dataSetCreation])
+
+
+def createPublicationSample(parameters, sessionToken, v3):
+ publicationOrganization = parameters.get('publicationOrganization')
+ publicationType = parameters.get('publicationType') # The only valid value for now is "Public Repository"
+ publicationDescription = parameters.get('publicationDescription') # Can be empty
+ publicationURL = parameters.get('publicationURL')
+ publicationIdentifier = parameters.get('publicationIdentifier')
+
+ sampleCreation = SampleCreation()
+ sampleCreation.setTypeId(EntityTypePermId('PUBLICATION'))
+ sampleCreation.setExperimentId(ExperimentIdentifier('/PUBLICATIONS/PUBLIC_REPOSITORIES/PUBLICATIONS_COLLECTION'))
+ sampleCreation.setSpaceId(SpacePermId('PUBLICATIONS'))
+ sampleCreation.setProperty('$NAME', 'TEST NAME')
+ sampleCreation.setProperty('$PUBLICATION.ORGANIZATION', publicationOrganization)
+ sampleCreation.setProperty('$PUBLICATION.TYPE', publicationType)
+ sampleCreation.setProperty('$PUBLICATION.IDENTIFIER', publicationIdentifier)
+ sampleCreation.setProperty('$PUBLICATION.URL', publicationURL)
+ sampleCreation.setProperty('$PUBLICATION.DESCRIPTION', publicationDescription)
+ return v3.createSamples(sessionToken, [sampleCreation])
diff --git a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/img/research-collection-icon.png b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/img/research-collection-icon.png
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diff --git a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/index.html b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/index.html
index 65763885d61..65c0c67df06 100644
--- a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/index.html
+++ b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/index.html
@@ -249,6 +249,10 @@
<script type="text/javascript" src="./js/views/Export/ExportTreeModel.js"></script>
<script type="text/javascript" src="./js/views/Export/ExportTreeView.js"></script>
+ <script type="text/javascript" src="./js/views/ResearchCollectionExport/ResearchCollectionExportController.js"></script>
+ <script type="text/javascript" src="./js/views/ResearchCollectionExport/ResearchCollectionExportModel.js"></script>
+ <script type="text/javascript" src="./js/views/ResearchCollectionExport/ResearchCollectionExportView.js"></script>
+
<script type="text/javascript" src="./js/views/DrawingBoards/DrawingBoardsController.js"></script>
<script type="text/javascript" src="./js/views/DrawingBoards/DrawingBoardsModel.js"></script>
<script type="text/javascript" src="./js/views/DrawingBoards/DrawingBoardsView.js"></script>
diff --git a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/controllers/MainController.js b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/controllers/MainController.js
index 09690f4f1d5..142198f6bab 100644
--- a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/controllers/MainController.js
+++ b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/controllers/MainController.js
@@ -376,12 +376,19 @@ function MainController(profile) {
break;
case "showExportTreePage":
document.title = "Export Builder";
- var newView = new ExportTreeController(this);
- var views = this._getNewViewModel(true, true, false);
- newView.init(views);
- this.currentView = newView;
+ var newExportView = new ExportTreeController(this);
+ var exportViews = this._getNewViewModel(true, true, false);
+ newExportView.init(exportViews);
+ this.currentView = newExportView;
//window.scrollTo(0,0);
break;
+ case "showResearchCollectionExportPage":
+ document.title = "Research Collection Export Builder";
+ var newResearchCollectionExportView = new ResearchCollectionExportController(this);
+ var researchCollectionExportViews = this._getNewViewModel(true, true, false);
+ newResearchCollectionExportView.init(researchCollectionExportViews);
+ this.currentView = newResearchCollectionExportView;
+ break;
case "showLabNotebookPage":
document.title = "Lab Notebook";
var newView = new LabNotebookController(this);
diff --git a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/server/ServerFacade.js b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/server/ServerFacade.js
index 5f6bde3add7..b9f816840a1 100644
--- a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/server/ServerFacade.js
+++ b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/server/ServerFacade.js
@@ -302,7 +302,65 @@ function ServerFacade(openbisServer) {
"entities" : entities,
"metadataOnly" : metadataOnly,
}, callbackFunction, "exports-api");
- }
+ };
+
+ //
+ // Research collection export
+ //
+ this.exportRc = function(entities, includeRoot, metadataOnly, submissionUrl, submissionType, userInformation, callbackFunction) {
+ this.asyncExportRc({
+ "method": "exportAll",
+ "includeRoot": includeRoot,
+ "entities": entities,
+ "metadataOnly": metadataOnly,
+ "submissionUrl": submissionUrl,
+ "submissionType": submissionType,
+ "userInformation": userInformation,
+ "originUrl": window.location.origin,
+ "sessionToken": this.openbisServer.getSession(),
+ }, callbackFunction, "rc-exports-api");
+ };
+
+ this.asyncExportRc = function(parameters, callbackFunction, serviceId) {
+ require(["as/dto/service/execute/ExecuteAggregationServiceOperation",
+ "as/dto/operation/AsynchronousOperationExecutionOptions", "as/dto/service/id/DssServicePermId",
+ "as/dto/datastore/id/DataStorePermId", "as/dto/service/execute/AggregationServiceExecutionOptions"],
+ function(ExecuteAggregationServiceOperation, AsynchronousOperationExecutionOptions, DssServicePermId, DataStorePermId,
+ AggregationServiceExecutionOptions) {
+ var dataStoreId = new DataStorePermId("STANDARD");
+ var dssServicePermId = new DssServicePermId(serviceId, dataStoreId);
+ var options = new AggregationServiceExecutionOptions();
+
+ options.withParameter("sessionToken", parameters["sessionToken"]);
+
+ options.withParameter("entities", parameters["entities"]);
+ options.withParameter("includeRoot", parameters["includeRoot"]);
+ options.withParameter("metadataOnly", parameters["metadataOnly"]);
+ options.withParameter("method", parameters["method"]);
+ options.withParameter("originUrl", parameters["originUrl"]);
+ options.withParameter("submissionType", parameters["submissionType"]);
+ options.withParameter("submissionUrl", parameters["submissionUrl"]);
+ options.withParameter("entities", parameters["entities"]);
+ options.withParameter("userId", parameters["userInformation"]["id"]);
+ options.withParameter("userEmail", parameters["userInformation"]["email"]);
+ options.withParameter("userFirstName", parameters["userInformation"]["firstName"]);
+ options.withParameter("userLastName", parameters["userInformation"]["lastName"]);
+
+ var operation = new ExecuteAggregationServiceOperation(dssServicePermId, options);
+ mainController.openbisV3.executeOperations([operation], new AsynchronousOperationExecutionOptions()).done(function(results) {
+ callbackFunction(results.executionId.permId);
+ });
+ });
+ };
+
+ //
+ // Gets submission types
+ //
+ this.listSubmissionTypes = function(callbackFunction) {
+ this.customELNApi({
+ "method": "getSubmissionTypes",
+ }, callbackFunction, "rc-exports-api");
+ };
//
// Metadata Related Functions
@@ -659,7 +717,6 @@ function ServerFacade(openbisServer) {
this._callPasswordResetService = function(parameters, callbackFunction) {
var _this = this;
this.getOpenbisV3(function(openbisV3) {
-
openbisV3.loginAsAnonymousUser().done(function(sessionToken) {
_this.openbisServer._internal.sessionToken = sessionToken;
@@ -682,6 +739,7 @@ function ServerFacade(openbisServer) {
}
this.customELNApi = function(parameters, callbackFunction, service) {
+ var _this = this;
if(!service) {
service = "eln-lims-api";
}
@@ -693,24 +751,28 @@ function ServerFacade(openbisServer) {
var dataStoreCode = profile.getDefaultDataStoreCode();
this.openbisServer.createReportFromAggregationService(dataStoreCode, service, parameters, function(data) {
- var error = null;
- var result = {};
- if(data.error) { //Error Case 1
- error = data.error.message;
- } else if (data.result.columns[1].title === "Error") { //Error Case 2
- error = data.result.rows[0][1].value;
- } else if (data.result.columns[0].title === "STATUS" && data.result.rows[0][0].value === "OK") { //Success Case
- result.message = data.result.rows[0][1].value;
- result.data = data.result.rows[0][2].value;
- if(result.data) {
- result.data = JSON.parse(result.data);
- }
- } else {
- error = "Unknown Error.";
- }
- callbackFunction(error, result);
+ _this.customELNApiCallbackHandler(data, callbackFunction);
});
- }
+ };
+
+ this.customELNApiCallbackHandler = function(data, callbackFunction) {
+ var error = null;
+ var result = {};
+ if (data && data.error) { //Error Case 1
+ error = data.error.message;
+ } else if (data && data.result.columns[1].title === "Error") { //Error Case 2
+ error = data.result.rows[0][1].value;
+ } else if (data && data.result.columns[0].title === "STATUS" && data.result.rows[0][0].value === "OK") { //Success Case
+ result.message = data.result.rows[0][1].value;
+ result.data = data.result.rows[0][2].value;
+ if(result.data) {
+ result.data = JSON.parse(result.data);
+ }
+ } else {
+ error = "Unknown Error.";
+ }
+ callbackFunction(error, result);
+ };
this.customELNASAPI = function(parameters, callbackFunction) {
this.customASService(parameters, callbackFunction, "as-eln-lims-api");
@@ -2563,10 +2625,10 @@ function ServerFacade(openbisServer) {
this.getSessionInformation = function(callbackFunction) {
mainController.openbisV3.getSessionInformation().done(function(sessionInfo) {
-Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â callbackFunction(sessionInfo);
+ callbackFunction(sessionInfo);
        }).fail(function(result) {
- Util.showFailedServerCallError(result);
- callbackFunction(false);
+ Util.showFailedServerCallError(result);
+ callbackFunction(false);
});
}
diff --git a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/util/FormUtil.js b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/util/FormUtil.js
index e501e670936..9658d70d42f 100644
--- a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/util/FormUtil.js
+++ b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/util/FormUtil.js
@@ -322,25 +322,28 @@ var FormUtil = new function() {
Select2Manager.add($dropdown);
return $dropdown;
}
-
- this.getPlainDropdown = function(mapVals, placeHolder) {
- var $component = $("<select>", {class : 'form-control'});
- if(placeHolder) {
- $component.append($("<option>").attr('value', '').attr('selected', '').attr('disabled', '').text(placeHolder));
- }
- for(var mIdx = 0; mIdx < mapVals.length; mIdx++) {
+ this.setValuesToComponent = function ($component, mapVals) {
+ for (var mIdx = 0; mIdx < mapVals.length; mIdx++) {
var $option = $("<option>").attr('value', mapVals[mIdx].value).text(mapVals[mIdx].label);
- if(mapVals[mIdx].disabled) {
+ if (mapVals[mIdx].disabled) {
$option.attr('disabled', '');
}
- if(mapVals[mIdx].selected) {
+ if (mapVals[mIdx].selected) {
$option.attr('selected', '');
}
$component.append($option);
}
+ };
+
+ this.getPlainDropdown = function(mapVals, placeHolder) {
+ var $component = $("<select>", {class : 'form-control'});
+ if (placeHolder) {
+ $component.append($("<option>").attr('value', '').attr('selected', '').attr('disabled', '').text(placeHolder));
+ }
+ this.setValuesToComponent($component, mapVals);
return $component;
- }
+ };
this.getDataSetsDropDown = function(code, dataSetTypes) {
var $component = $("<select>", { class : 'form-control ' });
@@ -350,11 +353,11 @@ var FormUtil = new function() {
$component.append($("<option>").attr('value', '').attr('selected', '').attr('disabled', '').text('Select a dataset type'));
- for(var i = 0; i < dataSetTypes.length; i++) {
+ for (var i = 0; i < dataSetTypes.length; i++) {
var datasetType = dataSetTypes[i];
var label = Util.getDisplayNameFromCode(datasetType.code);
var description = Util.getEmptyIfNull(datasetType.description);
- if(description !== "") {
+ if (description !== "") {
label += " (" + description + ")";
}
diff --git a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/Export/ExportTreeView.js b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/Export/ExportTreeView.js
index f09bd1a1cf9..7bbbd3de8e2 100644
--- a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/Export/ExportTreeView.js
+++ b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/Export/ExportTreeView.js
@@ -39,7 +39,7 @@ function ExportTreeView(exportTreeController, exportTreeModel) {
'onClick': '$("form[name=\'exportTreeForm\']").submit()' });
$header.append($exportButton);
- var $infoBox = FormUtil.getInfoBox("You can select any parts of the accesible openBIS structure to export:", [
+ var $infoBox = FormUtil.getInfoBox("You can select any parts of the accessible openBIS structure to export:", [
"If you select a tree node and do not expand it, everything below this node will be exported by default.",
"To export selectively only parts of a tree, open the nodes and select what to export."
]);
diff --git a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/ResearchCollectionExport/ResearchCollectionExportController.js b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/ResearchCollectionExport/ResearchCollectionExportController.js
new file mode 100644
index 00000000000..514b6a15d2d
--- /dev/null
+++ b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/ResearchCollectionExport/ResearchCollectionExportController.js
@@ -0,0 +1,127 @@
+/*
+ * Copyright 2011 ETH Zuerich, CISD
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+function ResearchCollectionExportController(parentController) {
+ var researchCollectionExportModel = new ResearchCollectionExportModel();
+ var researchCollectionExportView = new ResearchCollectionExportView(this, researchCollectionExportModel);
+
+ this.init = function(views) {
+ researchCollectionExportView.repaint(views);
+ };
+
+ this.initialiseSubmissionTypesDropdown = function(callback) {
+ Util.blockUI();
+ mainController.serverFacade.listSubmissionTypes(function(error, result) {
+ Util.unblockUI();
+ if (error) {
+ Util.showError(error);
+ } else {
+ researchCollectionExportModel.submissionTypes = result.data.map(function (resultItem) {
+ return {
+ value: resultItem.url,
+ label: resultItem.title
+ };
+ });
+ researchCollectionExportView.refreshSubmissionTypeDropdown();
+ }
+ });
+ };
+
+ this.exportSelected = function() {
+ var _this = this;
+ var selectedNodes = $(researchCollectionExportModel.tree).fancytree('getTree').getSelectedNodes();
+
+ var selectedOption = researchCollectionExportView.$submissionTypeDropdown.find(":selected");
+ var submissionUrl = selectedOption.val();
+ var submissionType = selectedOption.text();
+
+ var toExport = [];
+ for (var eIdx = 0; eIdx < selectedNodes.length; eIdx++) {
+ var node = selectedNodes[eIdx];
+ toExport.push({type: node.data.entityType, permId: node.key, expand: !node.expanded});
+ }
+
+ if (toExport.length === 0) {
+ Util.showInfo('First select something to export.');
+ } else if (!submissionUrl) {
+ Util.showInfo('First select submission type.');
+ } else {
+ Util.blockUI();
+ this.getUserInformation(function(userInformation) {
+ mainController.serverFacade.exportRc(toExport, true, false, submissionUrl, submissionType, userInformation,
+ function(operationExecutionPermId) {
+ _this.waitForOpExecutionResponse(operationExecutionPermId, function(error, result) {
+ Util.unblockUI();
+ if (result && result.data && result.data.url) {
+ var win = window.open(result.data.url, '_blank');
+ win.focus();
+ mainController.refreshView();
+ } else {
+ if (error) {
+ Util.showError(error);
+ } else {
+ Util.showError('Returned result format is not correct.');
+ }
+ }
+ });
+ });
+ });
+ }
+ };
+
+ this.waitForOpExecutionResponse = function(operationExecutionPermIdString, callbackFunction) {
+ var _this = this;
+ require(["as/dto/operation/id/OperationExecutionPermId",
+ "as/dto/operation/fetchoptions/OperationExecutionFetchOptions"],
+ function(OperationExecutionPermId, OperationExecutionFetchOptions) {
+ var operationExecutionPermId = new OperationExecutionPermId(operationExecutionPermIdString);
+ var fetchOptions = new OperationExecutionFetchOptions();
+ var fetchOptionsDetails = fetchOptions.withDetails();
+ fetchOptionsDetails.withResults();
+ fetchOptionsDetails.withError();
+ mainController.openbisV3.getOperationExecutions([operationExecutionPermId], fetchOptions).done(function(results) {
+ var result = results[operationExecutionPermIdString];
+ var v2Result = null;
+ if (result && result.details && result.details.results) {
+ v2Result = result.details.results[0];
+ }
+
+ if (result && result.state === 'FINISHED') {
+ mainController.serverFacade.customELNApiCallbackHandler(v2Result, callbackFunction);
+ } else if (!result || result.state === 'FAILED') {
+ mainController.serverFacade.customELNApiCallbackHandler(v2Result, callbackFunction);
+ } else {
+ setTimeout(function() {
+ _this.waitForOpExecutionResponse(operationExecutionPermIdString, callbackFunction);
+ }, 3000);
+ }
+ });
+ });
+ };
+
+ this.getUserInformation = function(callback) {
+ var userId = mainController.serverFacade.getUserId();
+ mainController.serverFacade.getSessionInformation(function(sessionInfo) {
+ var userInformation = {
+ firstName: sessionInfo.person.firstName,
+ lastName: sessionInfo.person.lastName,
+ email: sessionInfo.person.email,
+ id: userId,
+ };
+ callback(userInformation);
+ });
+ };
+}
\ No newline at end of file
diff --git a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/ResearchCollectionExport/ResearchCollectionExportModel.js b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/ResearchCollectionExport/ResearchCollectionExportModel.js
new file mode 100644
index 00000000000..7099e83d875
--- /dev/null
+++ b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/ResearchCollectionExport/ResearchCollectionExportModel.js
@@ -0,0 +1,23 @@
+/*
+ * Copyright 2011 ETH Zuerich, CISD
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+function ResearchCollectionExportModel() {
+ this.submissionTypes = [];
+
+ this.addSubmissionType = function(submissionType) {
+ submissionTypes.push(submissionType);
+ };
+}
\ No newline at end of file
diff --git a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/ResearchCollectionExport/ResearchCollectionExportView.js b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/ResearchCollectionExport/ResearchCollectionExportView.js
new file mode 100644
index 00000000000..7945f200cb3
--- /dev/null
+++ b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/ResearchCollectionExport/ResearchCollectionExportView.js
@@ -0,0 +1,75 @@
+/*
+ * Copyright 2011 ETH Zuerich, CISD
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+function ResearchCollectionExportView(researchCollectionExportController, researchCollectionExportModel) {
+ var exportTreeView = new ExportTreeView(researchCollectionExportController, researchCollectionExportModel);
+
+ this.repaint = function(views) {
+ researchCollectionExportController.initialiseSubmissionTypesDropdown();
+
+ var $header = views.header;
+ var $container = views.content;
+
+ var $form = $("<div>");
+ var $formColumn = $("<form>", {
+ 'name': 'rcExportForm',
+ 'role': 'form',
+ 'action': 'javascript:void(0);',
+ 'onsubmit': 'mainController.currentView.exportSelected();'
+ });
+ $form.append($formColumn);
+
+ var $infoBox = FormUtil.getInfoBox('You can select any parts of the accessible openBIS structure to export:', [
+ 'If you select a tree node and do not expand it, everything below this node will be exported by default.',
+ 'To export selectively only parts of a tree, open the nodes and select what to export.'
+ ]);
+ $infoBox.css('border', 'none');
+ $container.append($infoBox);
+
+ var $tree = $('<div>', { 'id' : 'exportsTree' });
+ $formColumn.append($('<br>'));
+ $formColumn.append(FormUtil.getBox().append($tree));
+
+ $container.append($form);
+
+ this.paintSubmissionTypeDropdown($container);
+
+ researchCollectionExportModel.tree = TreeUtil.getCompleteTree($tree);
+
+ var $formTitle = $('<h2>').append('Research Collection Export Builder');
+ $header.append($formTitle);
+
+ var $exportButton = $('<input>', { 'type': 'submit', 'class': 'btn btn-primary', 'value': 'Export Selected',
+ 'onClick': '$("form[name=\'rcExportForm\']").submit()'});
+ $header.append($exportButton);
+ };
+
+ this.paintSubmissionTypeDropdown = function($container) {
+ this.$submissionTypeDropdown = this.getSubmissionTypeDropdown();
+ var entityTypeDropdownFormGroup = FormUtil.getFieldForComponentWithLabel(this.$submissionTypeDropdown, 'Submission Type', null, true);
+ entityTypeDropdownFormGroup.css('width', '50%');
+ $container.append(entityTypeDropdownFormGroup);
+ };
+
+ this.getSubmissionTypeDropdown = function() {
+ return FormUtil.getDropdown(researchCollectionExportModel.submissionTypes, 'Select a submission type');
+ };
+
+ this.refreshSubmissionTypeDropdown = function() {
+ FormUtil.setValuesToComponent(this.$submissionTypeDropdown, researchCollectionExportModel.submissionTypes);
+ }
+
+}
\ No newline at end of file
diff --git a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/SideMenu/SideMenuWidgetView.js b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/SideMenu/SideMenuWidgetView.js
index da2bc285601..41e50655fc3 100644
--- a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/SideMenu/SideMenuWidgetView.js
+++ b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/SideMenu/SideMenuWidgetView.js
@@ -267,7 +267,14 @@ function SideMenuWidgetView(sideMenuWidgetController, sideMenuWidgetModel) {
if(profile.mainMenu.showExports) {
    var exportBuilderLink = _this.getLinkForNode("Export Builder", "EXPORT_BUILDER", "showExportTreePage", null);
- Â Â Â Â treeModelUtils.push({ displayName: "Export Builder", title : exportBuilderLink, entityType: "EXPORT_BUILDER", key : "EXPORT_BUILDER", folder : false, lazy : false, view : "showExportTreePage", icon : "glyphicon glyphicon-export" });
+ Â Â Â Â treeModelUtils.push({ displayName: "Export Builder", title : exportBuilderLink, entityType: "EXPORT_BUILDER", key : "EXPORT_BUILDER",
+ folder : false, lazy : false, view : "showExportTreePage", icon : "glyphicon glyphicon-export" });
+
+ var researchCollectionExportBuilderLink = _this.getLinkForNode("Research Collection Export Builder", "RESEARCH_COLLECTION_EXPORT_BUILDER",
+ "showResearchCollectionExportPage", null);
+ treeModelUtils.push({ displayName: "Research Collection Export Builder", title: researchCollectionExportBuilderLink,
+ entityType: "RESEARCH_COLLECTION_EXPORT_BUILDER", key: "RESEARCH_COLLECTION_EXPORT_BUILDER", folder: false, lazy: false,
+ view: "showResearchCollectionExportPage" });
}
if(profile.mainMenu.showStorageManager) {
@@ -811,6 +818,7 @@ function SideMenuWidgetView(sideMenuWidgetController, sideMenuWidgetModel) {
            stock.setExpanded(true);
        }
       Â
+ setCustomIcon($tree, "RESEARCH_COLLECTION_EXPORT_BUILDER", "./img/research-collection-icon.png");
        setCustomIcon($tree, "JUPYTER_WORKSPACE", "./img/jupyter-icon.png");
        setCustomIcon($tree, "NEW_JUPYTER_NOTEBOOK", "./img/jupyter-icon.png");
}
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/exportsApi.py
similarity index 80%
rename from openbis_standard_technologies/dist/core-plugins/eln-lims/1/dss/reporting-plugins/exports-api/exports-api.py
rename to openbis_standard_technologies/dist/core-plugins/eln-lims/1/dss/reporting-plugins/exports-api/exportsApi.py
index 1494b24e95d..932c0fa3023 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/exportsApi.py
@@ -13,42 +13,28 @@
# See the License for the specific language governing permissions and
# limitations under the License.
#
-from collections import deque
-import time
import jarray
-import threading
-
-#Java Core
-from java.io import ByteArrayInputStream
-from org.apache.commons.io import IOUtils
-from org.apache.commons.io import FileUtils
-
-from java.lang import String
-from java.lang import StringBuilder
-
+# To obtain the openBIS URL
+from ch.systemsx.cisd.openbis.dss.generic.server import DataStoreServer;
from ch.systemsx.cisd.openbis.generic.client.web.client.exception import UserFailureException
-
-#Zip Format
+from collections import deque
+# Zip Format
from java.io import File;
from java.io import FileInputStream;
-from java.io import FileNotFoundException;
from java.io import FileOutputStream;
+from java.lang import String
+from java.lang import StringBuilder
from java.util.zip import ZipEntry;
from java.util.zip import ZipOutputStream;
-from ch.systemsx.cisd.common.mail import EMailAddress;
+from org.apache.commons.io import FileUtils
+# Java Core
+from org.apache.commons.io import IOUtils
-#To obtain the openBIS URL
-from ch.systemsx.cisd.openbis.dss.generic.server import DataStoreServer;
-from ch.systemsx.cisd.openbis.dss.generic.server import SessionTokenManager
-from ch.systemsx.cisd.openbis.generic.shared.api.v1.dto import SearchCriteria
OPENBISURL = DataStoreServer.getConfigParameters().getServerURL() + "/openbis/openbis";
V3_DSS_BEAN = "data-store-server_INTERNAL";
#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.dto.property import DataType;
from HTMLParser import HTMLParser
from ch.ethz.sis.openbis.generic.asapi.v3.dto.space.search import SpaceSearchCriteria;
@@ -75,7 +61,6 @@ from ch.ethz.sis.openbis.generic.asapi.v3.dto.dataset.fetchoptions import DataSe
from ch.ethz.sis.openbis.generic.asapi.v3.dto.property import DataType
#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;
@@ -94,7 +79,7 @@ from ch.systemsx.cisd.openbis.dss.client.api.v1 import DssComponentFactory
#Logging
from ch.systemsx.cisd.common.logging import LogCategory;
from org.apache.log4j import Logger;
-operationLog = Logger.getLogger(str(LogCategory.OPERATION) + ".exports-api.py");
+operationLog = Logger.getLogger(str(LogCategory.OPERATION) + ".exportsApi.py");
#AVI API - DTO
from ch.ethz.sis.openbis.generic.asapi.v3.dto.project import Project
@@ -107,9 +92,6 @@ from ch.ethz.sis import DOCXBuilder
#Images export for word
from org.jsoup import Jsoup;
-from org.jsoup.nodes import Document;
-from org.jsoup.nodes import Element;
-from org.jsoup.select import Elements;
class MLStripper(HTMLParser):
def __init__(self):
@@ -125,32 +107,23 @@ def strip_tags(html):
s.feed(html)
return s.get_data()
-def process(tr, params, tableBuilder):
- method = params.get("method");
- isOk = False;
- result = None;
-
- # Set user using the service
-
- tr.setUserId(userId);
- if method == "exportAll":
- isOk = expandAndexport(tr, params);
+def displayResult(isOk, tableBuilder, result=None):
if isOk:
tableBuilder.addHeader("STATUS");
tableBuilder.addHeader("MESSAGE");
tableBuilder.addHeader("RESULT");
row = tableBuilder.addRow();
- row.setCell("STATUS","OK");
+ row.setCell("STATUS", "OK");
row.setCell("MESSAGE", "Operation Successful");
row.setCell("RESULT", result);
- else :
+ else:
tableBuilder.addHeader("STATUS");
tableBuilder.addHeader("MESSAGE");
row = tableBuilder.addRow();
- row.setCell("STATUS","FAIL");
+ row.setCell("STATUS", "FAIL");
row.setCell("MESSAGE", "Operation Failed");
-
+
def addToExportWithoutRepeating(entitiesToExport, entityFound):
found = False;
@@ -161,38 +134,56 @@ def addToExportWithoutRepeating(entitiesToExport, entityFound):
if not found:
entitiesToExport.append(entityFound);
-def expandAndexport(tr, params):
- #Services used during the export process
- # TO-DO Login on the services as ETL server but on behalf of the user that makes the call
+
+def validateDataSize(entitiesToExport, tr):
+ limitDataSizeInMegabytes = getConfigurationProperty(tr, 'limit-data-size-megabytes')
+ if limitDataSizeInMegabytes is None:
+ limitDataSizeInMegabytes = 500;
+ else:
+ limitDataSizeInMegabytes = int(limitDataSizeInMegabytes);
+ limitDataSizeInBytes = 1000000 * limitDataSizeInMegabytes;
+ estimatedSizeInBytes = 0;
+ for entityToExport in entitiesToExport:
+ if entityToExport["type"] == "FILE" and entityToExport["isDirectory"] == False:
+ estimatedSizeInBytes += entityToExport["length"];
+ elif entityToExport["type"] != "FILE":
+ estimatedSizeInBytes += 12000; # AVG File Metadata size
+ estimatedSizeInMegabytes = estimatedSizeInBytes / 1000000;
+ operationLog.info(
+ "Size Limit check - limitDataSizeInBytes: " + str(limitDataSizeInBytes) + " > " + " estimatedSizeInBytes: " + str(estimatedSizeInBytes));
+ if estimatedSizeInBytes > limitDataSizeInBytes:
+ raise UserFailureException("The selected data is " + str(estimatedSizeInMegabytes) + " MB that is bigger than the configured limit of " + str(
+ limitDataSizeInMegabytes) + " MB");
+
+
+def findEntitiesToExport(params):
sessionToken = params.get("sessionToken");
v3 = ServiceProvider.getV3ApplicationService();
v3d = ServiceProvider.getApplicationContext().getBean(V3_DSS_BEAN);
- mailClient = tr.getGlobalState().getMailClient();
metadataOnly = params.get("metadataOnly");
- entitiesToExport = [];
entitiesToExpand = deque([]);
-
+ entitiesToExport = [];
entities = params.get("entities");
- includeRoot = params.get("includeRoot");
- userEmail = v3.getSessionInformation(sessionToken).getPerson().getEmail();
+
for entity in entities:
entityAsPythonMap = { "type" : entity.get("type"), "permId" : entity.get("permId"), "expand" : entity.get("expand") };
- addToExportWithoutRepeating(entitiesToExport, entityAsPythonMap);
+ entitiesToExport.append(entityAsPythonMap);
if entity.get("expand"):
entitiesToExpand.append(entityAsPythonMap);
-
+
+ operationLog.info("Found %d entities to expand." % len(entitiesToExpand))
while entitiesToExpand:
entityToExpand = entitiesToExpand.popleft();
- type = entityToExpand["type"];
+ type = entityToExpand["type"];
permId = entityToExpand["permId"];
operationLog.info("Expanding type: " + str(type) + " permId: " + str(permId));
-
+
if type == "ROOT":
criteria = SpaceSearchCriteria();
results = v3.searchSpaces(sessionToken, criteria, SpaceFetchOptions());
operationLog.info("Found: " + str(results.getTotalCount()) + " spaces");
for space in results.getObjects():
- entityFound = { "type" : "SPACE", "permId" : space.getCode() };
+ entityFound = {"type": "SPACE", "permId": space.getCode(), "registrationDate": space.getRegistrationDate()};
addToExportWithoutRepeating(entitiesToExport, entityFound);
entitiesToExpand.append(entityFound);
if type == "SPACE":
@@ -201,7 +192,7 @@ def expandAndexport(tr, params):
results = v3.searchProjects(sessionToken, criteria, ProjectFetchOptions());
operationLog.info("Found: " + str(results.getTotalCount()) + " projects");
for project in results.getObjects():
- entityFound = { "type" : "PROJECT", "permId" : project.getPermId().getPermId() };
+ entityFound = {"type": "PROJECT", "permId": project.getPermId().getPermId(), "registrationDate": project.getRegistrationDate()};
addToExportWithoutRepeating(entitiesToExport, entityFound);
entitiesToExpand.append(entityFound);
if type == "PROJECT":
@@ -210,7 +201,8 @@ def expandAndexport(tr, params):
results = v3.searchExperiments(sessionToken, criteria, ExperimentFetchOptions());
operationLog.info("Found: " + str(results.getTotalCount()) + " experiments");
for experiment in results.getObjects():
- entityFound = { "type" : "EXPERIMENT", "permId" : experiment.getPermId().getPermId() };
+ entityFound = {"type": "EXPERIMENT", "permId": experiment.getPermId().getPermId(),
+ "registrationDate": experiment.getRegistrationDate()};
addToExportWithoutRepeating(entitiesToExport, entityFound);
entitiesToExpand.append(entityFound);
if type == "EXPERIMENT":
@@ -218,29 +210,33 @@ def expandAndexport(tr, params):
criteria.withExperiment().withPermId().thatEquals(permId);
results = v3.searchSamples(sessionToken, criteria, SampleFetchOptions());
operationLog.info("Found: " + str(results.getTotalCount()) + " samples");
-
+
dCriteria = DataSetSearchCriteria();
dCriteria.withExperiment().withPermId().thatEquals(permId);
dCriteria.withoutSample();
- dResults = v3.searchDataSets(sessionToken, dCriteria, DataSetFetchOptions());
+ fetchOptions = DataSetFetchOptions()
+ fetchOptions.withDataStore()
+ dResults = v3.searchDataSets(sessionToken, dCriteria, fetchOptions);
operationLog.info("Found: " + str(dResults.getTotalCount()) + " datasets");
for dataset in dResults.getObjects():
- entityFound = { "type" : "DATASET", "permId" : dataset.getPermId().getPermId() };
+ entityFound = {"type": "DATASET", "permId": dataset.getPermId().getPermId(), "registrationDate": dataset.getRegistrationDate()};
addToExportWithoutRepeating(entitiesToExport, entityFound);
entitiesToExpand.append(entityFound);
-
+
operationLog.info("Found: " + str(results.getTotalCount()) + " samples");
for sample in results.getObjects():
- entityFound = { "type" : "SAMPLE", "permId" : sample.getPermId().getPermId() };
+ entityFound = {"type": "SAMPLE", "permId": sample.getPermId().getPermId(), "registrationDate": sample.getRegistrationDate()};
addToExportWithoutRepeating(entitiesToExport, entityFound);
entitiesToExpand.append(entityFound);
if type == "SAMPLE":
criteria = DataSetSearchCriteria();
criteria.withSample().withPermId().thatEquals(permId);
- results = v3.searchDataSets(sessionToken, criteria, DataSetFetchOptions());
+ fetchOptions = DataSetFetchOptions()
+ fetchOptions.withDataStore()
+ results = v3.searchDataSets(sessionToken, criteria, fetchOptions);
operationLog.info("Found: " + str(results.getTotalCount()) + " datasets");
for dataset in results.getObjects():
- entityFound = { "type" : "DATASET", "permId" : dataset.getPermId().getPermId() };
+ entityFound = {"type": "DATASET", "permId": dataset.getPermId().getPermId(), "registrationDate": dataset.getRegistrationDate()};
addToExportWithoutRepeating(entitiesToExport, entityFound);
entitiesToExpand.append(entityFound);
if type == "DATASET" and not metadataOnly:
@@ -249,70 +245,51 @@ def expandAndexport(tr, params):
results = v3d.searchFiles(sessionToken, criteria, DataSetFileFetchOptions());
operationLog.info("Found: " + str(results.getTotalCount()) + " files");
for file in results.getObjects():
- entityFound = { "type" : "FILE", "permId" : permId, "path" : file.getPath(), "isDirectory" : file.isDirectory(), "length" : file.getFileLength() };
+ entityFound = {"type": "FILE", "permId": permId, "path": file.getPath(), "isDirectory": file.isDirectory(),
+ "length": file.getFileLength()};
addToExportWithoutRepeating(entitiesToExport, entityFound);
-
-
- limitDataSizeInMegabytes = getConfigurationProperty(tr, 'limit-data-size-megabytes');
- if limitDataSizeInMegabytes is None:
- limitDataSizeInMegabytes = 500;
- else:
- limitDataSizeInMegabytes = int(limitDataSizeInMegabytes);
-
- limitDataSizeInBytes = 1000000 * limitDataSizeInMegabytes;
- estimatedSizeInBytes = 0;
- for entityToExport in entitiesToExport:
- if entityToExport["type"] == "FILE" and entityToExport["isDirectory"] == False:
- estimatedSizeInBytes += entityToExport["length"];
- elif entityToExport["type"] != "FILE":
- estimatedSizeInBytes += 12000; #AVG File Metadata size
- estimatedSizeInMegabytes = estimatedSizeInBytes / 1000000;
-
- operationLog.info("Size Limit check - limitDataSizeInBytes: " + str(limitDataSizeInBytes) + " > " + " estimatedSizeInBytes: " + str(estimatedSizeInBytes));
- if estimatedSizeInBytes > limitDataSizeInBytes:
- raise UserFailureException("The selected data is " + str(estimatedSizeInMegabytes) + " MB that is bigger than the configured limit of " + str(limitDataSizeInMegabytes) + " MB");
-
- operationLog.info("Found " + str(len(entitiesToExport)) + " entities to export, export thread will start");
- thread = threading.Thread(target=export, args=(sessionToken, entitiesToExport, includeRoot, userEmail, mailClient));
- thread.daemon = True;
- thread.start();
-
- return True;
+ return entitiesToExport
+
+
+# Removes temporal folder and zip
+def cleanUp(tempDirPath, tempZipFilePath):
+ FileUtils.forceDelete(File(tempDirPath));
+ FileUtils.forceDelete(File(tempZipFilePath));
+
+
+# Generates ZIP file and stores it in workspace
+def generateZipFile(entities, includeRoot, sessionToken, tempDirPath, tempZipFilePath):
+ # Create Zip File
+ fos = FileOutputStream(tempZipFilePath);
+ zos = ZipOutputStream(fos);
+
+ generateFilesInZip(zos, entities, includeRoot, sessionToken, tempDirPath)
-def export(sessionToken, entities, includeRoot, userEmail, mailClient):
- #Services used during the export process
+ zos.close();
+ fos.close();
+
+
+def generateFilesInZip(zos, entities, includeRoot, sessionToken, tempDirPath):
+ # Services used during the export process
v3 = ServiceProvider.getV3ApplicationService();
v3d = ServiceProvider.getApplicationContext().getBean(V3_DSS_BEAN);
- dssComponent = DssComponentFactory.tryCreate(sessionToken, OPENBISURL);
-
objectCache = {};
objectMapper = GenericObjectMapper();
objectMapper.enable(SerializationFeature.INDENT_OUTPUT);
-
- #Create temporal folder
- tempDirName = "export_" + str(time.time());
- tempDirPathFile = File.createTempFile(tempDirName, None);
- tempDirPathFile.delete();
- tempDirPathFile.mkdir();
- tempDirPath = tempDirPathFile.getCanonicalPath();
- #To avoid empty directories on the zip file, it makes the first found entity the base directory
+ # To avoid empty directories on the zip file, it makes the first found entity the base directory
baseDirToCut = None;
-
- #Create Zip File
- tempZipFileName = tempDirName + ".zip";
- tempZipFilePath = tempDirPath + ".zip";
- fos = FileOutputStream(tempZipFilePath);
- zos = ZipOutputStream(fos);
-
+ fileMetadata = []
+ emptyZip = True
+
for entity in entities:
- type = entity["type"];
+ type = entity["type"];
permId = entity["permId"];
operationLog.info("exporting type: " + str(type) + " permId: " + str(permId));
entityObj = None;
entityFilePath = None;
-
+
if type == "SPACE":
- pass #Do nothing
+ pass # Do nothing
if type == "PROJECT":
criteria = ProjectSearchCriteria();
criteria.withPermId().thatEquals(permId);
@@ -333,7 +310,8 @@ def export(sessionToken, entities, includeRoot, userEmail, mailClient):
fetchOps.withProperties();
fetchOps.withTags();
entityObj = v3.searchExperiments(sessionToken, criteria, fetchOps).getObjects().get(0);
- entityFilePath = getFilePath(entityObj.getProject().getSpace().getCode(), entityObj.getProject().getCode(), entityObj.getCode(), None, None);
+ entityFilePath = getFilePath(entityObj.getProject().getSpace().getCode(), entityObj.getProject().getCode(), entityObj.getCode(), None,
+ None);
if type == "SAMPLE":
criteria = SampleSearchCriteria();
criteria.withPermId().thatEquals(permId);
@@ -347,7 +325,9 @@ def export(sessionToken, entities, includeRoot, userEmail, mailClient):
fetchOps.withParents().withProperties();
fetchOps.withChildren().withProperties();
entityObj = v3.searchSamples(sessionToken, criteria, fetchOps).getObjects().get(0);
- entityFilePath = getFilePath(entityObj.getExperiment().getProject().getSpace().getCode(), entityObj.getExperiment().getProject().getCode(), entityObj.getExperiment().getCode(), entityObj.getCode(), None);
+ entityFilePath = getFilePath(entityObj.getExperiment().getProject().getSpace().getCode(),
+ entityObj.getExperiment().getProject().getCode(), entityObj.getExperiment().getCode(), entityObj.getCode(),
+ None);
if type == "DATASET":
criteria = DataSetSearchCriteria();
criteria.withPermId().thatEquals(permId);
@@ -362,71 +342,84 @@ def export(sessionToken, entities, includeRoot, userEmail, mailClient):
fetchOps.withParents().withProperties();
fetchOps.withChildren().withProperties();
entityObj = v3.searchDataSets(sessionToken, criteria, fetchOps).getObjects().get(0);
-
+
sampleCode = None
- if(entityObj.getSample() is not None):
+ if (entityObj.getSample() is not None):
sampleCode = entityObj.getSample().getCode();
-
- entityFilePath = getFilePath(entityObj.getExperiment().getProject().getSpace().getCode(), entityObj.getExperiment().getProject().getCode(), entityObj.getExperiment().getCode(), sampleCode, entityObj.getCode());
+
+ entityFilePath = getFilePath(entityObj.getExperiment().getProject().getSpace().getCode(),
+ entityObj.getExperiment().getProject().getCode(), entityObj.getExperiment().getCode(), sampleCode,
+ entityObj.getCode());
if type == "FILE" and not entity["isDirectory"]:
datasetEntityObj = objectCache[entity["permId"]];
sampleCode = None
- if(datasetEntityObj.getSample() is not None):
+ if (datasetEntityObj.getSample() is not None):
sampleCode = datasetEntityObj.getSample().getCode();
-
- datasetEntityFilePath = getFilePath(datasetEntityObj.getExperiment().getProject().getSpace().getCode(), datasetEntityObj.getExperiment().getProject().getCode(), datasetEntityObj.getExperiment().getCode(), sampleCode, datasetEntityObj.getCode());
+
+ datasetEntityFilePath = getFilePath(datasetEntityObj.getExperiment().getProject().getSpace().getCode(),
+ datasetEntityObj.getExperiment().getProject().getCode(), datasetEntityObj.getExperiment().getCode(),
+ sampleCode, datasetEntityObj.getCode());
filePath = datasetEntityFilePath + "/" + entity["path"];
-
+
if not includeRoot:
- filePath = filePath[len(baseDirToCut):] #To avoid empty directories on the zip file, it makes the first found entity the base directory
-
- rawFileInputStream = DataSetFileDownloadReader(v3d.downloadFiles(sessionToken, [DataSetFilePermId(DataSetPermId(permId), entity["path"])], DataSetFileDownloadOptions())).read().getInputStream();
+ filePath = filePath[
+ len(baseDirToCut):] # To avoid empty directories on the zip file, it makes the first found entity the base directory
+
+ rawFileInputStream = DataSetFileDownloadReader(v3d.downloadFiles(sessionToken, [DataSetFilePermId(DataSetPermId(permId), entity["path"])],
+ DataSetFileDownloadOptions())).read().getInputStream();
rawFile = File(tempDirPath + filePath + ".json");
rawFile.getParentFile().mkdirs();
IOUtils.copyLarge(rawFileInputStream, FileOutputStream(rawFile));
addToZipFile(filePath, rawFile, zos);
-
- #To avoid empty directories on the zip file, it makes the first found entity the base directory
+ emptyZip = False
+
+ # To avoid empty directories on the zip file, it makes the first found entity the base directory
if not includeRoot:
if baseDirToCut is None and entityFilePath is not None:
baseDirToCut = entityFilePath[:entityFilePath.rfind('/')];
if entityFilePath is not None:
entityFilePath = entityFilePath[len(baseDirToCut):]
#
-
+
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("--> Entity type: " + type + " permId: " + permId + " obj: " + str(entityObj is not None) + " path: " + str(
+ entityFilePath) + " before files.");
if entityObj is not None and entityFilePath is not None:
- #JSON
+ # JSON
entityJson = String(objectMapper.writeValueAsString(entityObj));
- addFile(tempDirPath, entityFilePath, "json", entityJson.getBytes(), zos);
- #TEXT
+ fileMetadatum = addFile(tempDirPath, entityFilePath, "json", entityJson.getBytes(), zos);
+ fileMetadata.append(fileMetadatum)
+ emptyZip = False
+ # TEXT
entityTXT = String(getTXT(entityObj, v3, sessionToken, False));
- addFile(tempDirPath, entityFilePath, "txt", entityTXT.getBytes(), zos);
- #DOCX
+ fileMetadatum = addFile(tempDirPath, entityFilePath, "txt", entityTXT.getBytes(), zos);
+ fileMetadata.append(fileMetadatum)
+ # DOCX
entityDOCX = getDOCX(entityObj, v3, sessionToken, False);
- addFile(tempDirPath, entityFilePath, "docx", entityDOCX, zos);
- #HTML
+ fileMetadatum = addFile(tempDirPath, entityFilePath, "docx", entityDOCX, zos);
+ fileMetadata.append(fileMetadatum)
+ # HTML
entityHTML = getDOCX(entityObj, v3, sessionToken, True);
- addFile(tempDirPath, entityFilePath, "html", entityHTML, zos);
+ fileMetadatum = addFile(tempDirPath, entityFilePath, "html", entityHTML, zos);
+ fileMetadata.append(fileMetadatum)
operationLog.info("--> Entity type: " + type + " permId: " + permId + " post html.");
-
- zos.close();
- fos.close();
-
- #Store on workspace to be able to generate a download link
+ if emptyZip:
+ raise IOError('Nothing added to ZIP file.')
+ return fileMetadata
+
+
+def generateDownloadUrl(sessionToken, tempZipFileName, tempZipFilePath):
+ dssComponent = DssComponentFactory.tryCreate(sessionToken, OPENBISURL);
+
+ # Store on workspace to be able to generate a download link
operationLog.info("Zip file can be found on the temporal directory: " + tempZipFilePath);
dssComponent.putFileToSessionWorkspace(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);
- #Send Email
- sendMail(mailClient, userEmail, tempZipFileWorkspaceURL);
- #Remove temporal folder and zip
- FileUtils.forceDelete(File(tempDirPath));
- FileUtils.forceDelete(File(tempZipFilePath));
- return True
+ return tempZipFileWorkspaceURL
+
def getDOCX(entityObj, v3, sessionToken, isHTML):
docxBuilder = DOCXBuilder();
@@ -600,12 +593,25 @@ def getTXT(entityObj, v3, sessionToken, isRichText):
return txtBuilder.toString();
def addFile(tempDirPath, entityFilePath, extension, fileContent, zos):
- entityFile = File(tempDirPath + entityFilePath + "." + extension);
+ entityFileNameWithExtension = entityFilePath + "." + extension
+ entityFile = File(tempDirPath + entityFileNameWithExtension);
entityFile.getParentFile().mkdirs();
IOUtils.write(fileContent, FileOutputStream(entityFile));
- addToZipFile(entityFilePath + "." + extension, entityFile, zos);
+ addToZipFile(entityFileNameWithExtension, entityFile, zos);
FileUtils.forceDelete(entityFile);
+ extensionToMimeType = {
+ 'json': 'application/json',
+ 'txt': 'text/plain',
+ 'docx': 'application/vnd.openxmlformats-officedocument.wordprocessingml.document',
+ 'html': 'text/html',
+ }
+
+ return {
+ 'fileName': entityFileNameWithExtension[1:],
+ 'mimeType': extensionToMimeType.get(extension, 'application/octet-stream')
+ }
+
def getFilePath(spaceCode, projCode, expCode, sampCode, dataCode):
fileName = "";
if spaceCode is not None:
@@ -621,27 +627,18 @@ def getFilePath(spaceCode, projCode, expCode, sampCode, dataCode):
return fileName;
def addToZipFile(path, file, zos):
- fis = FileInputStream(file);
- zipEntry = ZipEntry(path[1:]); # Making paths relative to make them compatible with Windows zip implementation
- zos.putNextEntry(zipEntry);
-
- bytes = jarray.zeros(1024, "b");
+ fis = FileInputStream(file);
+ zipEntry = ZipEntry(path[1:]); # Making paths relative to make them compatible with Windows zip implementation
+ zos.putNextEntry(zipEntry);
+
+ bytes = jarray.zeros(1024, "b");
+ length = fis.read(bytes);
+ while length >= 0:
+ zos.write(bytes, 0, length);
length = fis.read(bytes);
- while length >= 0:
- zos.write(bytes, 0, length);
- length = fis.read(bytes);
-
- zos.closeEntry();
- fis.close();
-
-def sendMail(mailClient, userEmail, downloadURL):
- replyTo = None;
- fromAddress = None;
- recipient1 = EMailAddress(userEmail);
- topic = "Export Ready";
- message = "Download a zip file with your exported data at: " + downloadURL;
- mailClient.sendEmailMessage(topic, message, replyTo, fromAddress, recipient1);
- operationLog.info("--- MAIL ---" + " Recipient: " + userEmail + " Topic: " + topic + " Message: " + message);
+
+ zos.closeEntry();
+ fis.close();
def getConfigurationProperty(transaction, propertyName):
threadProperties = transaction.getGlobalState().getThreadParameters().getThreadProperties();
diff --git a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/dss/reporting-plugins/exports-api/generalExports.py b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/dss/reporting-plugins/exports-api/generalExports.py
new file mode 100644
index 00000000000..4a5845d984b
--- /dev/null
+++ b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/dss/reporting-plugins/exports-api/generalExports.py
@@ -0,0 +1,87 @@
+#
+# Copyright 2016 ETH Zuerich, Scientific IT Services
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+#
+
+import threading
+import time
+from ch.systemsx.cisd.common.logging import LogCategory
+from ch.systemsx.cisd.common.mail import EMailAddress
+from ch.systemsx.cisd.openbis.dss.generic.shared import ServiceProvider
+from java.io import File
+from org.apache.log4j import Logger
+
+from exportsApi import generateZipFile, cleanUp, displayResult, findEntitiesToExport, validateDataSize, generateDownloadUrl
+
+operationLog = Logger.getLogger(str(LogCategory.OPERATION) + ".generalExports.py")
+
+def process(tr, params, tableBuilder):
+ method = params.get("method")
+ isOk = False
+
+ # Set user using the service
+
+ tr.setUserId(userId)
+ if method == "exportAll":
+ isOk = expandAndExport(tr, params)
+
+ displayResult(isOk, tableBuilder)
+
+def expandAndExport(tr, params):
+ #Services used during the export process
+ # TO-DO Login on the services as ETL server but on behalf of the user that makes the call
+ sessionToken = params.get("sessionToken")
+ v3 = ServiceProvider.getV3ApplicationService()
+ userEmail = v3.getSessionInformation(sessionToken).getPerson().getEmail()
+
+ entitiesToExport = findEntitiesToExport(params)
+ validateDataSize(entitiesToExport, tr)
+
+ mailClient = tr.getGlobalState().getMailClient()
+ includeRoot = params.get("includeRoot")
+
+ operationLog.info("Found " + str(len(entitiesToExport)) + " entities to export, export thread will start")
+ thread = threading.Thread(target=export, args=(sessionToken, entitiesToExport, includeRoot, userEmail, mailClient))
+ thread.daemon = True
+ thread.start()
+
+ return True
+
+def export(sessionToken, entities, includeRoot, userEmail, mailClient):
+ #Create temporal folder
+ tempDirName = "export_" + str(time.time())
+ tempDirPathFile = File.createTempFile(tempDirName, None)
+ tempDirPathFile.delete()
+ tempDirPathFile.mkdir()
+ tempDirPath = tempDirPathFile.getCanonicalPath()
+ tempZipFileName = tempDirName + ".zip"
+ tempZipFilePath = tempDirPath + ".zip"
+
+ generateZipFile(entities, includeRoot, sessionToken, tempDirPath, tempZipFilePath)
+ tempZipFileWorkspaceURL = generateDownloadUrl(sessionToken, tempZipFileName, tempZipFilePath)
+
+ #Send Email
+ sendMail(mailClient, userEmail, tempZipFileWorkspaceURL)
+
+ cleanUp(tempDirPath, tempZipFilePath)
+ return True
+
+def sendMail(mailClient, userEmail, downloadURL):
+ replyTo = None
+ fromAddress = None
+ recipient1 = EMailAddress(userEmail)
+ topic = "Export Ready"
+ message = "Download a zip file with your exported data at: " + downloadURL
+ mailClient.sendEmailMessage(topic, message, replyTo, fromAddress, recipient1)
+ operationLog.info("--- MAIL ---" + " Recipient: " + userEmail + " Topic: " + topic + " Message: " + message)
\ No newline at end of file
diff --git a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/dss/reporting-plugins/exports-api/plugin.properties b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/dss/reporting-plugins/exports-api/plugin.properties
index 223af21c0cf..e44c1b3b476 100644
--- a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/dss/reporting-plugins/exports-api/plugin.properties
+++ b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/dss/reporting-plugins/exports-api/plugin.properties
@@ -1,4 +1,4 @@
label = Exports API
class = ch.systemsx.cisd.openbis.dss.generic.server.plugins.jython.JythonIngestionService
-script-path = exports-api.py
+script-path = generalExports.py
limit-data-size-megabytes = 10000
\ No newline at end of file
diff --git a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/dss/reporting-plugins/rc-exports-api/exportsApi.py b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/dss/reporting-plugins/rc-exports-api/exportsApi.py
new file mode 120000
index 00000000000..ccb8a49feb3
--- /dev/null
+++ b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/dss/reporting-plugins/rc-exports-api/exportsApi.py
@@ -0,0 +1 @@
+../exports-api/exportsApi.py
\ No newline at end of file
diff --git a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/dss/reporting-plugins/rc-exports-api/plugin.properties b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/dss/reporting-plugins/rc-exports-api/plugin.properties
new file mode 100644
index 00000000000..eabafa539e8
--- /dev/null
+++ b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/dss/reporting-plugins/rc-exports-api/plugin.properties
@@ -0,0 +1,8 @@
+label = Research Collection Exports API
+class = ch.systemsx.cisd.openbis.dss.generic.server.plugins.jython.JythonIngestionService
+script-path = rcExports.py
+limit-data-size-megabytes = 4000
+service-document-url=https://test.research-collection.ethz.ch/swordv2/servicedocument
+realm=SWORD2
+user=youruser
+password=yourpassword
diff --git a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/dss/reporting-plugins/rc-exports-api/rcExports.py b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/dss/reporting-plugins/rc-exports-api/rcExports.py
new file mode 100644
index 00000000000..e354f38dcdd
--- /dev/null
+++ b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/dss/reporting-plugins/rc-exports-api/rcExports.py
@@ -0,0 +1,384 @@
+#
+# Copyright 2016 ETH Zuerich, Scientific IT Services
+#
+# Licensed under the Apache License, Version 2.0 (the 'License');
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an 'AS IS' BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+#
+import json
+import os
+import traceback
+import xml.etree.ElementTree as ET
+
+import datetime
+import time
+from ch.systemsx.cisd.common.logging import LogCategory
+from java.io import File
+from java.io import FileOutputStream
+from java.net import URI
+from java.nio.file import Paths
+from java.text import SimpleDateFormat
+from java.util import UUID
+from java.util.zip import ZipOutputStream
+from org.apache.commons.io import FileUtils
+from org.apache.log4j import Logger
+from org.eclipse.jetty.client import HttpClient
+from org.eclipse.jetty.client.util import BasicAuthentication
+from org.eclipse.jetty.http import HttpMethod
+from org.eclipse.jetty.util.ssl import SslContextFactory
+
+from exportsApi import displayResult, findEntitiesToExport, validateDataSize, getConfigurationProperty, generateFilesInZip, addToZipFile, cleanUp
+
+operationLog = Logger.getLogger(str(LogCategory.OPERATION) + '.rcExports.py')
+
+
+def process(tr, params, tableBuilder):
+ method = params.get('method')
+
+ # Set user using the service
+ tr.setUserId(userId)
+
+ if method == 'exportAll':
+ resultUrl = expandAndExport(tr, params)
+ displayResult(resultUrl is not None, tableBuilder, '{"url": "' + resultUrl + '"}' if resultUrl is not None else None)
+ elif method == 'getSubmissionTypes':
+ collectionUrls = getSubmissionTypes(tr)
+ displayResult(collectionUrls is not None, tableBuilder, collectionUrls)
+
+
+def getSubmissionTypes(tr):
+ url = getConfigurationProperty(tr, 'service-document-url')
+
+ httpClient = None
+ try:
+ httpClient = authenticateUserJava(url, tr)
+ httpClient.setFollowRedirects(True)
+ httpClient.start()
+
+ collections = fetchServiceDocument(url, httpClient)
+ finally:
+ if httpClient is not None:
+ httpClient.stop()
+ return collections
+
+
+def expandAndExport(tr, params):
+ entitiesToExport = findEntitiesToExport(params)
+ validateDataSize(entitiesToExport, tr)
+
+ userInformation = {
+ 'firstName': params.get('userFirstName'),
+ 'lastName': params.get('userLastName'),
+ 'email': params.get('userEmail'),
+ }
+
+ operationLog.info('Found ' + str(len(entitiesToExport)) + ' entities to export')
+ return export(entities=entitiesToExport, tr=tr, params=params, userInformation=userInformation)
+
+
+def export(entities, tr, params, userInformation):
+ #Create temporal folder
+ timeNow = time.time()
+
+ exportDirName = 'export_' + str(timeNow)
+ exportDir = File.createTempFile(exportDirName, None)
+ exportDirPath = exportDir.getCanonicalPath()
+ exportDir.delete()
+ exportDir.mkdir()
+
+ contentZipFileName = 'content.zip'
+ contentDirName = 'content_' + str(timeNow)
+ contentDir = File.createTempFile(contentDirName, None, exportDir)
+ contentDirPath = contentDir.getCanonicalPath()
+ contentDir.delete()
+ contentDir.mkdir()
+
+ contentZipFilePath = exportDirPath + '/' + contentZipFileName
+
+ exportZipFilePath = exportDirPath + '.zip'
+ exportZipFileName = exportDirName + '.zip'
+
+ generateInternalZipFile(entities, params, contentDirPath, contentZipFilePath)
+ FileUtils.forceDelete(File(contentDirPath))
+
+ generateExternalZipFile(params=params, exportDirPath=exportDirPath, contentZipFilePath=contentZipFilePath, contentZipFileName=contentZipFileName,
+ exportZipFileName=exportZipFilePath, userInformation=userInformation, entities=entities)
+ resultUrl = sendToDSpace(params=params, tr=tr, tempZipFileName=exportZipFileName, tempZipFilePath=exportZipFilePath)
+ cleanUp(exportDirPath, exportZipFilePath)
+ return resultUrl
+
+
+def sendToDSpace(params, tr, tempZipFileName, tempZipFilePath):
+ depositUrl = str(params.get('submissionUrl'))
+
+ headers = {
+ 'In-Progress': 'true',
+ 'Content-Disposition': 'filename=' + tempZipFileName,
+ 'Content-Type': 'application/zip',
+ 'Content-Length': os.stat(tempZipFilePath).st_size,
+ 'Content-Transfer-Encoding': 'binary',
+ 'Packaging': 'http://purl.org/net/sword/package/METSDSpaceSIP',
+ 'On-Behalf-Of': str(params.get('userId')),
+ }
+
+ httpClient = None
+ try:
+ httpClient = authenticateUserJava(depositUrl, tr)
+
+ httpClient.setFollowRedirects(True)
+ httpClient.start()
+
+ request = httpClient.newRequest(depositUrl)
+ for key, value in headers.iteritems():
+ request.header(key, str(value))
+ response = request.method(HttpMethod.POST).file(Paths.get(tempZipFilePath), 'application/zip').send()
+ status = response.getStatus()
+ if status >= 300:
+ reason = response.getReason()
+ raise ValueError('Unsuccessful response from the server: %s %s' % (status, reason))
+
+ xmlText = response.getContentAsString().encode('utf-8')
+ xmlRoot = ET.fromstring(xmlText)
+ linkElement = xmlRoot.find('xmlns:link[@rel="alternate"]', namespaces=dict(xmlns='http://www.w3.org/2005/Atom'))
+ if linkElement is None:
+ raise ValueError('No redirection URL is found in the response.')
+
+ href = linkElement.attrib['href']
+
+ return href
+ except Exception as e:
+ operationLog.error('Exception at: ' + traceback.format_exc())
+ operationLog.error('Exception: ' + str(e))
+ raise e
+ finally:
+ if httpClient is not None:
+ httpClient.stop()
+
+
+def authenticateUserJava(url, tr):
+ sslContextFactory = SslContextFactory()
+ httpClient = HttpClient(sslContextFactory)
+ uri = URI(url)
+ user = getConfigurationProperty(tr, 'user')
+ password = getConfigurationProperty(tr, 'password')
+ realm = getConfigurationProperty(tr, 'realm')
+ auth = httpClient.getAuthenticationStore()
+ auth.addAuthentication(BasicAuthentication(uri, realm, user, password))
+ return httpClient
+
+
+def fetchServiceDocument(url, httpClient):
+ response = httpClient.newRequest(url).method(HttpMethod.GET).send()
+
+ xmlText = response.getContentAsString().encode('utf-8')
+ xmlRoot = ET.fromstring(xmlText)
+ collections = xmlRoot.findall('./xmlns:workspace/xmlns:collection[@href]', namespaces=dict(xmlns='http://www.w3.org/2007/app'))
+
+ def collectionToDictionaryMapper(collection):
+ return {
+ 'title': collection.find('./atom:title', namespaces=dict(atom='http://www.w3.org/2005/Atom')).text,
+ 'url': collection.attrib['href'],
+ }
+
+ return json.dumps(map(collectionToDictionaryMapper, collections))
+
+
+def generateInternalZipFile(entities, params, tempDirPath, tempZipFilePath):
+ # Generates ZIP file with selected item for export
+
+ sessionToken = params.get('sessionToken')
+ includeRoot = params.get('includeRoot')
+
+ fos = None
+ zos = None
+ try:
+ fos = FileOutputStream(tempZipFilePath)
+ zos = ZipOutputStream(fos)
+
+ fileMetadata = generateFilesInZip(zos, entities, includeRoot, sessionToken, tempDirPath)
+ finally:
+ if zos is not None:
+ zos.close()
+ if fos is not None:
+ fos.close()
+
+ return fileMetadata
+
+
+def generateExternalZipFile(params, exportDirPath, contentZipFilePath, contentZipFileName, exportZipFileName, userInformation, entities):
+ # Generates ZIP file which will go to the research collection server
+
+ originUrl=params.get('originUrl')
+ submissionType = str(params.get('submissionType'))
+
+ fileMetadata = [
+ {
+ 'fileName': contentZipFileName,
+ 'mimeType': 'application/zip'
+ }
+ ]
+
+ fos = None
+ zos = None
+ try:
+ fos = FileOutputStream(exportZipFileName)
+ zos = ZipOutputStream(fos)
+
+ addToZipFile(' ' + contentZipFileName, File(contentZipFilePath), zos)
+
+ generateXML(zipOutputStream=zos, fileMetadata=fileMetadata, exportDirPath=exportDirPath, submissionType=submissionType,
+ userInformation=userInformation, entities=entities, originUrl=originUrl)
+ except Exception as e:
+ operationLog.error('Exception at: ' + traceback.format_exc())
+ operationLog.error('Exception: ' + str(e))
+ raise e
+ finally:
+ if zos is not None:
+ zos.close()
+ if fos is not None:
+ fos.close()
+
+
+def generateXML(zipOutputStream, fileMetadata, exportDirPath, submissionType, userInformation, entities, originUrl):
+ ns = {
+ 'mets': 'http://www.loc.gov/METS/',
+ 'xlink': 'http://www.w3.org/1999/xlink',
+ 'dim': 'http://www.dspace.org/xmlns/dspace/dim'
+ }
+
+ entityPermIds = map(lambda entity: entity['permId'], entities)
+ permIdsStr = reduce(lambda str, permId: str + ',' + permId, entityPermIds)
+
+ withRegistrationDates = filter(lambda entity: 'registrationDate' in entity, entities)
+ registrationDates = map(lambda entity: entity['registrationDate'], withRegistrationDates)
+
+ if len(registrationDates) > 0:
+ minDateStr = javaDateToStr(min(registrationDates, key=lambda date: date.getTime()))
+ maxDateStr = javaDateToStr(max(registrationDates, key=lambda date: date.getTime()))
+ else:
+ minDateStr = None
+ maxDateStr = None
+
+ metsNS = ns['mets']
+ xlinkNS = ns['xlink']
+ dimNS = ns['dim']
+ ET.register_namespace('mets', metsNS)
+ ET.register_namespace('xlink', xlinkNS)
+ ET.register_namespace('dim', dimNS)
+
+ root = ET.Element(ET.QName(metsNS, 'METS'))
+ root.set('LABEL', 'DSpace Item')
+ root.set('ID', UUID.randomUUID().toString())
+
+ dmdSec = ET.SubElement(root, ET.QName(metsNS, 'dmdSec'))
+ dmdSec.set('GROUPID', 'group_dmd_0')
+ dmdSec.set('ID', 'dmd_1')
+
+ mdWrap = ET.SubElement(dmdSec, ET.QName(metsNS, 'mdWrap'))
+ mdWrap.set('MDTYPE', 'OTHER')
+ mdWrap.set('OTHERMDTYPE', 'DIM')
+
+ xmlData = ET.SubElement(mdWrap, ET.QName(metsNS, 'xmlData'))
+
+ dim = ET.SubElement(xmlData, ET.QName(dimNS, 'dim'))
+ dim.set('dspaceType', 'ITEM')
+
+ titleField = ET.SubElement(dim, ET.QName(dimNS, 'field'))
+ titleField.set('mdschema', 'dc')
+ titleField.set('element', 'title')
+ titleField.text = str(time.time())
+
+ typeField = ET.SubElement(dim, ET.QName(dimNS, 'field'))
+ typeField.set('mdschema', 'dc')
+ typeField.set('element', 'type')
+ typeField.text = submissionType
+
+ userIdField = ET.SubElement(dim, ET.QName(dimNS, 'field'))
+ userIdField.set('mdschema', 'ethz')
+ userIdField.set('element', 'identifier')
+ userIdField.set('qualifier', 'openbis')
+ userIdField.text = permIdsStr
+
+ userInfoField = ET.SubElement(dim, ET.QName(dimNS, 'field'))
+ userInfoField.set('mdschema', 'dc')
+ userInfoField.set('element', 'contributor')
+ userInfoField.set('qualifier', 'author')
+ userInfoField.text = userInformation['lastName'] + ', ' + userInformation['firstName']
+
+ publicationDateField = ET.SubElement(dim, ET.QName(dimNS, 'field'))
+ publicationDateField.set('mdschema', 'dc')
+ publicationDateField.set('element', 'date')
+ publicationDateField.set('qualifier', 'issued')
+ publicationDateField.text = datetime.date.today().strftime('%Y-%m-%d')
+
+ elnLimsURLPattern = '/openbis-test/webapp/eln-lims/?menuUniqueId=null&viewName='
+
+ for entity in entities:
+ type = entity['type']
+ viewName = ''
+ if type == 'SPACE':
+ viewName = 'showSpacePage'
+ if type == 'PROJECT':
+ viewName = 'showProjectPageFromPermId'
+ if type == 'EXPERIMENT':
+ viewName = 'showExperimentPageFromPermId'
+ if type == 'SAMPLE':
+ viewName = 'showViewSamplePageFromPermId'
+ if type == 'DATASET':
+ viewName = 'showViewDataSetPageFromPermId'
+ if type != 'FILE':
+ urlField = ET.SubElement(dim, ET.QName(dimNS, 'field'))
+ urlField.set('mdschema', 'ethz')
+ urlField.set('element', 'identifier')
+ urlField.set('qualifier', 'url')
+ urlField.text = originUrl + elnLimsURLPattern + viewName + '&viewData=' + entity['permId']
+
+ if minDateStr is not None and maxDateStr is not None:
+ creationDateField = ET.SubElement(dim, ET.QName(dimNS, 'field'))
+ creationDateField.set('mdschema', 'dc')
+ creationDateField.set('element', 'date')
+ creationDateField.set('qualifier', 'created')
+ creationDateField.text = minDateStr + '/' + maxDateStr if minDateStr != maxDateStr else minDateStr
+
+ fileSec = ET.SubElement(root, ET.QName(metsNS, 'fileSec'))
+ fileGrp = ET.SubElement(fileSec, ET.QName(metsNS, 'fileGrp'))
+ fileGrp.set('USE', 'CONTENT')
+
+ i = 0
+ for fileMetadatum in fileMetadata:
+ i += 1
+ file = ET.SubElement(fileGrp, ET.QName(metsNS, 'file'))
+ file.set('ID', 'file_' + str(i))
+ fLocat = ET.SubElement(file, ET.QName(metsNS, 'FLocat'))
+ fLocat.set('LOCTYPE', 'URL')
+ fLocat.set('MIMETYPE', fileMetadatum.get('mimeType'))
+ fLocat.set('RETENTIONPERIOD', '10 years')
+ fLocat.set(ET.QName(xlinkNS, 'href'), fileMetadatum.get('fileName'))
+
+ structMap = ET.SubElement(root, ET.QName(metsNS, 'structMap'))
+ structMap.set('LABEL', 'DSpace')
+ structMap.set('TYPE', 'LOGICAL')
+ div1 = ET.SubElement(structMap, ET.QName(metsNS, 'div'))
+ div1.set('DMDID', 'dmd_1')
+ div1.set('TYPE', 'DSpace Item')
+
+ xmlFileName = 'mets.xml'
+ xmlFilePath = exportDirPath + '/' + xmlFileName
+ ET.ElementTree(root).write(xmlFilePath)
+
+ xmlFile = File(xmlFilePath)
+ addToZipFile(' ' + xmlFileName, xmlFile, zipOutputStream)
+ # Space is added to the file name because the method chops out the first character
+
+
+def javaDateToStr(javaDate):
+ dateFormat = SimpleDateFormat('yyyy-MM-dd')
+ return dateFormat.format(javaDate)
--
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