diff --git a/openbis_standard_technologies/dist/core-plugins/eln-lims-life-sciences/1/as/master-data/data-model.xls b/openbis_standard_technologies/dist/core-plugins/eln-lims-life-sciences/1/as/master-data/data-model.xls
index 3ee993ae6e5fcd4df2a656c6551274769709d661..dc41839238990f7688c5a4b4f956986f3414f318 100644
Binary files a/openbis_standard_technologies/dist/core-plugins/eln-lims-life-sciences/1/as/master-data/data-model.xls and b/openbis_standard_technologies/dist/core-plugins/eln-lims-life-sciences/1/as/master-data/data-model.xls differ
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 4f80487f892ef4976e6b18b21e387ed772b85e39..21bc5da6b913898b698b337c5eaa1dd604c75b92 100644
Binary files a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/master-data/data-model.xls and b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/master-data/data-model.xls differ
diff --git a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/config/Profile.js b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/config/Profile.js
index b713b303923d04fa508d679c6db1851f4d2ce138..6027757010cb5d97163a8d04c21d03cdcbc93eae 100644
--- a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/config/Profile.js
+++ b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/config/Profile.js
@@ -61,7 +61,8 @@ $.extend(DefaultProfile.prototype, {
showVocabularyViewer : true,
showUserManager : true,
showUserProfile : true,
- showResearchCollectionExportBuilder : false,
+ // Not fully implemented yet.
+ // showResearchCollectionExportBuilder : false,
showZenodoExportBuilder : false,
}
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 8c6bfbcf1f2791f064a86b0aff88d215f6bd5568..4a42b1c0c13a61c3ff253c9f5535a822f8707862 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
@@ -83,13 +83,35 @@ function MainController(profile) {
//Functionality to keep state
this.backStack = [];
+
+ this.zenodoApiTokenKey = "personal-zenodo-api-token";
//
// Validates and enters the app
//
-
+
this.enterApp = function(data, username, password) {
+ var _this = this;
+ if(data && !username && !password) {
+ this.openbisV1.listDataStores(function(result) {
+ if(result && result.error && result.error.message) {
+ var callback = function() {Util.unblockUI();};
+ Util.showUserError(result.error.message, callback);
+ } else {
+ _this.initApp(data, username, password);
+ }
+ });
+ } else {
+ this.initApp(data, username, password);
+ }
+ }
+
+ this.initApp = function(data, username, password) {
var localReference = this;
+ //
+ // Check
+ //
+
//
// Check Credentials
//
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 5fc84d5f807768cfcaf096ac497f5a33875fd4d8..cf273afe3bfe7883c1fbe5f6e7775c43a7243742 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
@@ -417,7 +417,7 @@ function ServerFacade(openbisServer) {
});
};
- this.exportZenodo = function(entities, includeRoot, metadataOnly, userInformation, title, callbackFunction) {
+ this.exportZenodo = function(entities, includeRoot, metadataOnly, userInformation, title, accessToken, callbackFunction) {
this.asyncExportZenodo({
"method": "exportAll",
"includeRoot": includeRoot,
@@ -427,6 +427,7 @@ function ServerFacade(openbisServer) {
"originUrl": window.location.origin,
"sessionToken": this.openbisServer.getSession(),
"submissionTitle": title,
+ "accessToken": accessToken
}, callbackFunction, "zenodo-exports-api");
};
@@ -451,6 +452,7 @@ function ServerFacade(openbisServer) {
options.withParameter("submissionUrl", parameters["submissionUrl"]);
options.withParameter("entities", parameters["entities"]);
options.withParameter("submissionTitle", parameters["submissionTitle"]);
+ options.withParameter("accessToken", parameters["accessToken"]);
options.withParameter("userId", parameters["userInformation"]["id"]);
options.withParameter("userEmail", parameters["userInformation"]["email"]);
options.withParameter("userFirstName", parameters["userInformation"]["firstName"]);
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 ecd57517a2c01f717c852ea89b205c396594b486..8cbb61294a164f081712b1385f5ad793adc4eb3d 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
@@ -240,7 +240,8 @@ function SideMenuWidgetView(sideMenuWidgetController, sideMenuWidgetModel) {
    treeModelUtils.push({ title : jupyterNotebook, entityType: "NEW_JUPYTER_NOTEBOOK", key : "NEW_JUPYTER_NOTEBOOK", folder : false, lazy : false, view : "showNewJupyterNotebookCreator" });
}
- if(profile.mainMenu.showUserProfile && profile.isFileAuthenticationService && profile.isFileAuthenticationUser) {
+ if(profile.mainMenu.showUserProfile) {
+ // && profile.isFileAuthenticationService && profile.isFileAuthenticationUser
    var userProfileLink = _this.getLinkForNode("User Profile", "USER_PROFILE", "showUserProfilePage", null);
    treeModelUtils.push({ title : userProfileLink, entityType: "USER_PROFILE", key : "USER_PROFILE", folder : false, lazy : false, view : "showUserProfilePage", icon : "glyphicon glyphicon-user" });
}
@@ -276,15 +277,16 @@ function SideMenuWidgetView(sideMenuWidgetController, sideMenuWidgetModel) {
});
}
- if (profile.mainMenu.showResearchCollectionExportBuilder) {
- var researchCollectionExportBuilderLink = _this.getLinkForNode("Export to Research Collection",
- "EXPORT_TO_RESEARCH_COLLECTION", "showResearchCollectionExportPage", null);
- treeModelExports.push({
- displayName: "Export to Research Collection", title: researchCollectionExportBuilderLink,
- entityType: "EXPORT_TO_RESEARCH_COLLECTION", key: "EXPORT_TO_RESEARCH_COLLECTION", folder: false, lazy: false,
- view: "showResearchCollectionExportPage", icon: "./img/research-collection-icon.png"
- });
- }
+ // Not fully implemented yet.
+ // if (profile.mainMenu.showResearchCollectionExportBuilder) {
+ // var researchCollectionExportBuilderLink = _this.getLinkForNode("Export to Research Collection",
+ // "EXPORT_TO_RESEARCH_COLLECTION", "showResearchCollectionExportPage", null);
+ // treeModelExports.push({
+ // displayName: "Export to Research Collection", title: researchCollectionExportBuilderLink,
+ // entityType: "EXPORT_TO_RESEARCH_COLLECTION", key: "EXPORT_TO_RESEARCH_COLLECTION", folder: false, lazy: false,
+ // view: "showResearchCollectionExportPage", icon: "./img/research-collection-icon.png"
+ // });
+ // }
if (profile.mainMenu.showZenodoExportBuilder) {
var zenodoExportBuilderLink = _this.getLinkForNode("Export to Zenodo", "EXPORT_TO_ZENODO", "showZenodoExportPage", null);
diff --git a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/UserProfile/UserProfileController.js b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/UserProfile/UserProfileController.js
index 74c870c9621ff3375bbb3817d4d63ead3cee369c..93d3c3fc9e2ebfd73e007cdd00da66bee76928ac 100644
--- a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/UserProfile/UserProfileController.js
+++ b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/UserProfile/UserProfileController.js
@@ -18,6 +18,7 @@ function UserProfileController(mainController, mode) {
this._mainController = mainController;
this._userProfileModel = new UserProfileModel(mode);
this._userProfileView = new UserProfileView(this, this._userProfileModel);
+ this._zenodoApiTokenKey = this._mainController.zenodoApiTokenKey;
this.init = function(views) {
this._userProfileView.repaint(views);
@@ -49,6 +50,8 @@ function UserProfileController(mainController, mode) {
return;
}
var userId = this._mainController.serverFacade.getUserId();
+
+ this.setSettingValue(this._zenodoApiTokenKey, userInformation.zenodoToken);
this._mainController.serverFacade.updateUserInformation(userId, userInformation, (function(ok) {
if (ok) {
Util.showInfo("Profile saved. You will be logged out automatically in order to reload the profile data upon login.", (function() {
@@ -69,4 +72,17 @@ function UserProfileController(mainController, mode) {
return errors;
}
+ this.isFileAuthentication = function() {
+ return this._mainController.profile.isFileAuthenticationService &&
+ this._mainController.profile.isFileAuthenticationUser;
+ }
+
+ this.getSettingValue = function (key, callback) {
+ this._mainController.serverFacade.getSetting(key, callback);
+ };
+
+ this.setSettingValue = function (key, value) {
+ this._mainController.serverFacade.setSetting(key, value);
+ };
+
}
\ 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/UserProfile/UserProfileView.js b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/UserProfile/UserProfileView.js
index 22e972b17ff4a1c0ed7cd41180acf7d7211b6d91..65d80e7574d388b5922b96ea0459bc8b35175128 100644
--- a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/UserProfile/UserProfileView.js
+++ b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/UserProfile/UserProfileView.js
@@ -21,6 +21,7 @@ function UserProfileView(userProfileController, userProfileModel) {
this._$firstNameInput = null;
this._$lastNameInput = null;
this._$emailInput = null;
+ this._$zenodoToken = null;
this.repaint = function(views) {
@@ -71,14 +72,28 @@ function UserProfileView(userProfileController, userProfileModel) {
this._$emailInput = $("<input>", { type : "text", class : "form-control" });
this._$emailInput.val(getUserInformation.email);
$formColumn.append(this._getFormGroup(this._$emailInput, "Email:"));
+ // personal Zenodo API token
+ this._$zenodoToken = $("<input>", { type : "text", class : "form-control" });
+
+ this._userProfileController.getSettingValue(this._userProfileController._zenodoApiTokenKey, (function (settingsValue) {
+ if (settingsValue) {
+ this._$zenodoToken.val(settingsValue.trim());
+ }
+ }).bind(this));
+ $formColumn.append(this._getFormGroup(this._$zenodoToken, "Zenodo API Token:"));
+
// disable in view mode
- if (this._userProfileModel.mode === FormMode.VIEW) {
+ if (this._userProfileModel.mode === FormMode.VIEW ||
+ !this._userProfileController.isFileAuthentication()) {
this._$firstNameInput.prop("disabled", true);
this._$lastNameInput.prop("disabled", true);
this._$emailInput.prop("disabled", true);
}
- }).bind(this));
+ if (this._userProfileModel.mode === FormMode.VIEW) {
+ this._$zenodoToken.prop("disabled", true);
+ }
+ }).bind(this));
}
this._getOptionsMenu = function() {
@@ -96,6 +111,7 @@ function UserProfileView(userProfileController, userProfileModel) {
firstName : this._$firstNameInput.val(),
lastName : this._$lastNameInput.val(),
email : this._$emailInput.val(),
+ zenodoToken : this._$zenodoToken.val()
};
}
diff --git a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/ZenodoExport/ZenodoExportController.js b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/ZenodoExport/ZenodoExportController.js
index 22d8015cdae2798ad66dbae025a5c121076a69fe..fb99fc614e7ea5cb2e89a2a84a54680df5e6d190 100644
--- a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/ZenodoExport/ZenodoExportController.js
+++ b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/ZenodoExport/ZenodoExportController.js
@@ -15,17 +15,26 @@
*/
function ZenodoExportController(parentController) {
- var exportModel = new ZenodoExportModel();
- var exportView = new ZenodoExportView(this, exportModel);
+ this.exportModel = null;
+ this.exportView = null;
+ this.zenodoApiTokenKey = parentController.zenodoApiTokenKey;
this.init = function(views) {
- exportView.repaint(views);
+ this.getSettingValue(this.zenodoApiTokenKey, (function (accessToken) {
+ if (accessToken && accessToken !== '') {
+ this.exportModel = new ZenodoExportModel(accessToken);
+ this.exportView = new ZenodoExportView(this, this.exportModel);
+ this.exportView.repaint(views);
+ } else {
+ Util.showError('Personal Zenodo API Token missing, please set it on your user profile.');
+ }
+ }).bind(this));
};
this.exportSelected = function() {
var _this = this;
- var selectedNodes = $(exportModel.tree).fancytree('getTree').getSelectedNodes();
- var title = exportView.$titleTextBox.val().trim();
+ var selectedNodes = $(this.exportModel.tree).fancytree('getTree').getSelectedNodes();
+ var title = this.exportView.$titleTextBox.val().trim();
var toExport = [];
for (var eIdx = 0; eIdx < selectedNodes.length; eIdx++) {
@@ -41,8 +50,8 @@ function ZenodoExportController(parentController) {
Util.showInfo('Not only spaces and the root should be selected. It will result in an empty export file.');
} else {
Util.blockUI();
- this.getUserInformation(function(userInformation) {
- mainController.serverFacade.exportZenodo(toExport, true, false, userInformation, title,
+ this.getUserInformation((function(userInformation) {
+ mainController.serverFacade.exportZenodo(toExport, true, false, userInformation, title, this.exportModel.accessToken,
function(operationExecutionPermId) {
_this.waitForOpExecutionResponse(operationExecutionPermId, function(error, result) {
Util.unblockUI();
@@ -59,7 +68,7 @@ function ZenodoExportController(parentController) {
}
});
});
- });
+ }).bind(this));
}
};
@@ -112,4 +121,8 @@ function ZenodoExportController(parentController) {
callback(userInformation);
});
};
+
+ this.getSettingValue = function (key, callback) {
+ parentController.serverFacade.getSetting(key, callback);
+ };
}
\ 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/ZenodoExport/ZenodoExportModel.js b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/ZenodoExport/ZenodoExportModel.js
index f555844b57e82e8c640965767f2077b1b66f213e..dc4f73489ca42ef5f9dc9cd1abe15ef67a0a8c35 100644
--- a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/ZenodoExport/ZenodoExportModel.js
+++ b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/ZenodoExport/ZenodoExportModel.js
@@ -14,5 +14,6 @@
* limitations under the License.
*/
-function ZenodoExportModel() {
+function ZenodoExportModel(accessToken) {
+ this.accessToken = accessToken;
}
\ 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/ZenodoExport/ZenodoExportView.js b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/ZenodoExport/ZenodoExportView.js
index 833660f9406412a911d2006d59f9747ee194fca1..a2ae6996d23f4730a24de4e2ff05f4b6df87fae4 100644
--- a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/ZenodoExport/ZenodoExportView.js
+++ b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/ZenodoExport/ZenodoExportView.js
@@ -21,7 +21,7 @@ function ZenodoExportView(exportController, exportModel) {
var $form = $("<div>");
var $formColumn = $("<form>", {
- 'name': 'rcExportForm',
+ 'name': 'zenodoExportForm',
'role': 'form',
'action': 'javascript:void(0);',
'onsubmit': 'mainController.currentView.exportSelected();'
@@ -56,7 +56,7 @@ function ZenodoExportView(exportController, exportModel) {
this.paintTitleTextBox($container);
var $exportButton = $('<input>', { 'type': 'submit', 'class': 'btn btn-primary', 'value': 'Export Selected',
- 'onClick': '$("form[name=\'rcExportForm\']").submit()'});
+ 'onClick': '$("form[name=\'zenodoExportForm\']").submit()'});
$header.append($exportButton);
};
diff --git a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/dss/reporting-plugins/zenodo-exports-api/plugin.properties b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/dss/reporting-plugins/zenodo-exports-api/plugin.properties
index cc77ea6f8cfc5d2c91b4292696d89990276b2b7b..1e4e8fa3aa70869ce9c174f3bdcf7d2c5941224b 100644
--- a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/dss/reporting-plugins/zenodo-exports-api/plugin.properties
+++ b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/dss/reporting-plugins/zenodo-exports-api/plugin.properties
@@ -2,5 +2,4 @@ label = Zenodo Exports API
class = ch.systemsx.cisd.openbis.dss.generic.server.plugins.jython.JythonIngestionService
script-path = zenodoExports.py
limit-data-size-megabytes=${zenodo-exports-api-limit-data-size-megabytes:4000}
-zenodoUrl=${zenodo-exports-api-zenodoUrl:https://localhost}
-accessToken=${zenodo-exports-api-accessToken}
\ No newline at end of file
+zenodoUrl=${zenodo-exports-api-zenodoUrl:https://localhost}
\ No newline at end of file
diff --git a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/dss/reporting-plugins/zenodo-exports-api/zenodoExports.py b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/dss/reporting-plugins/zenodo-exports-api/zenodoExports.py
index be1dd798a3369d52923b64d6be25380fc00e7337..5922f0f8827de532880931ddc8150ef0501f88fc 100644
--- a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/dss/reporting-plugins/zenodo-exports-api/zenodoExports.py
+++ b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/dss/reporting-plugins/zenodo-exports-api/zenodoExports.py
@@ -93,7 +93,7 @@ def export(entities, tr, params):
def sendToZenodo(tr, params, tempZipFilePath, entities):
depositRootUrl = str(getConfigurationProperty(tr, 'zenodoUrl')) + '/api/deposit/depositions'
- accessToken = str(getConfigurationProperty(tr, 'accessToken'))
+ accessToken = params.get('accessToken')
operationLog.info('accessToken: %s' % accessToken)
httpClient = None
@@ -225,7 +225,7 @@ class ZenodoCallable(object):
actionCompleted = True
elif publicationJson.get('submitted'):
operationLog.info('Publication #%d submitted. Registering metadata.' % publicationJson.get('id'))
- self.registerPublicationInOpenbis(publicationJson.get('metadata'))
+ self.registerPublicationInOpenbis(publicationJson.get('metadata'), publicationJson.get('links'))
actionCompleted = True
else:
operationLog.info('Publication #%d not submitted yet.' % publicationJson.get('id'))
@@ -244,13 +244,13 @@ class ZenodoCallable(object):
return actionCompleted
- def registerPublicationInOpenbis(self, publicationMetadataJson):
+ def registerPublicationInOpenbis(self, publicationMetadataJson, publicationLinksJson):
sessionToken = self.params.get('sessionToken')
v3 = ServiceProvider.getV3ApplicationService()
id = CustomASServiceCode('publication-api')
options = CustomASServiceExecutionOptions() \
.withParameter('method', 'insertPublication') \
- .withParameter('publicationURL', self.selfUrl) \
+ .withParameter('publicationURL', publicationLinksJson.get('doi')) \
.withParameter('openBISRelatedIdentifiers', self.permIdsStr) \
.withParameter('name', publicationMetadataJson.get('title')) \
.withParameter('publicationDescription', publicationMetadataJson.get('description')) \
diff --git a/pybis/src/python/CHANGELOG.md b/pybis/src/python/CHANGELOG.md
index 1c68708da418d638fa3158a6d438d9e08b63e341..2f0abd9b62c0f900166306e048abc5978f6c8f06 100644
--- a/pybis/src/python/CHANGELOG.md
+++ b/pybis/src/python/CHANGELOG.md
@@ -1,3 +1,16 @@
+## Changes with pybis-1.9.3
+
+* fixed documentation: add_members (not add_persons)
+* bugfix role assignments of groups
+
+## Changes with pybis-1.9.2
+
+* searches for datasets and samples are highly improved
+* search parameters can accept a code, an identifier or an openbis entity
+* searching for all datasets in a project now works
+* bugfixes
+
+
## Changes with pybis-1.9.1
* bugfix: controlled vocabulary
diff --git a/pybis/src/python/README.md b/pybis/src/python/README.md
index 5a525c397433f583f80bd80189d97610a8ab7500..ef065b428f2ec16b9d9b00028f908a1a20cddc0e 100644
--- a/pybis/src/python/README.md
+++ b/pybis/src/python/README.md
@@ -126,9 +126,9 @@ group.assign_role(role='ADMIN', space='DEFAULT')
group.get_roles()
group.revoke_role(role='ADMIN', space='DEFAULT')
-group.add_persons(['admin'])
-group.get_persons()
-group.del_persons(['admin'])
+group.add_members(['admin'])
+group.get_members()
+group.del_members(['admin'])
group.delete()
o.get_persons()
diff --git a/pybis/src/python/pybis/__init__.py b/pybis/src/python/pybis/__init__.py
index 4aa2b995675dc04f0874952732c359ada99bdd0f..c09faa979fdad428ea5009396b3390cdd526bfbe 100644
--- a/pybis/src/python/pybis/__init__.py
+++ b/pybis/src/python/pybis/__init__.py
@@ -1,7 +1,7 @@
name = 'pybis'
__author__ = 'Swen Vermeul'
__email__ = 'swen@ethz.ch'
-__version__ = '1.9.1'
+__version__ = '1.9.3'
from . import pybis
from .pybis import Openbis
diff --git a/pybis/src/python/pybis/definitions.py b/pybis/src/python/pybis/definitions.py
index 681c47d4526a66a7faadfac3d081a8c8eec9cba2..ca0a43e785563549577e91d6a07968c7ea574d20 100644
--- a/pybis/src/python/pybis/definitions.py
+++ b/pybis/src/python/pybis/definitions.py
@@ -461,12 +461,12 @@ def get_fetchoption_for_entity(entity):
except KeyError as e:
return {}
-def get_type_for_entity(entity, action):
+def get_type_for_entity(entity, action, parents_or_children=''):
if action not in "create update delete search".split():
raise ValueError('unknown action: {}'.format(action))
definition = openbis_definitions(entity)
- if action in definition:
+ if action in definition and not parents_or_children:
return definition[action]
else:
# try to guess type, according to the naming scheme
@@ -478,10 +478,16 @@ def get_type_for_entity(entity, action):
"search": "SearchCriteria",
}
- return {
- "@type": "as.dto.{}.{}.{}{}"
- .format(entity.lower(), action, cap_entity, noun[action])
- }
+ if parents_or_children:
+ return {
+ "@type": "as.dto.{}.{}.{}{}{}"
+ .format(entity.lower(), action, cap_entity, parents_or_children, noun[action])
+ }
+ else:
+ return {
+ "@type": "as.dto.{}.{}.{}{}"
+ .format(entity.lower(), action, cap_entity, noun[action])
+ }
def get_method_for_entity(entity, action):
diff --git a/pybis/src/python/pybis/pybis.py b/pybis/src/python/pybis/pybis.py
index 398cf56cda8b98dd3afb248a5240373966886f75..d44a332a0219219e1c65b2ece10331a6a23e5e4c 100644
--- a/pybis/src/python/pybis/pybis.py
+++ b/pybis/src/python/pybis/pybis.py
@@ -381,9 +381,9 @@ def _subcriteria_for_tags(tags):
if not isinstance(tags, list):
tags = [tags]
- criterias = []
+ criteria = []
for tag in tags:
- criterias.append({
+ criteria.append({
"fieldName": "code",
"fieldType": "ATTRIBUTE",
"fieldValue": {
@@ -396,7 +396,7 @@ def _subcriteria_for_tags(tags):
return {
"@type": "as.dto.tag.search.TagSearchCriteria",
"operator": "AND",
- "criteria": criterias
+ "criteria": criteria
}
@@ -423,14 +423,99 @@ def _subcriteria_for_properties(prop, val):
}
}
+def _subcriteria_for(thing, entity, parents_or_children='', operator='AND'):
+ """Returns the sub-search criteria for «thing», which can be either:
+ - a python object (sample, dataSet, experiment)
+ - a permId
+ - an identifier
+ - a code
+ """
+
+ if isinstance(thing, str):
+ if is_permid(thing):
+ return _subcriteria_for_permid(
+ thing,
+ entity=entity,
+ parents_or_children=parents_or_children,
+ operator=operator
+ )
+ elif is_identifier(thing):
+ return _subcriteria_for_identifier(
+ thing,
+ entity=entity,
+ parents_or_children=parents_or_children,
+ operator=operator
+ )
+ else:
+ # look for code
+ return _subcriteria_for_code_new(
+ thing,
+ entity=entity,
+ parents_or_children=parents_or_children,
+ operator=operator
+ )
+
+ elif isinstance(thing, list):
+ criteria = []
+ for element in thing:
+ crit = _subcriteria_for(element, entity, parents_or_children, operator)
+ criteria += crit["criteria"]
+
+ return {
+ "criteria": criteria,
+ "@type": crit["@type"],
+ "operator": "OR"
+ }
+ elif thing is None:
+ # we just need the type
+ search_type = get_type_for_entity(entity, 'search', parents_or_children)
+ return {
+ "criteria": [],
+ **search_type,
+ "operator": operator
+ }
+ else:
+ # we passed an object
+ return _subcriteria_for_permid(
+ thing.permId,
+ entity=entity,
+ parents_or_children=parents_or_children,
+ operator=operator
+ )
+
+
+def _subcriteria_for_identifier(ids, entity, parents_or_children='', operator='AND'):
+ if not isinstance(ids, list):
+ ids = [ids]
+
+ criteria = []
+ for id in ids:
+ criteria.append({
+ "@type": "as.dto.common.search.IdentifierSearchCriteria",
+ "fieldValue": {
+ "value": id,
+ "@type": "as.dto.common.search.StringEqualToValue"
+ },
+ "fieldType": "ATTRIBUTE",
+ "fieldName": "identifier"
+ })
+
+ search_type = get_type_for_entity(entity, 'search', parents_or_children)
+ return {
+ "criteria": criteria,
+ **search_type,
+ "operator": operator
+ }
+ return criteria
+
def _subcriteria_for_permid(permids, entity, parents_or_children='', operator='AND'):
if not isinstance(permids, list):
permids = [permids]
- criterias = []
+ criteria = []
for permid in permids:
- criterias.append({
+ criteria.append({
"@type": "as.dto.common.search.PermIdSearchCriteria",
"fieldValue": {
"value": permid,
@@ -440,14 +525,36 @@ def _subcriteria_for_permid(permids, entity, parents_or_children='', operator='A
"fieldName": "code"
})
- criteria = {
- "criteria": criterias,
- "@type": "as.dto.{}.search.{}{}SearchCriteria".format(
- entity.lower(), entity, parents_or_children
- ),
+ search_type = get_type_for_entity(entity, 'search', parents_or_children)
+ return {
+ "criteria": criteria,
+ **search_type,
+ "operator": operator
+ }
+
+
+def _subcriteria_for_code_new(codes, entity, parents_or_children='', operator='AND'):
+ if not isinstance(codes, list):
+ codes = [codes]
+
+ criteria = []
+ for code in codes:
+ criteria.append({
+ "@type": "as.dto.common.search.CodeSearchCriteria",
+ "fieldValue": {
+ "value": code,
+ "@type": "as.dto.common.search.StringEqualToValue"
+ },
+ "fieldType": "ATTRIBUTE",
+ "fieldName": "code"
+ })
+
+ search_type = get_type_for_entity(entity, 'search', parents_or_children)
+ return {
+ "criteria": criteria,
+ **search_type,
"operator": operator
}
- return criteria
def _subcriteria_for_code(code, entity):
@@ -1028,7 +1135,7 @@ class Openbis:
else:
groupId = search_args[attr].code
sub_crit.append(
- _subcriteria_for_permid(groupId, 'AuthorizationGroup')
+ _subcriteria_for_permid(groupId, 'authorizationGroup')
)
elif attr == 'role':
# TODO
@@ -1403,37 +1510,34 @@ class Openbis:
def get_samples(
self, identifier=None, code=None, permId=None,
- space=None, project=None, experiment=None, type=None,
+ space=None, project=None, experiment=None, collection=None, type=None,
start_with=None, count=None,
withParents=None, withChildren=None, tags=None, props=None, **properties
):
""" Get a list of all samples for a given space/project/experiment (or any combination)
"""
+ if collection is not None:
+ experiment = collection
+
sub_criteria = []
- # v3 API does not offer a search for identifiers. We need to do a combined search instead:
- # space && code or
- # space && project && code
if identifier:
- identifier = identifier.lstrip('/')
- elements = identifier.split('/')
- if len(elements) == 2:
- space = elements[0]
- code = elements[1]
- elif len(elements) == 3:
- space = elements[0]
- code = elements[2]
- else:
- raise ValueError("{} is not a valid sample identifier.".format(identifier))
+ crit = _subcriteria_for(identifier, 'sample')
+ sub_criteria += crit['criteria']
if space:
- sub_criteria.append(_subcriteria_for_code(space, 'space'))
+ sub_criteria.append(_subcriteria_for(space, 'space'))
if project:
- proj_crit = _subcriteria_for_code(project, 'project')
- sub_criteria.append(proj_crit)
+ sub_criteria.append(_subcriteria_for(project, 'project'))
if experiment:
- sub_criteria.append(_subcriteria_for_code(experiment, 'experiment'))
+ sub_criteria.append(_subcriteria_for(experiment, 'experiment'))
+
+ if withParents:
+ sub_criteria.append(_subcriteria_for(withParents, 'sample', 'Parents'))
+ if withChildren:
+ sub_criteria.append(_subcriteria_for(withChildren, 'sample', 'Children'))
+
if properties is not None:
for prop in properties:
sub_criteria.append(_subcriteria_for_properties(prop, properties[prop]))
@@ -1445,26 +1549,6 @@ class Openbis:
sub_criteria.append(_criteria_for_code(code))
if permId:
sub_criteria.append(_common_search("as.dto.common.search.PermIdSearchCriteria", permId))
- if withParents:
- if not isinstance(withParents, list):
- withParents = [withParents]
- for parent in withParents:
- sub_criteria.append(
- _gen_search_criteria({
- "sample": "SampleParents",
- "identifier": parent
- })
- )
- if withChildren:
- if not isinstance(withChildren, list):
- withChildren = [withChildren]
- for child in withChildren:
- sub_criteria.append(
- _gen_search_criteria({
- "sample": "SampleChildren",
- "identifier": child
- })
- )
criteria = {
"criteria": sub_criteria,
@@ -1596,29 +1680,35 @@ class Openbis:
def get_datasets(
self, code=None, type=None, withParents=None, withChildren=None,
start_with=None, count=None, kind=None,
- status=None, sample=None, experiment=None, project=None,
+ status=None, sample=None, experiment=None, collection=None, project=None,
tags=None, props=None, **properties
):
+ if 'object' in properties:
+ sample = properties['object']
+ if collection is not None:
+ experiment = collection
+
sub_criteria = []
if code:
sub_criteria.append(_criteria_for_code(code))
if type:
- sub_criteria.append(_subcriteria_for_type(type, 'DataSet'))
+ sub_criteria.append(_subcriteria_for_type(type, 'dataSet'))
+
if withParents:
- sub_criteria.append(_subcriteria_for_permid(withParents, 'DataSet', 'Parents'))
+ sub_criteria.append(_subcriteria_for(withParents, 'dataSet', 'Parents'))
if withChildren:
- sub_criteria.append(_subcriteria_for_permid(withChildren, 'DataSet', 'Children'))
+ sub_criteria.append(_subcriteria_for(withChildren, 'dataSet', 'Children'))
if sample:
- sub_criteria.append(_subcriteria_for_code(sample, 'Sample'))
+ sub_criteria.append(_subcriteria_for(sample, 'sample'))
if experiment:
- sub_criteria.append(_subcriteria_for_code(experiment, 'Experiment'))
+ sub_criteria.append(_subcriteria_for(experiment, 'experiment'))
+
if project:
- exp_crit = _subcriteria_for_code(experiment, 'Experiment')
- proj_crit = _subcriteria_for_code(project, 'Project')
- exp_crit['criteria'] = []
+ exp_crit = _subcriteria_for(experiment, 'experiment')
+ proj_crit = _subcriteria_for(project, 'project')
exp_crit['criteria'].append(proj_crit)
sub_criteria.append(exp_crit)
if tags:
diff --git a/pybis/src/python/setup.py b/pybis/src/python/setup.py
index 723fcda825c708e6a385739579d327aa8d44c80e..d98d25fa4d55669e55272c2d728a0b6a57241c5c 100644
--- a/pybis/src/python/setup.py
+++ b/pybis/src/python/setup.py
@@ -11,7 +11,7 @@ with open("README.md", "r", encoding="utf-8") as fh:
setup(
name='PyBIS',
- version= '1.9.1',
+ version= '1.9.3',
author='Swen Vermeul • ID SIS • ETH Zürich',
author_email='swen@ethz.ch',
description='openBIS connection and interaction, optimized for using with Jupyter',
diff --git a/pybis/src/python/tests/conftest.py b/pybis/src/python/tests/conftest.py
index 677de709a3f316e1eb0806ec0ed2cf7e95f4388c..1568409e701a0c6e37da8fcab45941ae1cf6d83a 100644
--- a/pybis/src/python/tests/conftest.py
+++ b/pybis/src/python/tests/conftest.py
@@ -3,9 +3,12 @@ import time
from pybis import Openbis
-openbis_url = 'https://localhost:8443'
-admin_username = 'admin'
-admin_password = 'changeit'
+#openbis_url = 'https://localhost:8443'
+#admin_username = 'admin'
+#admin_password = 'changeit'
+openbis_url = 'http://localhost:20000'
+admin_username = 'openbis_test_js'
+admin_password = 'password'
@pytest.yield_fixture(scope="module")
def openbis_instance():
diff --git a/pybis/src/python/tests/test_group.py b/pybis/src/python/tests/test_group.py
index 9e3268332131fe216aa8479ba01bd9125e8807d1..cb3e8dad9fd2cb8b55de3e054437e8e837d6dfeb 100644
--- a/pybis/src/python/tests/test_group.py
+++ b/pybis/src/python/tests/test_group.py
@@ -27,12 +27,12 @@ def test_crud_group(openbis_instance, group):
changed_description = 'changed description of group ' + group.code
group.description = changed_description
group.save()
- group_changed = openbis_instance.get_group(code=group.code)
+ group_changed = openbis_instance.get_group(group.code)
assert group_changed.description == changed_description
group.delete('test')
with pytest.raises(ValueError):
- group_not_exists = openbis_instance.get_group(code=group.code)
+ group_not_exists = openbis_instance.get_group(group.code)
assert group_not_exists is None