diff --git a/installation/resource/installer/bin/restore-config-from-backup.sh b/installation/resource/installer/bin/restore-config-from-backup.sh
index 0f3b651a728f2b12bc87e3e905f319c3a8687654..db665da4e9e82ce73416b327f1ddd935fe6d2668 100755
--- a/installation/resource/installer/bin/restore-config-from-backup.sh
+++ b/installation/resource/installer/bin/restore-config-from-backup.sh
@@ -45,6 +45,7 @@ if [ -d $ROOT/openBIS-server ]; then
copyConfig $CONF/core-plugins "html/etc$" $ROOT/core-plugins
copyFolderIfExists $CONF/start.d $ROOT/openBIS-server/jetty/start.d
+ copyFolderIfExists $CONF/../openBIS-server/jetty/indices $ROOT/openBIS-server/jetty/indices
fi
# -- DSS
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 fd572d224fd285a552e935d30376e0d664c97bdc..2ab4398fbc07ecb634560b74312915b744522ed0 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
@@ -215,7 +215,7 @@ $.extend(DefaultProfile.prototype, {
// this.jupyterIntegrationServerEndpoint = "https://bs-openbis-sis-dev.ethz.ch:8002";
// this.jupyterEndpoint = "https://bs-openbis-sis-dev.ethz.ch:8000/";
- this.systemProperties = ["$ANNOTATIONS_STATE", "$FREEFORM_TABLE_STATE"];
+ this.systemProperties = ["$ANNOTATIONS_STATE", "FREEFORM_TABLE_STATE"];
this.forcedDisableRTF = [];
this.forceMonospaceFont = [];
this.imageViewerDataSetCodes = [];
diff --git a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/config/SettingsManager.js b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/config/SettingsManager.js
index ee84c275dfa6cdc722e8710c99f6c9b1a01787fa..0132e137bf2d5cd5cf59334d303bce0c04e5a2e1 100644
--- a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/config/SettingsManager.js
+++ b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/config/SettingsManager.js
@@ -140,11 +140,6 @@ function SettingsManager(serverFacade) {
if(!settings.sampleTypeDefinitionsExtension[sampleTypeCode].SHOW) {
targetProfile.hideTypes["sampleTypeCodes"].push(sampleTypeCode);
}
-
- // Show on navigation by default
- if(targetProfile.sampleTypeDefinitionsExtension[sampleTypeCode]["SHOW_ON_NAV"] === undefined) {
- targetProfile.sampleTypeDefinitionsExtension[sampleTypeCode]["SHOW_ON_NAV"] = true;
- }
}
}
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 71cd78f2124619b078ec63e4a49d35aa6eb8a409..a0848120b09948e965b8f2e83b8526bdc6e9c43e 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
@@ -599,7 +599,7 @@ function MainController(profile) {
var argsMap = JSON.parse(cleanText);
var sampleTypeCode = argsMap["sampleTypeCode"];
var experimentIdentifier = argsMap["experimentIdentifier"];
- document.title = "Create " + ELNDictionary.Sample + " " + arg;
+ document.title = "Create " + Util.getDisplayNameFromCode(sampleTypeCode);
this._showCreateSubExperimentPage(sampleTypeCode, experimentIdentifier);
//window.scrollTo(0,0);
break;
@@ -638,7 +638,7 @@ function MainController(profile) {
if(!data[0]) {
window.alert("The item is no longer available, refresh the page, if the problem persists tell your admin that the Lucene index is probably corrupted.");
} else {
- document.title = "" + ELNDictionary.Sample + " " + data[0].code;
+ document.title = "" + Util.getDisplayNameFromCode(data[0].sampleTypeCode) + " " + data[0].code;
var isELNSubExperiment = $.inArray(data[0].spaceCode, _this.profile.inventorySpaces) === -1 && _this.profile.inventorySpaces.length > 0;
_this._showEditSamplePage(data[0], isELNSubExperiment, paginationInfo);
//window.scrollTo(0,0);
@@ -660,7 +660,7 @@ function MainController(profile) {
if(!data[0]) {
window.alert("The item is no longer available, refresh the page, if the problem persists tell your admin that the Lucene index is probably corrupted.");
} else {
- document.title = "" + ELNDictionary.Sample + " " + data[0].code;
+ document.title = "" + Util.getDisplayNameFromCode(data[0].sampleTypeCode) + " " + data[0].code;
var isELNSubExperiment = $.inArray(data[0].spaceCode, _this.profile.inventorySpaces) === -1 && _this.profile.inventorySpaces.length > 0;
_this._showViewSamplePage(data[0], isELNSubExperiment, paginationInfo);
//window.scrollTo(0,0);
@@ -682,7 +682,7 @@ function MainController(profile) {
if(!data[0]) {
window.alert("The item is no longer available, refresh the page, if the problem persists tell your admin that the Lucene index is probably corrupted.");
} else {
- document.title = "" + ELNDictionary.Sample + " " + data[0].code;
+ document.title = "" + Util.getDisplayNameFromCode(data[0].sampleTypeCode) + " " + data[0].code;
var isELNSubExperiment = $.inArray(data[0].spaceCode, _this.profile.inventorySpaces) === -1&& _this.profile.inventorySpaces.length > 0;
_this._showViewSamplePage(data[0], isELNSubExperiment, paginationInfo);
//window.scrollTo(0,0);
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 42cbc42728a7a1d64e13dbd477000880080d94a2..1990d21e8ea47a29f311a7346edda6dca5aeca40 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
@@ -1311,6 +1311,9 @@ function ServerFacade(openbisServer) {
if(advancedFetchOptions.withParentsType) {
parentFetchOptions.withType();
}
+ if (advancedFetchOptions.withParentsExperiment) {
+ parentFetchOptions.withExperiment();
+ }
}
if(advancedFetchOptions.withChildren) {
var childrenFetchOptions = fetchOptions.withChildren();
@@ -1318,8 +1321,11 @@ function ServerFacade(openbisServer) {
childrenFetchOptions.withType();
}
if(advancedFetchOptions.withChildrenProperties) {
- childrenFetchOptions.withProperties();
- }
+ childrenFetchOptions.withProperties();
+ }
+ if (advancedFetchOptions.withChildrenExperiment) {
+ childrenFetchOptions.withExperiment();
+ }
}
if(advancedFetchOptions.withAncestors) {
var ancestorsFetchOptions = fetchOptions.withParents();
diff --git a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/test/AdminTests.js b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/test/AdminTests.js
index b9ef1e42f4615e02436a204b9185fbdc3392ff46..5d07c73be797f5198196883ba2ac8bf0c8f89aa8 100644
--- a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/test/AdminTests.js
+++ b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/test/AdminTests.js
@@ -86,8 +86,6 @@ var AdminTests = new function() {
testChain = Promise.resolve();
testChain.then(() => e.waitForId("USER_MANAGER"))
.then(() => e.click("USER_MANAGER"))
- .then(() => e.waitForId("optionsMenu"))
- .then(() => e.click("optionsMenu"))
.then(() => e.waitForId("createUser"))
.then(() => e.click("createUser"))
.then(() => e.waitForId("userId"))
diff --git a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/test/TestUtil.js b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/test/TestUtil.js
index 98f64900e7071964300504d7138146564ab02df8..535d2266442e29799d0780b4122e4914a6eba77c 100644
--- a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/test/TestUtil.js
+++ b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/test/TestUtil.js
@@ -56,10 +56,10 @@ var TestUtil = new function() {
xhr.responseType = 'blob';
xhr.onload = function(e) {
- if (this.status == 200) {
+ if (this.status == 200) {
// get binary data as a response
action(this.response);
- }
+ }
};
xhr.send();
@@ -85,7 +85,7 @@ var TestUtil = new function() {
throw "CKEditor #" + elementId + " should be equal " + data;
}
} catch(error) {
- reject();
+ reject(error);
}
});
}
diff --git a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/test/UserTests.js b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/test/UserTests.js
index aa8dde9adbb4b384aaf6f013338d606aa6b36b09..1fc3a681305149d2be49806f5c055bc6d000b10e 100644
--- a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/test/UserTests.js
+++ b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/test/UserTests.js
@@ -16,6 +16,24 @@ var UserTests = new function() {
.then(() => this.storageTest())
//16. Storage Manager - Moving Box
.then(() => this.movingBoxTest())
+ //17. Storage Manager - Moving Sample
+ .then(() => this.movingSampleTest())
+ //18. Create Protocol
+ .then(() => this.createProtocol())
+ //19. Project Form - Create/Update
+ .then(() => this.createProject())
+ //20. Experiment Form - Create/Update
+ .then(() => this.createExperiment())
+ //21. Experiment Step Form - Create/Update
+ .then(() => this.createExperimentStep())
+ //22. is now disabled
+ //23. Experiment Step Form - Dataset Uploader and Viewer
+ .then(() => this.datasetUploader())
+ //24. Experiment Step Form - Children Generator (not exist)
+ //25. Project Form - Show in project overview
+ .then(() => this.showInProjectOverview())
+ //26. Search
+ .then(() => this.search())
.catch(error => { console.log(error) });
}
@@ -66,36 +84,48 @@ var UserTests = new function() {
this.createBacteria = function(code, name) {
return new Promise(function executor(resolve, reject) {
var e = EventUtil;
+ var testChain = Promise.resolve();
var richText = '<p><span style="color:#000080;"><strong>F- tonA21 thi-1 thr-1 leuB6 lacY1</strong></span><strong> </strong><span style="color:#008000;"><i><strong>glnV44 rfbC1 fhuA1 ?? mcrB e14-(mcrA-)</strong></i></span><i><strong> </strong></i><span style="color:#cc99ff;"><strong><u>hsdR(rK -mK +) λ-</u></strong></span></p>';
- Promise.resolve().then(() => e.waitForId("_MATERIALS_BACTERIA_BACTERIA_COLLECTION"))
- .then(() => e.click("_MATERIALS_BACTERIA_BACTERIA_COLLECTION"))
- .then(() => e.waitForId("create-btn"))
- .then(() => e.click("create-btn"))
- .then(() => e.waitForId("sampleFormTitle"))
- .then(() => e.equalTo("sampleFormTitle", "Create Object Bacteria", true, false))
- .then(() => e.waitForId("codeId"))
- .then(() => e.waitForFill("codeId"))
- .then(() => e.equalTo("codeId", code, true, false))
- .then(() => e.waitForId("NAME"))
- .then(() => e.change("NAME", name, false))
- //Paste from Word
- .then(() => TestUtil.ckeditorSetData("BACTERIA.GENOTYPE", richText))
- .then(() => e.waitForId("save-btn"))
- .then(() => e.click("save-btn"))
- //Check saving results
- .then(() => e.waitForId("edit-btn"))
- .then(() => e.waitForId("NAME"))
- .then(() => e.equalTo("NAME", name, true, false))
- .then(() => TestUtil.ckeditorTestData("BACTERIA.GENOTYPE", richText))
- .then(() => resolve());
+ testChain.then(() => e.waitForId("_MATERIALS_BACTERIA_BACTERIA_COLLECTION"))
+ .then(() => e.click("_MATERIALS_BACTERIA_BACTERIA_COLLECTION"))
+ .then(() => e.waitForId("create-btn"))
+ .then(() => e.click("create-btn"))
+ .then(() => e.waitForId("sampleFormTitle"))
+ .then(() => e.equalTo("sampleFormTitle", "New Bacteria", true, false));
+
+ if (code === "BAC1") {
+ // Show Code
+ testChain.then(() => e.waitForId("options-menu-btn-sample-view-bacteria"))
+ .then(() => e.click("options-menu-btn-sample-view-bacteria"))
+ .then(() => e.waitForId("options-menu-btn-identification-info"))
+ .then(() => e.click("options-menu-btn-identification-info"));
+ }
+
+ testChain.then(() => e.waitForId("codeId"))
+ .then(() => e.waitForFill("codeId"))
+ .then(() => e.equalTo("codeId", code, true, false))
+ .then(() => e.waitForId("NAME"))
+ .then(() => e.change("NAME", name, false))
+ //Paste from Word
+ .then(() => e.waitForCkeditor("BACTERIA.GENOTYPE"))
+ .then(() => TestUtil.ckeditorSetData("BACTERIA.GENOTYPE", richText))
+ .then(() => e.waitForId("save-btn"))
+ .then(() => e.click("save-btn"))
+ //Check saving results
+ .then(() => e.waitForId("edit-btn"))
+ .then(() => e.waitForId("NAME"))
+ .then(() => e.equalTo("NAME", name, true, false))
+ .then(() => TestUtil.ckeditorTestData("BACTERIA.GENOTYPE", richText))
+ .then(() => resolve());
});
}
this.importsAutomaticCodes = function() {
var baseURL = location.protocol + '//' + location.host + location.pathname;
var pathToResource = "js/test/resources/bacteria_for_test_without_identifier.tsv";
+
return new Promise(function executor(resolve, reject) {
var e = EventUtil;
Promise.resolve().then(() => UserTests.importBacteriasFromFile(baseURL + pathToResource))
@@ -111,6 +141,7 @@ var UserTests = new function() {
this.importsGivenCodes = function() {
var baseURL = location.protocol + '//' + location.host + location.pathname;
var pathToResource = "js/test/resources/bacteria_for_test_with_identifier.tsv";
+
return new Promise(function executor(resolve, reject) {
var e = EventUtil;
Promise.resolve().then(() => UserTests.importBacteriasFromFile(baseURL + pathToResource))
@@ -131,8 +162,8 @@ var UserTests = new function() {
Promise.resolve().then(() => e.waitForId("_MATERIALS_BACTERIA_BACTERIA_COLLECTION"))
.then(() => e.click("_MATERIALS_BACTERIA_BACTERIA_COLLECTION"))
- .then(() => e.waitForId("options-menu-btn"))
- .then(() => e.click("options-menu-btn"))
+ .then(() => e.waitForId("sample-options-menu-btn"))
+ .then(() => e.click("sample-options-menu-btn"))
.then(() => e.waitForId("register-object-btn"))
.then(() => e.click("register-object-btn"))
.then(() => e.waitForId("choose-type-btn"))
@@ -157,6 +188,7 @@ var UserTests = new function() {
// we wait for the save-button, cause page contains add-storage-btn
// even when page can't be edit. So we wait when page be reloaded.
.then(() => e.waitForId("save-btn"))
+ .then(() => e.sleep(2000))
.then(() => e.waitForId("add-storage-btn"))
.then(() => e.click("add-storage-btn"))
.then(() => e.waitForId("storage-drop-down-id"))
@@ -195,6 +227,320 @@ var UserTests = new function() {
.then(() => e.dragAndDrop("storage-drop-down-id-a-1-2-storage-box", "storage-drop-down-id-b-1-1", false))
.then(() => e.equalTo("change-log-container-id", "None", false, false))
.then(() => e.click("save-changes-btn"))
+ .then(() => e.sleep(3000))
+ .then(() => resolve());
+ });
+ }
+
+ this.movingSampleTest = function() {
+ return new Promise(function executor(resolve, reject) {
+ var e = EventUtil;
+
+ Promise.resolve().then(() => e.waitForId("STORAGE_MANAGER"))
+ .then(() => e.click("STORAGE_MANAGER"))
+ .then(() => e.waitForId("storage-drop-down-id-a"))
+ .then(() => e.change("storage-drop-down-id-a", "BENCH", false))
+ .then(() => e.waitForId("storage-drop-down-id-a-1-1"))
+ .then(() => e.waitForId("storage-drop-down-id-a-1-1-storage-box"))
+ .then(() => e.click("storage-drop-down-id-a-1-1-storage-box"))
+ .then(() => e.waitForId("storage-drop-down-id-a-C-2-storage-box"))
+ .then(() => e.dragAndDrop("storage-drop-down-id-a-C-2-storage-box", "storage-drop-down-id-a-A-3", false))
+ .then(() => e.equalTo("change-log-container-id", "None", false, false))
+ .then(() => e.click("save-changes-btn"))
+ // Open object BAC1 and verify storage.
+ .then(() => e.waitForId("_MATERIALS_BACTERIA_BACTERIA_COLLECTION"))
+ .then(() => e.click("_MATERIALS_BACTERIA_BACTERIA_COLLECTION"))
+ .then(() => e.waitForId("bac1-column-id"))
+ .then(() => e.click("bac1-column-id"))
+ .then(() => e.waitForId("testbox-a3-id"))
+ .then(() => e.equalTo("testbox-a3-id", "Test Box - A3", true, false))
+ .then(() => e.sleep(3000))
+ .then(() => resolve());
+ });
+ }
+
+ this.createProtocol = function() {
+ return new Promise(function executor(resolve, reject) {
+ var e = EventUtil;
+
+ Promise.resolve().then(() => e.waitForId("_METHODS_PROTOCOLS_GENERAL_PROTOCOLS"))
+ .then(() => e.click("_METHODS_PROTOCOLS_GENERAL_PROTOCOLS"))
+ .then(() => e.waitForId("create-btn"))
+ .then(() => e.click("create-btn"))
+ .then(() => e.waitForId("options-menu-btn-sample-view-general_protocol"))
+ .then(() => e.click("options-menu-btn-sample-view-general_protocol"))
+ .then(() => e.waitForId("options-menu-btn-identification-info"))
+ .then(() => e.click("options-menu-btn-identification-info"))
+ .then(() => e.waitForId("codeId"))
+ .then(() => e.waitForFill("codeId"))
+ .then(() => e.waitForId("save-btn"))
+ .then(() => e.click("save-btn"))
+ .then(() => e.waitForId("edit-btn"))
+ .then(() => resolve());
+ });
+ }
+
+ this.createProject = function() {
+ return new Promise(function executor(resolve, reject) {
+ var e = EventUtil;
+
+ Promise.resolve().then(() => e.waitForId("TESTID"))
+ .then(() => e.click("TESTID"))
+ .then(() => e.waitForId("create-btn"))
+ .then(() => e.click("create-btn"))
+ .then(() => e.waitForId("project-code-id"))
+ .then(() => e.write("project-code-id", "PROJECT_101", false))
+ .then(() => e.waitForId("save-btn"))
+ .then(() => e.click("save-btn"))
+ .then(() => e.waitForId("edit-btn"))
+ .then(() => e.click("edit-btn"))
+ .then(() => e.waitForId("options-menu-btn-project-view"))
+ .then(() => e.click("options-menu-btn-project-view"))
+ .then(() => e.waitForId("options-menu-btn-description"))
+ .then(() => e.click("options-menu-btn-description"))
+ .then(() => e.waitForCkeditor("description-id"))
+ .then(() => TestUtil.ckeditorSetData("description-id", "Test Description 101"))
+ .then(() => e.waitForId("save-btn"))
+ .then(() => e.click("save-btn"))
+ .then(() => e.waitForId("edit-btn"))
+ .then(() => resolve());
+ });
+ }
+
+ this.createExperiment = function() {
+ return new Promise(function executor(resolve, reject) {
+ var e = EventUtil;
+
+ var yesterday = Util.getFormatedDate(new Date(new Date().setDate(new Date().getDate() - 1)));
+ var tomorrow = Util.getFormatedDate(new Date(new Date().setDate(new Date().getDate() + 1)));
+
+ Promise.resolve().then(() => e.waitForId("options-menu-btn"))
+ .then(() => e.click("options-menu-btn"))
+ // Create Default Experiment
+ .then(() => e.waitForId("default-experiment"))
+ .then(() => e.click("default-experiment"))
+ .then(() => e.waitForId("codeId"))
+ .then(() => e.waitForFill("codeId"))
+ // add Name
+ .then(() => e.waitForId("NAME"))
+ .then(() => e.change("NAME", "Experiment 101", false))
+ // show in project overview checked
+ .then(() => e.waitForId("SHOW_IN_PROJECT_OVERVIEW"))
+ .then(() => e.checked("SHOW_IN_PROJECT_OVERVIEW", true))
+ .then(() => e.change("SHOW_IN_PROJECT_OVERVIEW", true))
+ // add first comment
+ .then(() => e.waitForId("add-comment-btn"))
+ .then(() => e.click("add-comment-btn"))
+ .then(() => e.waitForId("comment-0-box"))
+ .then(() => e.write("comment-0-box", "My first comment", false))
+ .then(() => e.waitForId("save-comment-0-btn"))
+ .then(() => e.click("save-comment-0-btn"))
+ .then(() => e.waitForId("save-btn"))
+ .then(() => e.click("save-btn"))
+ // Update date and name for Experiment
+ .then(() => e.waitForId("edit-btn"))
+ .then(() => e.click("edit-btn"))
+ .then(() => e.waitForId("save-btn"))
+ // edit name
+ .then(() => e.waitForId("NAME"))
+ .then(() => e.change("NAME", "Experiment 101 Bis", false))
+ // set start date
+ .then(() => e.waitForId("START_DATE"))
+ .then(() => e.change("START_DATE", tomorrow, false))
+ // set end date
+ .then(() => e.waitForId("END_DATE"))
+ .then(() => e.change("END_DATE", yesterday, false))
+ // add second comment
+ .then(() => e.waitForId("add-comment-btn"))
+ .then(() => e.click("add-comment-btn"))
+ .then(() => e.waitForId("comment-0-box"))
+ .then(() => e.write("comment-0-box", "My second comment", false))
+ .then(() => e.waitForId("save-comment-0-btn"))
+ .then(() => e.click("save-comment-0-btn"))
+ .then(() => e.waitForId("save-btn"))
+ .then(() => e.click("save-btn"))
+ //You should see the error
+ .then(() => e.waitForId("jNotifyDismiss"))
+ .then(() => e.click("jNotifyDismiss"))
+ // fix the error (remove end date) and save experiment
+ .then(() => e.change("END_DATE", "", false))
+ .then(() => e.waitForId("save-btn"))
+ .then(() => e.click("save-btn"))
+ .then(() => resolve());
+ });
+ }
+
+ this.createExperimentStep = function() {
+ return new Promise(function executor(resolve, reject) {
+ var e = EventUtil;
+
+ var tomorrow = Util.getFormatedDate(new Date(new Date().setDate(new Date().getDate() + 1)));
+
+ Promise.resolve().then(() => e.waitForId("options-menu-btn"))
+ .then(() => e.click("options-menu-btn"))
+ // add Experimental Step
+ .then(() => e.waitForId("experimental-step"))
+ .then(() => e.click("experimental-step"))
+ .then(() => e.waitForId("options-menu-btn-sample-view-experimental_step"))
+ .then(() => e.click("options-menu-btn-sample-view-experimental_step"))
+ .then(() => e.waitForId("codeId"))
+ .then(() => e.click("codeId"))
+ // add name
+ .then(() => e.waitForId("NAME"))
+ .then(() => e.change("NAME", "Step 101", false))
+ // show in project overview checked
+ .then(() => e.waitForId("SHOW_IN_PROJECT_OVERVIEW"))
+ .then(() => e.checked("SHOW_IN_PROJECT_OVERVIEW", true))
+ .then(() => e.change("SHOW_IN_PROJECT_OVERVIEW", true))
+ // set start date
+ .then(() => e.waitForId("START_DATE"))
+ .then(() => e.change("START_DATE", tomorrow, false))
+ // add protocol
+ .then(() => e.waitForId("plus-btn-general_protocol"))
+ .then(() => e.click("plus-btn-general_protocol"))
+ .then(() => e.waitForId("gen1-column-id"))
+ .then(() => e.click("gen1-column-id"))
+ // Operations
+ .then(() => e.waitForId("gen1-operations-column-id"))
+ .then(() => e.click("gen1-operations-column-id"))
+ .then(() => e.waitForId("gen1-operations-column-id-use-as-template"))
+ .then(() => e.click("gen1-operations-column-id-use-as-template"))
+ .then(() => e.waitForId("newSampleCodeForCopy"))
+ .then(() => e.write("newSampleCodeForCopy", "CODE1", false))
+ .then(() => e.waitForId("copyAccept"))
+ .then(() => e.click("copyAccept"))
+ // add first comment
+ .then(() => e.waitForId("add-comment-btn"))
+ .then(() => e.click("add-comment-btn"))
+ .then(() => e.waitForId("comment-0-box"))
+ .then(() => e.write("comment-0-box", "My first comment", false))
+ .then(() => e.waitForId("save-comment-0-btn"))
+ .then(() => e.click("save-comment-0-btn"))
+ .then(() => e.waitForId("code1-column-id"))
+ // save
+ .then(() => e.waitForId("save-btn"))
+ .then(() => e.click("save-btn"))
+ // edit
+ .then(() => e.waitForId("edit-btn"))
+ .then(() => e.click("edit-btn"))
+ .then(() => e.waitForId("save-btn"))
+ // edit name
+ .then(() => e.waitForId("NAME"))
+ .then(() => e.change("NAME", "Step 101 Bis", false))
+ // save
+ .then(() => e.waitForId("save-btn"))
+ .then(() => e.click("save-btn"))
+ .then(() => resolve());
+ });
+ }
+
+ this.datasetUploader = function() {
+ var baseURL = location.protocol + '//' + location.host + location.pathname;
+ var pathToResource = "js/test/resources/test-image.png";
+
+ return new Promise(function executor(resolve, reject) {
+ var e = EventUtil;
+
+ Promise.resolve().then(() => e.waitForId("upload-btn"))
+ .then(() => e.click("upload-btn"))
+ // choose type
+ .then(() => e.waitForId("DATASET_TYPE"))
+ .then(() => e.changeSelect2("DATASET_TYPE", "ELN_PREVIEW", false))
+ // add first comment
+ .then(() => e.waitForId("add-comment-btn"))
+ .then(() => e.click("add-comment-btn"))
+ .then(() => e.waitForId("comment-0-box"))
+ .then(() => e.write("comment-0-box", "My first comment", false))
+ .then(() => e.waitForId("save-comment-0-btn"))
+ .then(() => e.click("save-comment-0-btn"))
+ // upload image
+ .then(() => e.dropFile("test-image.png", baseURL + pathToResource, "filedrop", false))
+ .then(() => e.waitForClass("progressbar.ready"))
+ .then(() => e.waitForId("save-btn"))
+ .then(() => e.click("save-btn"))
+ // open data set and edit it
+ .then(() => e.waitForId("dataSetPosInTree-0"))
+ .then(() => e.click("dataSetPosInTree-0"))
+ .then(() => e.waitForId("dataset-edit-btn"))
+ .then(() => e.click("dataset-edit-btn"))
+ .then(() => e.waitForId("save-btn"))
+ // change Name
+ .then(() => e.waitForId("NAME"))
+ .then(() => e.change("NAME", "New Name", false))
+ .then(() => e.click("save-btn"))
+ .then(() => e.waitForId("dataset-edit-btn"))
+ .then(() => resolve());
+ });
+ }
+
+ this.showInProjectOverview = function() {
+ return new Promise(function executor(resolve, reject) {
+ var e = EventUtil;
+
+ Promise.resolve().then(() => e.waitForId("PATH_TESTID_PROJECT_101"))
+ .then(() => e.click("PATH_TESTID_PROJECT_101"))
+ // click "Show Experiments"
+ .then(() => e.waitForId("options-menu-btn-project-view"))
+ .then(() => e.waitForId("project-experiments"))
+ .then(() => e.waitForStyle("project-experiments", "display", "none", false))
+ .then(() => e.click("options-menu-btn-project-view"))
+ .then(() => e.waitForId("options-menu-btn-experiments"))
+ .then(() => e.click("options-menu-btn-experiments"))
+ .then(() => e.waitForId("project-experiments"))
+ .then(() => e.waitForStyle("project-experiments", "display", "", false))
+ // click "Show Objects"
+ .then(() => e.waitForId("options-menu-btn-project-view"))
+ .then(() => e.waitForId("project-samples"))
+ .then(() => e.waitForStyle("project-samples", "display", "none", false))
+ .then(() => e.click("options-menu-btn-project-view"))
+ .then(() => e.waitForId("options-menu-btn-objects"))
+ .then(() => e.click("options-menu-btn-objects"))
+ .then(() => e.waitForId("project-samples"))
+ .then(() => e.waitForStyle("project-samples", "display", "", false))
+ .then(() => resolve());
+ });
+ }
+
+ this.search = function() {
+ return new Promise(function executor(resolve, reject) {
+ var e = EventUtil;
+
+ Promise.resolve().then(() => e.waitForId("search"))
+ // start global search
+ .then(() => e.click("search"))
+ .then(() => e.change("search", "BAC5", false))
+ .then(() => e.keypress("search", 13, false))
+ .then(() => e.waitForId("save-btn"))
+ // check searching results
+ .then(() => e.waitForId("columns-dropdown-id"))
+ .then(() => e.click("columns-dropdown-id"))
+ .then(() => e.waitForId("code-cln"))
+ .then(() => e.checked("code-cln", true))
+ // todo should be modified after test 10. and BAC5_BAC4 will be available
+ .then(() => e.waitForId("bac5-id"))
+ // save query
+ .then(() => e.waitForId("save-btn"))
+ .then(() => e.click("save-btn"))
+ .then(() => e.waitForId("Name"))
+ .then(() => e.write("Name", "Search for BAC5", false))
+ .then(() => e.waitForId("advanced-entity-search-dropdown-id"))
+ .then(() => e.triggerSearchSelect2("advanced-entity-search-dropdown-id", "ba", false))
+ .then(() => e.waitForId("search-query-save-btn"))
+ .then(() => e.click("search-query-save-btn"))
+ // wait for saving
+ .then(() => e.sleep(3000))
+ // Click on BAC5
+ .then(() => e.waitForId("bac5-id"))
+ .then(() => e.click("bac5-id"))
+ .then(() => e.waitForId("edit-btn"))
+ // Click on Advanced Search
+ .then(() => e.waitForId("ADVANCED_SEARCH"))
+ .then(() => e.click("ADVANCED_SEARCH"))
+ .then(() => e.waitForId("saved-search-dropdown-id"))
+ .then(() => e.triggerSelectSelect2("saved-search-dropdown-id", 0, false))
+ .then(() => e.waitForId("search-btn"))
+ .then(() => e.click("search-btn"))
+ .then(() => e.waitForId("bac5-id"))
.then(() => resolve());
});
}
diff --git a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/test/resources/test-image.png b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/test/resources/test-image.png
new file mode 100644
index 0000000000000000000000000000000000000000..f39ca347e3721a748461bf5d8e7c185b89c00dd7
Binary files /dev/null and b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/test/resources/test-image.png differ
diff --git a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/util/EventUtil.js b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/util/EventUtil.js
index abe3051fd51783e5fba9f2a70b0d48fa7ea9c0d2..84520f191dda151db3378fc53bc12599d22de737 100644
--- a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/util/EventUtil.js
+++ b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/util/EventUtil.js
@@ -11,7 +11,7 @@ var EventUtil = new function() {
element.trigger('click');
resolve();
} catch(error) {
- reject();
+ reject(error);
}
});
};
@@ -24,7 +24,55 @@ var EventUtil = new function() {
element.val(value).change();
resolve();
} catch(error) {
- reject();
+ reject(error);
+ }
+ });
+ };
+
+ this.changeSelect2 = function(elementId, value, ignoreError) {
+ return new Promise(function executor(resolve, reject) {
+ try {
+ var element = EventUtil.getElement(elementId, ignoreError, resolve);
+ element.select2();
+ element.focus();
+ element.val(value);
+ element.select2().trigger('change');
+ resolve();
+ } catch(error) {
+ reject(error);
+ }
+ });
+ };
+
+ this.triggerSelectSelect2 = function(elementId, value, ignoreError) {
+ return new Promise(function executor(resolve, reject) {
+ try {
+ var element = EventUtil.getElement(elementId, ignoreError, resolve);
+ element.focus();
+ element.val(value);
+ element.select2().trigger('select2:select');
+ resolve();
+ } catch(error) {
+ reject(error);
+ }
+ });
+ };
+
+ this.triggerSearchSelect2 = function(elementId, value, ignoreError) {
+ return new Promise(function executor(resolve, reject) {
+ try {
+ var element = EventUtil.getElement(elementId, ignoreError, resolve);
+ element.select2('open');
+
+ var $search = element.data('select2').dropdown.$search || element.data('select2').selection.$search;
+ $search.val(value);
+ $search.trigger('input');
+ setTimeout(function() {
+ $('.select2-results__option').trigger("mouseup");
+ resolve();
+ }, 2000);
+ } catch(error) {
+ reject(error);
}
});
};
@@ -37,7 +85,7 @@ var EventUtil = new function() {
element.prop('checked', value);
resolve();
} catch(error) {
- reject();
+ reject(error);
}
});
};
@@ -53,7 +101,7 @@ var EventUtil = new function() {
throw "Element #" + elementId + " should" + (isEqual ? "" : " not") + " be equal " + value;
}
} catch(error) {
- reject();
+ reject(error);
}
});
};
@@ -70,11 +118,26 @@ var EventUtil = new function() {
}
resolve();
} catch(error) {
- reject();
+ reject(error);
}
});
};
+ this.keypress = function(elementId, key, ignoreError) {
+ return new Promise(function executor(resolve, reject) {
+ try {
+ var element = EventUtil.getElement(elementId, ignoreError, resolve);
+ element.focus();
+ var e = $.Event('keypress');
+ e.which = key;
+ $(element).trigger(e);
+ resolve();
+ } catch(error) {
+ reject(error);
+ }
+ });
+ }
+
this.verifyExistence = function(elementId, isExist, ignoreError) {
return new Promise(function executor(resolve, reject) {
var elementExistence = $("#" + elementId).length > 0;
@@ -102,6 +165,35 @@ var EventUtil = new function() {
});
};
+ this.waitForClass = function(className, ignoreError, timeout) {
+ return new Promise(function executor(resolve, reject) {
+ timeout = EventUtil.checkTimeout(className, timeout, ignoreError, resolve, reject);
+
+ if($("." + className).length <= 0) {
+ setTimeout(executor.bind(null, resolve, reject), DEFAULT_TIMEOUT_STEP);
+ } else {
+ resolve();
+ }
+ });
+ };
+
+ this.waitForStyle = function(elementId, styleName, styleValue, ignoreError, timeout) {
+ return new Promise(function executor(resolve, reject) {
+ try {
+ timeout = EventUtil.checkTimeout(elementId, timeout, ignoreError, resolve, reject);
+
+ var element = EventUtil.getElement(elementId, ignoreError, resolve);
+ if (element[0].style[styleName] === styleValue) {
+ resolve();
+ } else {
+ setTimeout(executor.bind(null, resolve, reject), DEFAULT_TIMEOUT_STEP);
+ }
+ } catch(error) {
+ reject(error);
+ }
+ });
+ }
+
this.waitForFill = function(elementId, ignoreError, timeout) {
return new Promise(function executor(resolve, reject) {
timeout = EventUtil.checkTimeout(elementId, timeout, ignoreError, resolve, reject);
@@ -115,6 +207,19 @@ var EventUtil = new function() {
});
};
+ this.waitForCkeditor = function(id, data, timeout) {
+ return new Promise(function executor(resolve, reject) {
+ timeout = EventUtil.checkTimeout(elementId, timeout, ignoreError, resolve, reject);
+ editor = CKEditorManager.getEditorById(id);
+
+ if(editor === undefined) {
+ setTimeout(executor.bind(null, resolve, reject), DEFAULT_TIMEOUT_STEP);
+ } else {
+ resolve();
+ }
+ });
+ }
+
this.checkTimeout = function(elementId, timeout, ignoreError, resolve, reject) {
if (!timeout) {
timeout = DEFAULT_TIMEOUT;
@@ -131,6 +236,10 @@ var EventUtil = new function() {
return timeout;
}
+ this.sleep = function(ms) {
+ return new Promise(resolve => setTimeout(resolve, ms));
+ }
+
this.dragAndDrop = function(dragId, dropId, ignoreError) {
return new Promise(function executor(resolve, reject) {
try {
@@ -151,11 +260,32 @@ var EventUtil = new function() {
dropElement.trigger(dropEvent);
resolve();
} catch(error) {
- reject();
+ reject(error);
}
});
};
+ this.dropFile = function(fileName, url, dropId, ignoreError) {
+ return new Promise(function executor(resolve, reject) {
+ try {
+ var dropElement = EventUtil.getElement(dropId, ignoreError, resolve).droppable();
+
+ TestUtil.fetchBytes(url, function(file) {
+ file.name = fileName;
+
+ var dt = { files: [file] };
+
+ dropEvent = jQuery.Event("drop");
+ dropEvent.originalEvent = jQuery.Event("DragEvent");
+ dropEvent.originalEvent.dataTransfer = dt;
+ dropElement.trigger(dropEvent);
+ resolve();
+ });
+ } catch(error) {
+ reject(error);
+ }
+ });
+ };
this.getElement = function(elementId, ignoreError, resolve) {
var element = $( "#" + elementId );
@@ -168,5 +298,4 @@ var EventUtil = new function() {
}
return element;
}
-
}
\ No newline at end of file
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 93a249d74d6902056773285df620888d03405be7..705c310c0e7d1f73c7602ce43a4989485a183a3e 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
@@ -501,12 +501,15 @@ var FormUtil = new function() {
return $btn;
}
- this.getButtonWithText = function(text, clickEvent, btnClass) {
+ this.getButtonWithText = function(text, clickEvent, btnClass, id) {
var auxBtnClass = "btn-default";
if(btnClass) {
auxBtnClass = btnClass;
}
var $pinBtn = $("<a>", { 'class' : 'btn ' + auxBtnClass });
+ if(id) {
+ $pinBtn.attr("id", id);
+ }
$pinBtn.append(text);
$pinBtn.click(clickEvent);
return $pinBtn;
@@ -786,6 +789,11 @@ var FormUtil = new function() {
// Form Fields
//
this._getBooleanField = function(id, alt, checked) {
+ if (id) {
+ if(id.charAt(0) === '$') {
+ id = id.substring(1);
+ }
+ }
var attr = {'type' : 'checkbox', 'id' : id, 'alt' : alt, 'placeholder' : alt };
if(checked) {
attr['checked'] = '';
@@ -1005,11 +1013,16 @@ var FormUtil = new function() {
if(!title) {
title = "More ... ";
}
+ var id = 'options-menu-btn';
+ if (namespace) {
+ id = id + "-" + namespace;
+ id = id.toLowerCase();
+ }
var $dropdownOptionsMenu = $("<span>", { class : 'dropdown' });
if(toolbarModel) {
toolbarModel.push({ component : $dropdownOptionsMenu, tooltip: null });
}
- var $dropdownOptionsMenuCaret = $("<a>", { 'href' : '#', 'data-toggle' : 'dropdown', class : 'dropdown-toggle btn btn-default', 'id' : 'options-menu-btn'})
+ var $dropdownOptionsMenuCaret = $("<a>", { 'href' : '#', 'data-toggle' : 'dropdown', class : 'dropdown-toggle btn btn-default', 'id' : id})
.append(title).append($("<b>", { class : 'caret' }));
var $dropdownOptionsMenuList = $("<ul>", { class : 'dropdown-menu', 'role' : 'menu' });
$dropdownOptionsMenu.append($dropdownOptionsMenuCaret);
@@ -1021,7 +1034,8 @@ var FormUtil = new function() {
} else {
var label = option.label;
var title = option.title ? option.title : label;
- var $dropdownElement = $("<li>", { 'role' : 'presentation' }).append($("<a>", {'title' : title }).append(label));
+ var id = title.split(" ").join("-").toLowerCase();
+ var $dropdownElement = $("<li>", { 'role' : 'presentation' }).append($("<a>", {'title' : title, 'id' : id}).append(label));
$dropdownElement.click(option.action);
$dropdownOptionsMenuList.append($dropdownElement);
}
@@ -1041,6 +1055,8 @@ var FormUtil = new function() {
var sectionSetting = sectionsSettings[option.label];
if (sectionSetting !== undefined) {
shown = sectionSetting === 'shown';
+ } else if (option.showByDefault) {
+ shown = true;
} else {
shown = ! profile.hideSectionsByDefault;
}
@@ -1048,7 +1064,8 @@ var FormUtil = new function() {
var $section = $(option.section);
$section.toggle(shown);
var $label = $("<span>").append((shown ? "Hide " : "Show ") + option.label);
- var $dropdownElement = $("<li>", { 'role' : 'presentation' }).append($("<a>").append($label));
+ var id = 'options-menu-btn-' + option.label.split(" ").join("-").toLowerCase();
+ var $dropdownElement = $("<li>", { 'role' : 'presentation' }).append($("<a>", { 'id' : id }).append($label));
var action = function(event) {
var option = event.data.option;
var $label = event.data.label;
@@ -1058,6 +1075,9 @@ var FormUtil = new function() {
$label.text("Show " + option.label);
sectionsSettings[option.label] = "hidden";
} else {
+ if (option.beforeShowingAction) {
+ option.beforeShowingAction();
+ }
$label.text("Hide " + option.label);
sectionsSettings[option.label] = "shown";
}
@@ -1158,7 +1178,9 @@ var FormUtil = new function() {
entityPath.append("/").append(this.getFormLink(spaceCode, 'Space', spaceCode));
}
if(projectCode) {
- entityPath.append("/").append(this.getFormLink(projectCode, 'Project', IdentifierUtil.getProjectIdentifier(spaceCode, projectCode)));
+ var projectIdentifier = IdentifierUtil.getProjectIdentifier(spaceCode, projectCode);
+ var id = "PATH" + projectIdentifier.split(" ").join("-").split("/").join("_");
+ entityPath.append("/").append(this.getFormLink(projectCode, 'Project', projectIdentifier, null, id));
}
if(experimentCode) {
entityPath.append("/").append(this.getFormLink(experimentCode, 'Experiment', IdentifierUtil.getExperimentIdentifier(spaceCode, projectCode, experimentCode)));
diff --git a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/util/PrintUtil.js b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/util/PrintUtil.js
index 22821e3fb66c7337c2003db056c9fda3bc952795..1c6fba5b79e9c0c96b2b6c6fc988cc19b6a269ae 100644
--- a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/util/PrintUtil.js
+++ b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/util/PrintUtil.js
@@ -66,7 +66,7 @@ var PrintUtil = new function() {
var samplesListOfCodes = "";
for(var sampleTypeCode in allSamplesByType) {
- samplesListOfCodes += sampleTypeCode + ": ";
+ samplesListOfCodes += Util.getDisplayNameFromCode(sampleTypeCode) + ": ";
var samples = allSamplesByType[sampleTypeCode];
for(var i = 0; i < samples.length; i++) {
var sample = samples[i];
@@ -76,13 +76,7 @@ var PrintUtil = new function() {
if(sampleTypeCode === "STORAGE_POSITION") {
samplesListOfCodes += Util.getStoragePositionDisplayName(sample);
} else {
- var name = sample.properties[profile.propertyReplacingCode];
- if(!name) {
- samplesListOfCodes += sample.code;
- } else {
- samplesListOfCodes += sample.code + "(" + name + ")";
- }
-
+ samplesListOfCodes += Util.getDisplayNameForEntity(sample);
}
}
samplesListOfCodes += "</br>";
@@ -127,6 +121,7 @@ var PrintUtil = new function() {
var $newInspectorTable = $("<table>", { "class" : "properties table table-condensed" });
$newInspector.append($newInspectorTable);
+ this._addLabelAndValue($newInspectorTable, "Code", entity.code);
if(extraProperties) {
for(code in extraProperties) {
@@ -136,11 +131,7 @@ var PrintUtil = new function() {
if(propLabel.length > 25) {
propLabel = propLabel.substring(0, 23) + "...";
}
- $newInspectorTable
- .append($("<tr>")
- .append($("<td>", { "class" : "property", "colspan" : "1" }).append($("<p>", { "class" : "inspectorLabel"}).append(propLabel + ":")))
- .append($("<td>", { "class" : "property", "colspan" : "1" }).append($("<p>", { "class" : "inspectorLineBreak"}).append(extraProp.value)))
- );
+ this._addLabelAndValue($newInspectorTable, propLabel, extraProp.value);
}
}
@@ -197,11 +188,7 @@ var PrintUtil = new function() {
.append($("<td>", { "class" : "property", "colspan" : "2" }).append($("<p>", { "class" : "inspectorLineBreak"}).append(propertyLabel + ":").append("<br>").append(propertyContent)))
);
} else {
- $newInspectorTable
- .append($("<tr>")
- .append($("<td>", { "class" : "property", "colspan" : "1" }).append($("<p>", { "class" : "inspectorLabel"}).append(propertyLabel + ":")))
- .append($("<td>", { "class" : "property", "colspan" : "1" }).append($("<p>", { "class" : "inspectorLineBreak" }).append(propertyContent)))
- );
+ this._addLabelAndValue($newInspectorTable, propertyLabel, propertyContent);
}
}
}
@@ -211,38 +198,22 @@ var PrintUtil = new function() {
//Show Parent Codes
var allParentCodesAsText = this._getCodesFromSamples(entity.parents);
if(allParentCodesAsText.length > 0) {
- $newInspectorTable
- .append($("<tr>")
- .append($("<td>", { "class" : "property", "colspan" : "1" }).append($("<p>", { "class" : "inspectorLabel"}).append("Parents:")))
- .append($("<td>", { "class" : "property", "colspan" : "1" }).append($("<p>", { "class" : "inspectorLineBreak" }).append(allParentCodesAsText)))
- );
+ this._addLabelAndValue($newInspectorTable, "Parents", allParentCodesAsText);
}
//Show Children Codes
var allChildrenCodesAsText = this._getCodesFromSamples(entity.children);
if(allChildrenCodesAsText.length > 0) {
- $newInspectorTable
- .append($("<tr>")
- .append($("<td>", { "class" : "property", "colspan" : "1" }).append($("<p>", { "class" : "inspectorLabel"}).append("Children:")))
- .append($("<td>", { "class" : "property", "colspan" : "1" }).append($("<p>", { "class" : "inspectorLineBreak"}).append(allChildrenCodesAsText)))
- );
+ this._addLabelAndValue($newInspectorTable, "Children", allChildrenCodesAsText);
}
}
//Show Modification Date
if(entity.registrationDetails) {
- $newInspectorTable
- .append($("<tr>")
- .append($("<td>", { "class" : "property", "colspan" : "1" }).append($("<p>", { "class" : "inspectorLabel"}).append("Modification Date:")))
- .append($("<td>", { "class" : "property", "colspan" : "1" }).append($("<p>", { "class" : "inspectorLineBreak"}).append(new Date(entity.registrationDetails["modificationDate"]))))
- );
+ this._addLabelAndValue($newInspectorTable, "Modification Date", new Date(entity.registrationDetails["modificationDate"]));
//Show Creation Date
- $newInspectorTable
- .append($("<tr>")
- .append($("<td>", { "class" : "property", "colspan" : "1" }).append($("<p>", { "class" : "inspectorLabel"}).append("Registration Date:")))
- .append($("<td>", { "class" : "property", "colspan" : "1" }).append($("<p>", { "class" : "inspectorLineBreak"}).append(new Date(entity.registrationDetails["registrationDate"]))))
- );
+ this._addLabelAndValue($newInspectorTable, "Registration Date", new Date(entity.registrationDetails["registrationDate"]));
}
if(extraCustomId && extraContent) {
@@ -251,6 +222,15 @@ var PrintUtil = new function() {
return $newInspector;
};
+
+ this._addLabelAndValue = function($newInspectorTable, label, value) {
+ $newInspectorTable
+ .append($("<tr>")
+ .append($("<td>", { "class" : "property", "colspan" : "1" }).append($("<p>", { "class" : "inspectorLabel"}).append(label + ":")))
+ .append($("<td>", { "class" : "property", "colspan" : "1" }).append($("<p>", { "class" : "inspectorLineBreak" }).append(value)))
+ );
+
+ }
this._convertJsonToHtml = function(json) {
data = json["data"];
diff --git a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/AdvancedSearch/AdvancedSearchView.js b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/AdvancedSearch/AdvancedSearchView.js
index a32c9c1bcc816ce5c26244fbf67a947e9894da4d..262b93a35f2ba9acf86b16e033def36a69f1ae62 100644
--- a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/AdvancedSearch/AdvancedSearchView.js
+++ b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/AdvancedSearch/AdvancedSearchView.js
@@ -125,7 +125,7 @@ function AdvancedSearchView(advancedSearchController, advancedSearchModel) {
    });
}
- Â Â Â Â var $btnSave = $('<input>', { 'type': 'submit', 'class' : 'btn btn-primary', 'value' : 'Save' });
+ Â Â Â Â var $btnSave = $('<input>', { 'type': 'submit', 'class' : 'btn btn-primary', 'value' : 'Save', 'id' : 'search-query-save-btn' });
    var $btnCancel = $('<a>', { 'class' : 'btn btn-default' }).append('Cancel');
    $btnCancel.click(function() {
      Util.unblockUI();
@@ -190,10 +190,11 @@ function AdvancedSearchView(advancedSearchController, advancedSearchModel) {
});
}
this._$savedSearchesDropdown = FormUtil.getPlainDropdown(savedSearchOptions);
- this._$savedSearchesDropdown.change(function(change) {
- var i = _this._$savedSearchesDropdown.val();
- _this._advancedSearchController.selectSavedSearch(i);
- });
+ this._$savedSearchesDropdown.attr("id", "saved-search-dropdown-id");
+ this._$savedSearchesDropdown.on("select2:select", function () {
+ var i = _this._$savedSearchesDropdown.val();
+ _this._advancedSearchController.selectSavedSearch(i);
+ });
$container.append(this._$savedSearchesDropdown);
this._$savedSearchesDropdown.select2({
width: '400px',
@@ -209,7 +210,7 @@ function AdvancedSearchView(advancedSearchController, advancedSearchModel) {
var $buttonSave = FormUtil.getButtonWithIcon('glyphicon-floppy-disk', function() {
_this._save();
- }, 'Save');
+ }, 'Save', null, "save-btn");
$buttonSave.css({ 'margin-left': '8px'});
$container.append($buttonSave);
@@ -243,7 +244,7 @@ function AdvancedSearchView(advancedSearchController, advancedSearchModel) {
var $submitButton = FormUtil.getButtonWithIcon('glyphicon-search', function() {
_this._advancedSearchController.search();
- });
+ }, null, null, "search-btn");
$submitButton.css("margin-top", "22px");
var $submitButtonGroup = FormUtil.getFieldForComponentWithLabel($submitButton, "", null, true);
@@ -743,7 +744,8 @@ function AdvancedSearchView(advancedSearchController, advancedSearchModel) {
}
}
}
- return _this._getLinkOnClick(data.code, data, paginationInfo);
+ var id = data.code.toLowerCase() + "-id";
+ return _this._getLinkOnClick(data.code, data, paginationInfo, id);
}
}, {
label : 'Identifier',
@@ -901,16 +903,16 @@ function AdvancedSearchView(advancedSearchController, advancedSearchModel) {
return dataGrid;
}
- this._getLinkOnClick = function(code, data, paginationInfo) {
+ this._getLinkOnClick = function(code, data, paginationInfo, id) {
if(data.entityKind !== "Sample") {
paginationInfo = null; // TODO - Only supported for samples for now
}
switch(data.entityKind) {
case "Experiment":
- return FormUtil.getFormLink(code, data.entityKind, data.identifier, paginationInfo);
+ return FormUtil.getFormLink(code, data.entityKind, data.identifier, paginationInfo, id);
break;
default:
- return FormUtil.getFormLink(code, data.entityKind, data.permId, paginationInfo);
+ return FormUtil.getFormLink(code, data.entityKind, data.permId, paginationInfo, id);
break;
}
}
diff --git a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/DataGrid/DataGridController.js b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/DataGrid/DataGridController.js
index cec7c15151fc7255427aa9088436df2f2844a8cd..5797ce89ac28b15e122bf355b97c452ce45d2f26 100644
--- a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/DataGrid/DataGridController.js
+++ b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/DataGrid/DataGridController.js
@@ -57,6 +57,10 @@ function DataGridController(title, columnsFirst, columnsLast, columnsDynamicFunc
});
}
+ this.refreshHeight = function() {
+ this._grid.calculateHeight();
+ }
+
this.refresh = function() {
this._dataGridModel.datagrid.repeater('render');
}
diff --git a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/DataGrid/SampleDataGridUtil.js b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/DataGrid/SampleDataGridUtil.js
index 2082287015c8e340fb9e0089cd0f4dc88a5dbfc7..d6bed74cc27f8916aba71e26cf33fa1322a99133 100644
--- a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/DataGrid/SampleDataGridUtil.js
+++ b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/DataGrid/SampleDataGridUtil.js
@@ -13,7 +13,9 @@ var SampleDataGridUtil = new function() {
sortable : false,
render : function(data) {
var nameToUse = Util.getNameOrCode(data);
- return (isLinksDisabled)?nameToUse:FormUtil.getFormLink(nameToUse, "Sample", data.permId);
+ var codeId = data.code.toLowerCase() + "-column-id";
+ var $controlLabel = $('<label>', { 'id' : codeId }).html(nameToUse);
+ return (isLinksDisabled) ? $controlLabel : FormUtil.getFormLink(nameToUse, "Sample", data.permId, null, codeId);
}
});
@@ -191,8 +193,7 @@ var SampleDataGridUtil = new function() {
}
}
}
- var codeId = data.code.toLowerCase() + "-column-id";
- return (isLinksDisabled)?data.code:FormUtil.getFormLink(data.code, "Sample", data.permId, paginationInfo, codeId);
+ return (isLinksDisabled)?data.code:FormUtil.getFormLink(data.code, "Sample", data.permId, paginationInfo);
},
filter : function(data, filter) {
return data.identifier.toLowerCase().indexOf(filter) !== -1;
diff --git a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/DataSetForm/DataSetFormController.js b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/DataSetForm/DataSetFormController.js
index 9e3f3598df89aaeb6e3f4ece1d132b2d3d1165ff..9a8150f81661adfe1aa8ec8550f395dd07a3ef5b 100644
--- a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/DataSetForm/DataSetFormController.js
+++ b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/DataSetForm/DataSetFormController.js
@@ -106,6 +106,10 @@ function DataSetFormController(parentController, mode, entity, dataSet, isMini,
});
}
+ this._showError = function(errorMessage) {
+ Util.blockUI();
+ Util.showUserError(errorMessage, function() { Util.unblockUI(); });
+ }
//
// Form Submit
//
@@ -115,14 +119,16 @@ function DataSetFormController(parentController, mode, entity, dataSet, isMini,
//
if(this._dataSetFormModel.mode === FormMode.CREATE) {
if(this._dataSetFormModel.files.length === 0) {
- Util.blockUI();
- Util.showUserError("You should upload at least one file.", function() { Util.unblockUI(); });
+ this._showError("You should upload at least one file.");
+ return;
+ }
+ if ($('#DATASET_TYPE').val() === "") {
+ this._showError("No Data Set Type specified.");
return;
}
if(Uploader.uploadsInProgress()) {
- Util.blockUI();
- Util.showUserError("Please wait the upload to finish.", function() { Util.unblockUI(); });
+ this._showError("Please wait the upload to finish.");
return;
}
}
diff --git a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/DataSetForm/DataSetFormView.js b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/DataSetForm/DataSetFormView.js
index d3b74ce13a9416a972b1c2978c8a39d8155a43f1..1c6b65ba1a828fcebe9749500ed1500ee166a8c8 100644
--- a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/DataSetForm/DataSetFormView.js
+++ b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/DataSetForm/DataSetFormView.js
@@ -66,7 +66,7 @@ function DataSetFormView(dataSetFormController, dataSetFormModel) {
//Edit Button
var $editBtn = FormUtil.getButtonWithIcon("glyphicon-edit", function () {
mainController.changeView('showEditDataSetPageFromPermId', _this._dataSetFormModel.dataSet.code);
- }, "Edit");
+ }, "Edit", null, "dataset-edit-btn");
if(toolbarConfig.EDIT) {
toolbarModel.push({ component : $editBtn });
}
@@ -158,7 +158,7 @@ function DataSetFormView(dataSetFormController, dataSetFormModel) {
} else if(!this._dataSetFormModel.isMini) {
var $saveBtn = FormUtil.getButtonWithIcon("glyphicon-floppy-disk", function() {
_this._dataSetFormController.submitDataSet();
- }, "Save");
+ }, "Save", null, "save-btn");
$saveBtn.removeClass("btn-default");
$saveBtn.addClass("btn-primary");
toolbarModel.push({ component : $saveBtn });
diff --git a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/DataSetForm/widgets/AdvancedEntitySearchDropdown.js b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/DataSetForm/widgets/AdvancedEntitySearchDropdown.js
index 6e8671454d92c3f14c65dc728b3692ad35eca014..53f93071e53f16b2238ee894f2f30b9806735cc3 100644
--- a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/DataSetForm/widgets/AdvancedEntitySearchDropdown.js
+++ b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/DataSetForm/widgets/AdvancedEntitySearchDropdown.js
@@ -233,6 +233,7 @@ function AdvancedEntitySearchDropdown(isMultiple,
//
this.init = function($container) {
$select.attr("multiple", "multiple");
+ $select.attr("id", "advanced-entity-search-dropdown-id");
if(isRequired) {
$select.attr("required", "required");
diff --git a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/DataSetForm/widgets/DatasetViewerView.js b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/DataSetForm/widgets/DatasetViewerView.js
index f7cf5d3e6686d1f62b481459e968edfa6183514a..72cfd53bfad5af6cbecf8b0878dcf2b3cf2b6fd9 100644
--- a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/DataSetForm/widgets/DatasetViewerView.js
+++ b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/DataSetForm/widgets/DatasetViewerView.js
@@ -96,6 +96,7 @@ function DataSetViewerView(dataSetViewerController, dataSetViewerModel) {
$container.append($tree);
var treeModel = [];
+ var dataSetPosInTree = 0;
for(var datasetCode in this._dataSetViewerModel.entityDataSets) {
var displayName = this._dataSetViewerModel.entityDataSets[datasetCode].properties[profile.propertyReplacingCode];
if(!displayName) {
@@ -106,9 +107,10 @@ function DataSetViewerView(dataSetViewerController, dataSetViewerModel) {
var dataset = this._dataSetViewerModel.entityDataSets[datasetCode];
var onClick = "mainController.changeView('showViewDataSetPageFromPermId', '" + datasetCode + "');";
- var dataSetTitle = "<span onclick=\"" + onClick + "\">"
+ var dataSetTitle = "<span id=\"dataSetPosInTree-" + dataSetPosInTree + "\" onclick=\"" + onClick + "\">"
+ dataset.dataSetTypeCode + " : " + displayName + "</span>";
treeModel.push({ title : dataSetTitle, key : "/", folder : true, lazy : true, datasetCode : datasetCode });
+ dataSetPosInTree += 1;
}
var glyph_opts = {
@@ -229,9 +231,12 @@ function DataSetViewerView(dataSetViewerController, dataSetViewerModel) {
content : $tooltip,
position : "left",
functionFormat : function(instance, helper, content) {
-
- var containerWidth = $(helper.origin).offset().left*0.9;
- var containerHeight = $(window).height()*0.9;
+ var containerWidth = $(helper.origin).offset().left;
+ if (containerWidth < 200) {
+ containerWidth = $(helper.origin).width();
+ }
+ containerWidth *= 0.9;
+ var containerHeight = $(window).height() * 0.9;
var $img = content.find("img");
var imageSize = Util.getImageSize(containerWidth, containerHeight, $img[0].width, $img[0].height);
diff --git a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/ExperimentForm/ExperimentFormView.js b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/ExperimentForm/ExperimentFormView.js
index 9426729a20e91ba56b22f5115e6a2d113f4017ce..3fab1fc232e282135364a5c578a1bdaad6e6c6f8 100644
--- a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/ExperimentForm/ExperimentFormView.js
+++ b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/ExperimentForm/ExperimentFormView.js
@@ -85,7 +85,7 @@ function ExperimentFormView(experimentFormController, experimentFormModel) {
//Edit
var $editBtn = FormUtil.getButtonWithIcon("glyphicon-edit", function () {
mainController.changeView("showEditExperimentPageFromIdentifier", _this._experimentFormModel.experiment.identifier);
- }, "Edit");
+ }, "Edit", null, "edit-btn");
toolbarModel.push({ component : $editBtn });
}
if (_this._allowedToMove()) {
@@ -174,7 +174,7 @@ function ExperimentFormView(experimentFormController, experimentFormModel) {
} else { //Create and Edit
var $saveBtn = FormUtil.getButtonWithIcon("glyphicon-floppy-disk", function() {
_this._experimentFormController.updateExperiment();
- }, "Save");
+ }, "Save", null, "save-btn");
$saveBtn.removeClass("btn-default");
$saveBtn.addClass("btn-primary");
toolbarModel.push({ component : $saveBtn });
@@ -234,7 +234,7 @@ function ExperimentFormView(experimentFormController, experimentFormModel) {
'class' : 'zoomableImage',
'id' : 'preview-image',
'src' : './img/image_loading.gif',
- 'style' : 'max-width:100%; display:none;'
+ 'style' : 'max-height:300px; display:none;'
});
$previewImage.click(function() {
Util.showImage($("#preview-image").attr("src"));
@@ -316,12 +316,12 @@ function ExperimentFormView(experimentFormController, experimentFormModel) {
if(this._experimentFormModel.mode === FormMode.VIEW || this._experimentFormModel.mode === FormMode.EDIT) {
$identificationInfo.append(FormUtil.getFieldForLabelWithText("Code", this._experimentFormModel.experiment.code));
- var $codeField = FormUtil._getInputField("text", null, "code", null, true);
+ var $codeField = FormUtil._getInputField("text", "codeId", "code", null, true);
$codeField.val(IdentifierUtil.getCodeFromIdentifier(this._experimentFormModel.experiment.identifier));
$codeField.hide();
$identificationInfo.append($codeField);
} else if(this._experimentFormModel.mode === FormMode.CREATE) {
- var $codeField = FormUtil._getInputField("text", null, "code", null, true);
+ var $codeField = FormUtil._getInputField("text", "codeId", "code", null, true);
$codeField.keyup(function() {
_this._experimentFormModel.isFormDirty = true;
var caretPosition = this.selectionStart;
@@ -381,11 +381,6 @@ function ExperimentFormView(experimentFormController, experimentFormModel) {
}
this._createSamplesSection = function(hideShowOptionsModel) {
- hideShowOptionsModel.push({
- label : ELNDictionary.Samples,
- section : "#experiment-samples"
- });
-
var _this = this;
var $samples = $("<div>", { id : "experiment-samples" });
$samples.append($('<legend>').text(ELNDictionary.Samples));
@@ -400,6 +395,13 @@ function ExperimentFormView(experimentFormController, experimentFormModel) {
var sampleList = new SampleTableController(this._experimentFormController, null, this._experimentFormModel.experiment.identifier, null, null, this._experimentFormModel.experiment);
sampleList.init(views);
$samples.hide();
+ hideShowOptionsModel.push({
+ label : ELNDictionary.Samples,
+ section : "#experiment-samples",
+ beforeShowingAction : function() {
+ sampleList.refreshHeight();
+ }
+ });
return $samples;
}
diff --git a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/ExperimentTable/ExperimentTableController.js b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/ExperimentTable/ExperimentTableController.js
index 9ffa01a89df825b562d0857ef2cd5a59dc775894..8174295b7a647f17c1083d460996eb7506ba89ff 100644
--- a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/ExperimentTable/ExperimentTableController.js
+++ b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/ExperimentTable/ExperimentTableController.js
@@ -81,8 +81,15 @@ function ExperimentTableController(parentController, title, project, showInProje
var rowClick = null;
//Create and display table
- var dataGridController = ExperimentDataGridUtil.getExperimentDataGrid(selectedTypeCode, experiments, rowClick, 50);
- dataGridController.init(this._experimentTableView.getTableContainer());
+ this._dataGridController = ExperimentDataGridUtil.getExperimentDataGrid(selectedTypeCode, experiments, rowClick, 50);
+ this._dataGridController.init(this._experimentTableView.getTableContainer());
+ }
+ }
+
+ this.refreshHeight = function()
+ {
+ if (this._dataGridController) {
+ this._dataGridController.refreshHeight();
}
}
}
\ 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/HierarchyTable/HierarchyTableView.js b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/HierarchyTable/HierarchyTableView.js
index 24877303093f678575a70a72f0291c1f4ad2584f..9835090f45922896464c9433814ad747f04a71cb 100644
--- a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/HierarchyTable/HierarchyTableView.js
+++ b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/HierarchyTable/HierarchyTableView.js
@@ -32,14 +32,7 @@ function HierarchyTableView(controller, model) {
$containerColumn.append(this._container);
views.content.append($containerColumn);
- switch(this._model.entity["@type"]) {
- case "as.dto.dataset.DataSet":
- views.header.append($("<h1>").append("Dataset Hierarchy Table for " + this._model.entity.code));
- break;
- case "as.dto.sample.Sample":
- views.header.append($("<h1>").append("" + ELNDictionary.Sample + " Hierarchy Table for " + this._model.entity.identifier));
- break;
- }
+ views.header.append($("<h1>").append("Dataset Hierarchy Table: " + Util.getDisplayNameForEntity(this._model.entity)));
this._hierarchyFilterController = new HierarchyFilterController(this._model.entity, function() { _this._dataGrid.refresh(); });
this._hierarchyFilterController.init(views.header);
diff --git a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/HierarchyTable/widgets/HierarchyFilterView.js b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/HierarchyTable/widgets/HierarchyFilterView.js
index 0b85ab4e57946aaad1d8ad1023dccc7ced7b7481..58b169b00e3891c19750ddaa9c95eb1d34b2062b 100644
--- a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/HierarchyTable/widgets/HierarchyFilterView.js
+++ b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/HierarchyTable/widgets/HierarchyFilterView.js
@@ -41,7 +41,7 @@ function HierarchyFilterView(controller, model) {
var types = this._model.getTypes();
var $filtersFormEntityTypes = $('<select>', { 'id' : 'entityTypesSelector' , class : 'multiselect' , 'multiple' : 'multiple'});
for (var type in types) {
- $filtersFormEntityTypes.append($('<option>', { 'value' : type , 'selected' : ''}).html(type));
+ $filtersFormEntityTypes.append($('<option>', { 'value' : type , 'selected' : ''}).html(Util.getDisplayNameFromCode(type)));
}
$filtersForm
diff --git a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/ProjectForm/ProjectFormView.js b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/ProjectForm/ProjectFormView.js
index 8222fccf51c2bfe67c644099bc537d02b5417db7..817d2dd5958490714f22b0ee7016c31a04592301 100644
--- a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/ProjectForm/ProjectFormView.js
+++ b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/ProjectForm/ProjectFormView.js
@@ -66,7 +66,6 @@ function ProjectFormView(projectFormController, projectFormModel) {
_this._projectFormController.createNewExperiment(typeCode);
}, 100);
}
- getNewSampleOfTypeWithParent(typeCode,);
});
}
if (_this._allowedToMove()) {
@@ -83,7 +82,7 @@ function ProjectFormView(projectFormController, projectFormModel) {
//Edit
var $editBtn = FormUtil.getButtonWithIcon("glyphicon-edit", function () {
_this._projectFormController.enableEditing();
- }, "Edit");
+ }, "Edit", null, "edit-btn");
toolbarModel.push({ component : $editBtn });
}
if(_this._allowedToDelete()) {
@@ -152,7 +151,7 @@ function ProjectFormView(projectFormController, projectFormModel) {
} else {
var $saveBtn = FormUtil.getButtonWithIcon("glyphicon-floppy-disk", function() {
_this._projectFormController.updateProject();
- }, "Save");
+ }, "Save", null, "save-btn");
$saveBtn.removeClass("btn-default");
$saveBtn.addClass("btn-primary");
toolbarModel.push({ component : $saveBtn });
@@ -205,7 +204,7 @@ function ProjectFormView(projectFormController, projectFormModel) {
}
if (this._projectFormModel.mode === FormMode.CREATE) {
- var $textField = FormUtil._getInputField('text', null, "Project Code", null, true);
+ var $textField = FormUtil._getInputField('text', "project-code-id", "Project Code", null, true);
$textField.keyup(function(event){
var textField = $(this);
var caretPosition = this.selectionStart;
@@ -251,7 +250,7 @@ function ProjectFormView(projectFormController, projectFormModel) {
$description.append($("<legend>").append("General"));
var description = Util.getEmptyIfNull(this._projectFormModel.project.description);
if(this._projectFormModel.mode !== FormMode.VIEW) {
- var $textBox = FormUtil._getTextBox(null, "Description", false);
+ var $textBox = FormUtil._getTextBox("description-id", "Description", false);
var textBoxEvent = function(jsEvent, newValue) {
var valueToUse = null;
if (newValue !== undefined && newValue !== null) {
@@ -276,11 +275,6 @@ function ProjectFormView(projectFormController, projectFormModel) {
this._createExperimentsSection = function(projectIdentifier, hideShowOptionsModel) {
var entityKindName = ELNDictionary.getExperimentKindName(projectIdentifier, true);
- hideShowOptionsModel.push({
- label : entityKindName,
- section : "#project-experiments"
- });
-
var $experiments = $("<div>", { id : "project-experiments" });
var $experimentsContainer = $("<div>");
$experiments.append($("<legend>").append(entityKindName));
@@ -289,15 +283,18 @@ function ProjectFormView(projectFormController, projectFormModel) {
var experimentTableController = new ExperimentTableController(this._projectFormController, null, jQuery.extend(true, {}, this._projectFormModel.project), true);
experimentTableController.init($experimentsContainer);
$experiments.hide();
+ hideShowOptionsModel.push({
+ label : entityKindName,
+ section : "#project-experiments",
+ beforeShowingAction : function() {
+ experimentTableController.refreshHeight();
+ }
+ });
return $experiments;
}
this._createSamplesSection = function(hideShowOptionsModel) {
var entityKindName = "" + ELNDictionary.Samples + "";
- hideShowOptionsModel.push({
- label : entityKindName,
- section : "#project-samples"
- });
var $samples = $("<div>", { id : "project-samples" });
var $experimentsContainer = $("<div>");
@@ -314,6 +311,13 @@ function ProjectFormView(projectFormController, projectFormModel) {
var sampleTableController = new SampleTableController(this._projectFormController, null, null, this._projectFormModel.project.permId, true, null, 40);
sampleTableController.init(views);
$samples.hide();
+ hideShowOptionsModel.push({
+ label : entityKindName,
+ section : "#project-samples",
+ beforeShowingAction : function() {
+ sampleTableController.refreshHeight();
+ }
+ });
return $samples;
}
diff --git a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/SampleForm/SampleFormView.js b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/SampleForm/SampleFormView.js
index 6971e177f35525bc29782b9fedb58b5ba7adfce0..ef9822bec7a660d2e97850ab7594d91d25214283 100644
--- a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/SampleForm/SampleFormView.js
+++ b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/SampleForm/SampleFormView.js
@@ -1,4 +1,4 @@
-/*
+ /*
* Copyright 2014 ETH Zuerich, Scientific IT Services
*
* Licensed under the Apache License, Version 2.0 (the "License");
@@ -113,9 +113,10 @@ function SampleFormView(sampleFormController, sampleFormModel) {
if(this._sampleFormModel.mode === FormMode.VIEW) {
// New
- if(_this._allowedToCreateChild() && toolbarConfig.CREATE) {
+ if(_this._allowedToCreateChild() && this._sampleFormModel.isELNSample && toolbarConfig.CREATE) {
var sampleTypes = profile.getAllSampleTypes(true);
- FormUtil.addCreationDropdown(toolbarModel, sampleTypes, ["ENTRY", "EXPERIMENTAL_STEP"], function(typeCode) {
+ var priorityTypes = ["ENTRY", "EXPERIMENTAL_STEP"];
+ FormUtil.addCreationDropdown(toolbarModel, sampleTypes, priorityTypes, function(typeCode) {
return function() {
Util.blockUI();
setTimeout(function() {
@@ -278,7 +279,7 @@ function SampleFormView(sampleFormController, sampleFormModel) {
//Create Dataset
var $uploadBtn = FormUtil.getButtonWithIcon("glyphicon-upload", function () {
mainController.changeView('showCreateDataSetPageFromPermId',_this._sampleFormModel.sample.permId);
- }, "Upload");
+ }, "Upload", null, "upload-btn");
if(toolbarConfig.UPLOAD_DATASET) {
toolbarModel.push({ component : $uploadBtn, tooltip: null });
}
@@ -619,7 +620,7 @@ function SampleFormView(sampleFormController, sampleFormModel) {
'class' : 'zoomableImage',
'id' : 'preview-image',
'src' : './img/image_loading.gif',
- 'style' : 'max-width:100%; display:none;'
+ 'style' : 'max-width:300px; display:none;'
});
$previewImage.click(function() {
Util.showImage($("#preview-image").attr("src"));
@@ -699,7 +700,7 @@ function SampleFormView(sampleFormController, sampleFormModel) {
continue;
}
- if(propertyType.code === "$ANNOTATIONS_STATE" || propertyType.code === "$FREEFORM_TABLE_STATE" || propertyType.code === "$ORDER.ORDER_STATE" ) {
+ if(propertyType.code === "$ANNOTATIONS_STATE" || propertyType.code === "FREEFORM_TABLE_STATE" || propertyType.code === "$ORDER.ORDER_STATE" ) {
continue;
} else if(propertyType.code === "$XMLCOMMENTS") {
var $commentsContainer = $("<div>");
@@ -902,12 +903,7 @@ function SampleFormView(sampleFormController, sampleFormModel) {
}
this._createParentsSection = function(hideShowOptionsModel, sampleTypeDefinitionsExtension, sampleTypeCode) {
- hideShowOptionsModel.push({
- forceToShow : this._sampleFormModel.mode === FormMode.CREATE && (sampleTypeDefinitionsExtension && sampleTypeDefinitionsExtension["FORCE_TO_SHOW_PARENTS_SECTION"]),
- label : "Parents",
- section : "#sample-parents"
- });
-
+ var _this = this;
var requiredParents = [];
if (sampleTypeDefinitionsExtension && sampleTypeDefinitionsExtension["SAMPLE_PARENTS_HINT"]) {
requiredParents = sampleTypeDefinitionsExtension["SAMPLE_PARENTS_HINT"];
@@ -935,15 +931,21 @@ function SampleFormView(sampleFormController, sampleFormModel) {
this._sampleFormModel.sampleLinksParents.init($sampleParentsWidget);
}
$sampleParentsWidget.hide();
+
+ hideShowOptionsModel.push({
+ forceToShow : this._sampleFormModel.mode === FormMode.CREATE && (sampleTypeDefinitionsExtension && sampleTypeDefinitionsExtension["FORCE_TO_SHOW_PARENTS_SECTION"]),
+ label : "Parents",
+ section : "#sample-parents",
+ showByDefault : true,
+ beforeShowingAction : function() {
+ _this._sampleFormModel.sampleLinksParents.refreshHeight();
+ }
+ });
+
return $sampleParentsWidget;
}
this._createChildrenSection = function(hideShowOptionsModel, sampleTypeDefinitionsExtension, sampleTypeCode) {
- hideShowOptionsModel.push({
- label : "Children",
- section : "#sample-children"
- });
-
var _this = this;
var requiredChildren = [];
if(sampleTypeDefinitionsExtension && sampleTypeDefinitionsExtension["SAMPLE_CHILDREN_HINT"]) {
@@ -994,6 +996,16 @@ function SampleFormView(sampleFormController, sampleFormModel) {
$sampleChildrenWidget.append($generateChildrenBox);
}
$sampleChildrenWidget.hide();
+
+ hideShowOptionsModel.push({
+ label : "Children",
+ section : "#sample-children",
+ showByDefault : true,
+ beforeShowingAction : function() {
+ _this._sampleFormModel.sampleLinksChildren.refreshHeight();
+ }
+ });
+
return $sampleChildrenWidget;
}
diff --git a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/SampleForm/widgets/CommentsView.js b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/SampleForm/widgets/CommentsView.js
index c8317cb392904530600a393be17a89047547db0f..d42b8e3dd377b1b92bea8fb4a942e21b06e25e18 100644
--- a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/SampleForm/widgets/CommentsView.js
+++ b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/SampleForm/widgets/CommentsView.js
@@ -77,19 +77,21 @@ function CommentsView(commentsController, commentsModel) {
this.addAddButton = function() {
if(this._commentsModel.mode !== FormMode.VIEW) {
var _this = this;
- var $buttonPlusOne = $("<a>", {"class" : "btn btn-default"});
+ var commentNumber = 0;
+ var $buttonPlusOne = $("<a>", {"class" : "btn btn-default", "id" : "add-comment-btn"});
$buttonPlusOne.append($("<span>", { "class" : "glyphicon glyphicon-plus-sign"}));
$buttonPlusOne.click(function() {
- _this.addNewComment();
+ _this.addNewComment(commentNumber);
+ commentNumber++;
});
this.commentsAddButton.append(FormUtil.getFieldForComponentWithLabel($buttonPlusOne, null));
}
}
- this.addNewComment = function() {
- var $textBox = FormUtil._getTextBox(null, null, false);
+ this.addNewComment = function(commentNumber) {
+ var $textBox = FormUtil._getTextBox("comment-" + commentNumber + "-box", null, false);
var $textBoxGroup = FormUtil.getFieldForComponentWithLabel($textBox, null, null);
- var $saveButton = FormUtil.getButtonWithText("Add Comment");
+ var $saveButton = FormUtil.getButtonWithText("Add Comment", null, null, "save-comment-" + commentNumber + "-btn");
var $saveButtonGroup = FormUtil.getFieldForComponentWithLabel($saveButton, null, null);
this.commentsContainer.append($textBoxGroup);
diff --git a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/SampleForm/widgets/LinksController.js b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/SampleForm/widgets/LinksController.js
index 66e618c48d8bea17245c8ddb040176d9126ef577..1becb0945bd0f4cb1f06094114b1a774ee143838 100644
--- a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/SampleForm/widgets/LinksController.js
+++ b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/SampleForm/widgets/LinksController.js
@@ -61,6 +61,10 @@ function LinksController(title, sampleTypeHints, isDisabled, samplesToEdit, show
}
}
+ this.refreshHeight = function() {
+ linksView.refreshHeight();
+ }
+
//
// API - Used by Sample Form
//
diff --git a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/SampleForm/widgets/LinksView.js b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/SampleForm/widgets/LinksView.js
index 473a8b2fdd634ed5e38bbf3858add551c18dd1b7..ccf71b29b781fbe35f640697e3edce81fd5e022e 100644
--- a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/SampleForm/widgets/LinksView.js
+++ b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/SampleForm/widgets/LinksView.js
@@ -24,6 +24,8 @@ function LinksView(linksController, linksModel) {
var $samplePicker = $("<div>");
var $savedContainer = null;
+ var dataGrids = [];
+
//
// External API
//
@@ -154,6 +156,13 @@ function LinksView(linksController, linksModel) {
var dataGrid = SampleDataGridUtil.getSampleDataGrid(containerCode, samplesOnGrid, null, linksView.getCustomOperationsForGrid(), allCustomAnnotations, postFix, linksModel.isDisabled, false, false, false, 40);
dataGrid.init($dataGridContainer);
linksModel.writeState(sample, null, null, false);
+ dataGrids.push(dataGrid);
+ }
+
+ this.refreshHeight = function() {
+ dataGrids.forEach(function(dataGrid) {
+ dataGrid.refreshHeight();
+ });
}
this.repaint = function($container) {
@@ -306,8 +315,13 @@ function LinksView(linksController, linksModel) {
sortable : false,
render : function(data) {
//Dropdown Setup
+ var codeId = data.code.toLowerCase() + "-operations-column-id";
+
var $dropDownMenu = $("<span>", { class : 'dropdown table-options-dropdown' });
- var $caret = $("<a>", { 'href' : '#', 'data-toggle' : 'dropdown', class : 'dropdown-toggle btn btn-default'}).append("Operations ").append($("<b>", { class : 'caret' }));
+ var $caret = $("<a>", { 'href' : '#',
+ 'data-toggle' : 'dropdown',
+ class : 'dropdown-toggle btn btn-default',
+ 'id' : codeId}).append("Operations ").append($("<b>", { class : 'caret' }));
var $list = $("<ul>", { class : 'dropdown-menu', 'role' : 'menu', 'aria-labelledby' :'sampleTableDropdown' });
$dropDownMenu.append($caret);
$dropDownMenu.append($list);
@@ -321,7 +335,8 @@ function LinksView(linksController, linksModel) {
$dropDownMenu.click(stopEventsBuble);
if(profile.isSampleTypeProtocol(data["$object"].sampleTypeCode)) {
- var $copyAndLink = $("<li>", { 'role' : 'presentation' }).append($("<a>", {'title' : 'Use as template'}).append("Use as template"));
+ var id = codeId + "-use-as-template";
+ var $copyAndLink = $("<li>", { 'role' : 'presentation' }).append($("<a>", {'id' : id, 'title' : 'Use as template'}).append("Use as template"));
$copyAndLink.click(function(e) {
stopEventsBuble(e);
var copyAndLink = function(code) {
@@ -434,14 +449,16 @@ function LinksView(linksController, linksModel) {
}
var dataGrid = SampleDataGridUtil.getSampleDataGrid(sampleTypeCode, advancedSampleSearchCriteria, rowClick, null, null, null, true, true, true, false, 60);
dataGrid.init($gridContainer, extraOptions);
+ dataGrids.push(dataGrid);
}
linksView.getAddBtn = function($container, sampleTypeCode) {
var enabledFunction = function() {
linksView.showSamplePicker($container, sampleTypeCode);
};
-
- var $addBtn = FormUtil.getButtonWithIcon("glyphicon-plus", (linksModel.isDisabled)?null:enabledFunction);
+
+ var id = "plus-btn-" + sampleTypeCode.toLowerCase();
+ var $addBtn = FormUtil.getButtonWithIcon("glyphicon-plus", (linksModel.isDisabled)?null:enabledFunction, null, null, id);
if(linksModel.isDisabled) {
return "";
} else {
diff --git a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/SampleTable/SampleTableController.js b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/SampleTable/SampleTableController.js
index c1d5b6f18b36f9864bf9cb0816f8c4450b251c2b..5c2e2d1c0e1b250f38dfcfd6c53321810fec30a2 100644
--- a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/SampleTable/SampleTableController.js
+++ b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/SampleTable/SampleTableController.js
@@ -82,18 +82,19 @@ function SampleTableController(parentController, title, experimentIdentifier, pr
}
this._reloadTableWithAllSamples = function(advancedSampleSearchCriteria) {
+ var _this = this;
//Create and display table
var withExperiment = !this._sampleTableModel.experimentIdentifier && !this._sampleTableModel.experiment;
var tableHeight = 90;
if(this._sampleTableModel.heightOverride) {
- tableHeight = this._sampleTableModel.heightOverride;
+ tableHeight = this._sampleTableModel.heightOverride;
}
- var dataGridController = SampleDataGridUtil.getSampleDataGrid(this._sampleTableModel.experimentIdentifier, advancedSampleSearchCriteria, null, null, null, null, null, null, true, withExperiment, tableHeight);
+ this._dataGridController = SampleDataGridUtil.getSampleDataGrid(this._sampleTableModel.experimentIdentifier, advancedSampleSearchCriteria, null, null, null, null, null, null, true, withExperiment, tableHeight);
var extraOptions = [];
extraOptions.push({ name : "Delete selected", action : function(selected) {
- var grid = dataGridController._grid;
+ var grid = _this._dataGridController._grid;
var selected = grid.getSelected();
if(selected != undefined && selected.length == 0){
Util.showUserError("Please select at least one sample to delete!");
@@ -138,6 +139,12 @@ function SampleTableController(parentController, title, experimentIdentifier, pr
}
}});
- dataGridController.init(this._sampleTableView.getTableContainer(), extraOptions);
+ this._dataGridController.init(this._sampleTableView.getTableContainer(), extraOptions);
+ }
+
+ this.refreshHeight = function() {
+ if (this._dataGridController) {
+ this._dataGridController.refreshHeight();
+ }
}
}
\ 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/SampleTable/SampleTableView.js b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/SampleTable/SampleTableView.js
index 103139ff8d278cd59a9ccb5167e2e794d88e8e2c..af8ea71df9774cef57a591464df11e5b5fb7a306 100644
--- a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/SampleTable/SampleTableView.js
+++ b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/SampleTable/SampleTableView.js
@@ -124,7 +124,7 @@ function SampleTableView(sampleTableController, sampleTableModel) {
this._getOptionsMenu = function() {
var _this = this;
var $dropDownMenu = $("<span>", { class : 'dropdown' });
- var $caret = $("<a>", { 'href' : '#', 'data-toggle' : 'dropdown', class : 'dropdown-toggle btn btn-default', 'id' : 'options-menu-btn'}).append("More ... ").append($("<b>", { class : 'caret' }));
+ var $caret = $("<a>", { 'href' : '#', 'data-toggle' : 'dropdown', class : 'dropdown-toggle btn btn-default', 'id' : 'sample-options-menu-btn'}).append("More ... ").append($("<b>", { class : 'caret' }));
var $list = $("<ul>", { class : 'dropdown-menu', 'role' : 'menu', 'aria-labelledby' :'sampleTableDropdown' });
$dropDownMenu.append($caret);
$dropDownMenu.append($list);
diff --git a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/SettingsForm/SettingsFormView.js b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/SettingsForm/SettingsFormView.js
index 90c372ed1171ab3911f9b0c981e8ee861fd5fc80..60fa6fe72efe557c6062bfd7c5c7305be0ca8571 100644
--- a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/SettingsForm/SettingsFormView.js
+++ b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/SettingsForm/SettingsFormView.js
@@ -643,9 +643,13 @@ function SettingsFormView(settingsFormController, settingsFormModel) {
}
if (rowValues["Disable section"]) {
settings["SAMPLE_PARENTS_DISABLED"] = true;
+ } else {
+ settings["SAMPLE_PARENTS_DISABLED"] = false;
}
if (rowValues["Disable addition of any " + ELNDictionary.sample + " type"]) {
settings["SAMPLE_PARENTS_ANY_TYPE_DISABLED"] = true;
+ } else {
+ settings["SAMPLE_PARENTS_ANY_TYPE_DISABLED"] = false;
}
} else if (rowValues["Settings for"] === "Children") {
if (rowValues["Section name"] && rowValues["Section name"].length > 0) {
@@ -653,9 +657,13 @@ function SettingsFormView(settingsFormController, settingsFormModel) {
}
if (rowValues["Disable section"]) {
settings["SAMPLE_CHILDREN_DISABLED"] = true;
+ } else {
+ settings["SAMPLE_CHILDREN_DISABLED"] = false;
}
if (rowValues["Disable addition of any " + ELNDictionary.sample + " type"]) {
settings["SAMPLE_CHILDREN_ANY_TYPE_DISABLED"] = true;
+ } else {
+ settings["SAMPLE_CHILDREN_ANY_TYPE_DISABLED"] = false;
}
}
}
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 e72bef3cc8866a17d6fca16023b45cd724193c56..ff6bc1831d09299d7d2d3a952483a7b2fd833752 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
@@ -611,7 +611,8 @@ function SideMenuWidgetView(sideMenuWidgetController, sideMenuWidgetModel) {
        case "EXPERIMENT":
            var sampleRules = { "UUIDv4" : { type : "Experiment", name : "ATTR.PERM_ID", value : permId } };
            mainController.serverFacade.searchForSamplesAdvanced({ entityKind : "SAMPLE", logicalOperator : "AND", rules : sampleRules },
- Â Â Â Â Â Â Â Â Â Â Â Â { only : true, withProperties : true, withType : true, withExperiment : true, withParents : true, withChildren : true, withParentsType : true, withChildrenType : true},
+ Â Â Â Â Â Â Â Â Â Â Â Â { only : true, withProperties : true, withType : true, withExperiment : true, withParents : true,
+ withParentsExperiment: true, withChildren : true, withParentsType : true, withChildrenType : true},
            function(searchResult) {
                var samples = searchResult.objects;
                var samplesToShow = [];
@@ -619,12 +620,16 @@ function SideMenuWidgetView(sideMenuWidgetController, sideMenuWidgetModel) {
                    var sample = samples[sIdx];
                    var sampleIsExperiment = sample.type.code.indexOf("EXPERIMENT") > -1;
                    var sampleTypeOnNav = profile.showOnNav(sample.type.code);
+ var sampleExperimentIdentifier = sample.experiment.identifier.identifier;
                    if(sampleIsExperiment || sampleTypeOnNav) {
                        var parentInELN = false;
                        if(sample.parents) {
                            for(var pIdx = 0; pIdx < sample.parents.length; pIdx++) {
- Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â var parentIdentifier = sample.parents[pIdx].identifier.identifier;
- Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â parentInELN = profile.isELNIdentifier(parentIdentifier);
+ var parent = sample.parents[pIdx];
+ Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â var parentIdentifier = parent.identifier.identifier;
+ var parentExperimentIdentifier = parent.experiment.identifier.identifier;
+ Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â parentInELN = profile.isELNIdentifier(parentIdentifier)
+ && parentExperimentIdentifier === sampleExperimentIdentifier;
                            if(parentInELN) {
break;
                            }
@@ -739,7 +744,9 @@ function SideMenuWidgetView(sideMenuWidgetController, sideMenuWidgetModel) {
        case "SAMPLE":
            var sampleRules = { "UUIDv4" : { type : "Attribute", name : "PERM_ID", value : permId } };
            mainController.serverFacade.searchForSamplesAdvanced({ entityKind : "SAMPLE", logicalOperator : "AND", rules : sampleRules },
- Â Â Â Â Â Â Â Â Â Â Â Â { only : true, withProperties : true, withType : true, withExperiment : true, withParents : true, withChildren : true, withChildrenProperties : true, withParentsType : true, withChildrenType : true}
+ Â Â Â Â Â Â Â Â Â Â Â Â { only : true, withProperties : true, withType : true, withExperiment : true, withParents : true,
+ withChildren : true, withChildrenProperties : true, withChildrenExperiment : true,
+ withParentsType : true, withChildrenType : true}
            , function(searchResult) {
                var results = [];
                var samples = searchResult.objects;
@@ -749,7 +756,9 @@ function SideMenuWidgetView(sideMenuWidgetController, sideMenuWidgetModel) {
    } else {
        for(var cIdx = 0; cIdx < samples[0].children.length; cIdx++) {
                        var sample = samples[0].children[cIdx];
- Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â
+ Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â if (sample.experiment.identifier.identifier !== samples[0].experiment.identifier.identifier) {
+ continue;
+ }
var sampleIsExperiment = sample.type.code.indexOf("EXPERIMENT") > -1;
var sampleIcon;
if(sampleIsExperiment) {
diff --git a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/SpaceForm/SpaceFormView.js b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/SpaceForm/SpaceFormView.js
index 64cee57a6f0cba4fba16e756fa2b323900cec427..5e19141733f74d98cee163766f58a7ad0d872b2b 100644
--- a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/SpaceForm/SpaceFormView.js
+++ b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/SpaceForm/SpaceFormView.js
@@ -40,7 +40,7 @@ function SpaceFormView(spaceFormController, spaceFormModel) {
if (_this._allowedToCreateProject()) {
var $createProj = FormUtil.getButtonWithIcon("glyphicon-plus", function() {
_this._spaceFormController.createProject();
- }, "New Project");
+ }, "New Project", null, "create-btn");
toolbarModel.push({ component : $createProj});
}
diff --git a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/StorageManager/widgets/GridView.js b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/StorageManager/widgets/GridView.js
index 59b4cf6a5a771eea2162486a95c859f2c818a5a4..708f9325e422ad528c6e10d03235debc7a74c267 100644
--- a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/StorageManager/widgets/GridView.js
+++ b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/StorageManager/widgets/GridView.js
@@ -147,7 +147,6 @@ function GridView(gridModel) {
sample = jQuery.extend(true, {}, labels[i].data.samples[0]);
}
- extraProperties = null;
if(sample && sample.sampleTypeCode === "STORAGE_POSITION" && sample.parents && sample.parents[0]) {
if(profile.propertyReplacingCode && sample.parents[0].properties && sample.parents[0].properties[profile.propertyReplacingCode]) {
// Label
@@ -158,7 +157,6 @@ function GridView(gridModel) {
}
sample = sample.parents[0];
- extraProperties = {code : {label : "Code", value : sample.code}};
var href = Util.getURLFor(null, "showViewSamplePageFromPermId", sample.permId);
optSampleTitle = $("<a>", { "href" : href, "class" : "browser-compatible-javascript-link" }).text(labels[i].displayName);
@@ -167,7 +165,7 @@ function GridView(gridModel) {
}).bind(this, sample));
}
- var rowLabel = i + 1;
+ var rowLabel = posX;
if(this._gridModel.useLettersOnRows) {
rowLabel = Util.getLetterForNumber(rowLabel);
}
@@ -175,7 +173,7 @@ function GridView(gridModel) {
var labelContainer = $("<div>", { class: "storageBox", id : storageBoxId }).text(labels[i].displayName);
if (sample) {
var tooltip = PrintUtil.getTable(sample, false, optSampleTitle, 'inspectorWhiteFont',
- 'colorEncodedWellAnnotations-holder-' + sample.permId, null, extraProperties);
+ 'colorEncodedWellAnnotations-holder-' + sample.permId, null, null);
labelContainer.tooltipster({
content: $(tooltip),
interactive: true,
diff --git a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/UserManager/UserManagerView.js b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/UserManager/UserManagerView.js
index 015007f543e161c13b21799dd3e2ce421f6851e7..9a123a8c257b98165948379e856efc28a276cdfe 100644
--- a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/UserManager/UserManagerView.js
+++ b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/UserManager/UserManagerView.js
@@ -40,10 +40,10 @@ function UserManagerView(userManagerController, userManagerModel) {
var $toolbox = $("<div>", { 'id' : 'toolBoxContainer', class : 'toolBox'});
var $createUser = FormUtil.getButtonWithIcon("glyphicon-plus", function() {
_this._userManagerController.showCreateNewUserModal();
- }, "New User");
+ }, "New User", null, "createUser");
$toolbox.append($createUser);
$header.append($toolbox);
-
+
//
// Data Grid
//
diff --git a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/legacy/SampleHierarchy.js b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/legacy/SampleHierarchy.js
index b9dbfc5f1c39df96d9fdd55e2b3707ad23a0148b..f9cd29ef8287f469006da8acd8132a87ef68f358 100644
--- a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/legacy/SampleHierarchy.js
+++ b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/legacy/SampleHierarchy.js
@@ -43,7 +43,7 @@ function SampleHierarchy(serverFacade, views, profile, sample) {
$form.append($formColumn);
- views.header.append($("<h1>").append("" + ELNDictionary.Sample + " Hierarchy Graph for " + this.sample.identifier));
+ views.header.append($("<h1>").append("Hierarchy Graph: " + Util.getDisplayNameForEntity(this.sample)));
localInstance.hierarchyFilterController = new HierarchyFilterController(this.sample, function() { localInstance.filterSampleAndUpdate(); });
localInstance.hierarchyFilterController.init(views.header);
@@ -311,12 +311,7 @@ function SampleHierarchy(serverFacade, views, profile, sample) {
'style' : 'cursor:pointer; width:13px; height:18px;',
}));
- var nameLabel = null;
- if(sample.properties[profile.propertyReplacingCode]) {
- nameLabel = sample.code + "(" + sample.properties[profile.propertyReplacingCode] + ")";
- } else {
- nameLabel = sample.code;
- }
+ var nameLabel = Util.getDisplayNameForEntity(sample);
var $sampleLink = $('<a>', { 'href' : "javascript:mainController.changeView('showViewSamplePageFromPermId', '" + sample.permId + "')"}).text(nameLabel);
@@ -326,7 +321,7 @@ function SampleHierarchy(serverFacade, views, profile, sample) {
.append($hideLink)
.append($dataLink)
.append($addChildLink)
- .append(sample.sampleTypeCode + ':')
+ .append(' ' + Util.getDisplayNameFromCode(sample.sampleTypeCode) + ':')
.append($sampleLink);
if(sample.showDataOnGraph) {
diff --git a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/lib/grid/js/Grid.html b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/lib/grid/js/Grid.html
index 085d860a497a2b4f6991703dbef4fbe1d6797bb9..bf2b5ec23877c2a8c7107672618e76d6beb0c632 100644
--- a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/lib/grid/js/Grid.html
+++ b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/lib/grid/js/Grid.html
@@ -60,7 +60,7 @@
</div>
<div class="dropdown columnDropdown" style = "display: inline; padding-left: 10px;">
- <button class="btn btn-default dropdown-toggle" type="button" data-toggle="dropdown">
+ <button class="btn btn-default dropdown-toggle" type="button" data-toggle="dropdown" id="columns-dropdown-id">
Columns <span class="caret"></span>
</button>
<ul style="max-height:500px; overflow:scroll; overflow-x: hidden;" class="dropdown-menu" role="menu"></ul>
diff --git a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/lib/grid/js/Grid.js b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/lib/grid/js/Grid.js
index 8857fff7a1553269711c611b4c2a87930bc9d054..56c9306db251d760c6145afbf3ad3a64320b6f77 100644
--- a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/lib/grid/js/Grid.js
+++ b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/lib/grid/js/Grid.js
@@ -175,10 +175,20 @@ $.extend(Grid.prototype, {
columnsForDropdown.forEach(function(column, columnIndex) {
if(!column.showByDefault && !column.hide) {
+
var checkbox = $("<input>")
.attr("type", "checkbox")
.attr("value", column.property)
.attr("style", "margin-left: 5px;");
+
+ if (column.property != null) {
+ var id = column.property.split(" ").join("-") + "-cln";
+ if (id[0] === '$') {
+ id = id.substring(1, id.length - 1);
+ }
+ id = id.toLowerCase();
+ checkbox.attr("id", id)
+ }
if(thisGrid.tableSettings && thisGrid.tableSettings.columns && Object.keys(thisGrid.tableSettings.columns).length !== 0) {
if((thisGrid.tableSettings.columns[column.property] === true)) { //If settings are present
@@ -752,17 +762,7 @@ $.extend(Grid.prototype, {
// Fix table width since fuelux 3.1.0
// var newWidth = $(thisGrid.panel).find(".repeater-list-wrapper > .table").width();
// $(thisGrid.panel).find(".repeater").width(newWidth);
-
- var headerHeight = $(thisGrid.panel).find(".repeater-header").outerHeight(true);
- var listHeight = Math.max(100, $(thisGrid.panel).find(".repeater-list").outerHeight(true));
- var footerHeight = $(thisGrid.panel).find(".repeater-footer").outerHeight(true);
- var viewport = $(thisGrid.panel).find(".repeater-canvas")[0];
- var scrollbarHeight = viewport.scrollWidth > viewport.offsetWidth ? thisGrid.scrollbarWidth : 0;
- var totalHeight = headerHeight + listHeight + footerHeight + scrollbarHeight;
- totalHeight = Math.min(totalHeight, thisGrid.maxHeight);
- if (thisGrid.viewOptions.staticHeight < totalHeight) {
- thisGrid.viewOptions.staticHeight = totalHeight;
- }
+ thisGrid.calculateHeight();
var optionsDropdowns = $(".dropdown.table-options-dropdown");
for(var i = 0; i < optionsDropdowns.length; i++) {
@@ -784,6 +784,23 @@ $.extend(Grid.prototype, {
}, 100);
}, options);
},
+
+ calculateHeight : function() {
+ var thisGrid = this;
+ var $panel = $(thisGrid.panel);
+ var $header = $panel.find(".repeater-header");
+ var headerHeight = $header.outerHeight(true);
+ var listHeight = Math.max(144, $(thisGrid.panel).find(".repeater-list").outerHeight(true));
+ var footerHeight = $panel.find(".repeater-footer").outerHeight(true);
+ var viewport = $panel.find(".repeater-canvas")[0];
+ var scrollbarHeight = viewport.scrollWidth > viewport.offsetWidth ? thisGrid.scrollbarWidth : 0;
+ var totalHeight = headerHeight + listHeight + footerHeight + scrollbarHeight;
+ totalHeight = Math.min(totalHeight, thisGrid.maxHeight);
+ if (thisGrid.viewOptions.staticHeight < totalHeight) {
+ thisGrid.viewOptions.staticHeight = totalHeight;
+ }
+
+ },
addRowClickListener : function(listener) {
if (!this.rowClickListeners) {
diff --git a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/plugins/bbb-hub/BBBServerFacade.js b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/plugins/bbb-hub/BBBServerFacade.js
new file mode 100644
index 0000000000000000000000000000000000000000..32c4989cf99266320443d5c48729e6440a8e559e
--- /dev/null
+++ b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/plugins/bbb-hub/BBBServerFacade.js
@@ -0,0 +1,142 @@
+var BBBServerFacade = new function() {
+ this.getExperiment = function($container, model) {
+ require(["openbis",
+ "as/dto/sample/fetchoptions/SampleFetchOptions",
+ "as/dto/experiment/fetchoptions/ExperimentFetchOptions",
+ "as/dto/experiment/id/ExperimentIdentifier",
+ "as/dto/dataset/fetchoptions/DataSetFetchOptions"],
+ function(openbis, SampleFetchOptions,
+ ExperimentFetchOptions,
+ ExperimentIdentifier,
+ DataSetFetchOptions) {
+
+ var v3 = new openbis(null);
+ v3._private.sessionToken = mainController.openbisV1._internal.sessionToken;
+
+ var webAppContext = v3.getWebAppContext();
+
+ var dataSetFetchOptions = new DataSetFetchOptions();
+ dataSetFetchOptions.withType();
+ dataSetFetchOptions.withPhysicalData();
+
+ var experimentId = new ExperimentIdentifier(model.experiment.identifier);
+ var fetchOptions = new ExperimentFetchOptions();
+ fetchOptions.withDataSetsUsing(dataSetFetchOptions);
+ fetchOptions.withType();
+
+ var sampleFetchOptions = new SampleFetchOptions();
+ sampleFetchOptions.withType().withPropertyAssignments().withPropertyType();
+ sampleFetchOptions.withProperties();
+ fetchOptions.withSamplesUsing(sampleFetchOptions);
+ v3.getExperiments([experimentId], fetchOptions).done(function(result) {
+ var experiment = result[model.experiment.identifier];
+ if (experiment.type.code == "BBB") {
+ SnakemakeTrigger.paintTriggerContainers($container, model, experiment);
+ }
+ });
+ });
+ }
+
+ this.getExperiments = function($content) {
+ require(["openbis", "as/dto/sample/fetchoptions/SampleFetchOptions",
+ "as/dto/experiment/fetchoptions/ExperimentFetchOptions",
+ "as/dto/experiment/id/ExperimentIdentifier",
+ "as/dto/dataset/fetchoptions/DataSetFetchOptions",
+ "as/dto/experiment/search/ExperimentSearchCriteria",
+ "as/dto/project/fetchoptions/ProjectFetchOptions"],
+ function(openbis, SampleFetchOptions,
+ ExperimentFetchOptions,
+ ExperimentIdentifier,
+ DataSetFetchOptions,
+ ExperimentSearchCriteria,
+ ProjectFetchOptions) {
+
+ var v3 = new openbis();
+
+ v3.loginAsAnonymousUser().done(function(sessionToken) {
+ v3._private.sessionToken = sessionToken;
+ var webAppContext = v3.getWebAppContext();
+
+ var fetchOptions = new ExperimentFetchOptions();
+ fetchOptions.withType();
+ fetchOptions.withProperties();
+ fetchOptions.withRegistrator();
+
+ var projectFetchOptions = new ProjectFetchOptions();
+ projectFetchOptions.withSpace();
+
+ fetchOptions.withProjectUsing(projectFetchOptions);
+
+ var searchCriteria = new ExperimentSearchCriteria();
+ searchCriteria.withType();
+
+ v3.searchExperiments(searchCriteria, fetchOptions).done(function(result) {
+ BBBServerFacade.getRoleAssignment($content, result.objects);
+ });
+ }).fail(function(result) {
+ console.log("Call failed to server: " + JSON.stringify(result));
+ });
+ });
+ }
+
+ this.getRoleAssignment = function ($content, experiments) {
+ require(["openbis", "as/dto/roleassignment/fetchoptions/RoleAssignmentFetchOptions",
+ "as/dto/roleassignment/search/RoleAssignmentSearchCriteria"],
+ function(openbis, RoleAssignmentFetchOptions, RoleAssignmentSearchCriteria) {
+
+ var v3 = new openbis();
+
+ v3.loginAsAnonymousUser().done(function(sessionToken) {
+ v3._private.sessionToken = sessionToken;
+ var webAppContext = v3.getWebAppContext();
+
+ var criteria = new RoleAssignmentSearchCriteria();
+ criteria.withOrOperator();
+ criteria.withProject();
+ criteria.withSpace();
+
+ var fetchOptions = new RoleAssignmentFetchOptions();
+ fetchOptions.withSpace();
+ fetchOptions.withProject();
+ fetchOptions.withUser();
+ fetchOptions.withAuthorizationGroup();
+
+ v3.searchRoleAssignments(criteria, fetchOptions).done(function(result) {
+ SnakemakeTable.paintTable($content, experiments, result.objects);
+ });
+ }).fail(function(result) {
+ console.log("Call failed to server: " + JSON.stringify(result));
+ });
+ });
+ }
+
+ this.callCustomASService = function(params, $model, action) {
+ var result_div = $('#callback_message');
+
+ require(["openbis",
+ "as/dto/service/id/CustomASServiceCode",
+ "as/dto/service/CustomASServiceExecutionOptions",
+ "as/dto/experiment/id/ExperimentIdentifier"],
+ function(openbis, CustomASServiceCode, CustomASServiceExecutionOptions, ExperimentIdentifier) {
+
+ var v3 = new openbis(null);
+ v3._private.sessionToken = mainController.openbisV1._internal.sessionToken;
+ var webAppContext = mainController.openbisV3.getWebAppContext();
+ webAppContext['entityIdentifier'] = $model.experiment.identifier;
+
+ var serviceCode = new CustomASServiceCode("snakemake_service");
+ var options = new CustomASServiceExecutionOptions();
+
+ options.withParameter("webapp_context", webAppContext)
+ Object.keys(params).forEach(function(key) {
+ options.withParameter(key, params[key]);
+ });
+
+ v3.executeCustomASService(serviceCode, options).done(function(result) {
+ result_json = JSON.parse(result);
+ action(result_json)
+ });
+ });
+ return false;
+ }
+}
\ No newline at end of file
diff --git a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/plugins/bbb-hub/UiComponents.js b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/plugins/bbb-hub/UiComponents.js
new file mode 100644
index 0000000000000000000000000000000000000000..36e1f12a6404c1896e609c4d8c3292b65b86335e
--- /dev/null
+++ b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/plugins/bbb-hub/UiComponents.js
@@ -0,0 +1,104 @@
+var UiComponents = new function() {
+
+ this.addDropdown = function(label, options, $container, selectAction) {
+ var $dropdown = UiComponents.getDropdown(options);
+ $inputGroup = UiComponents.getInputGroup($dropdown, label);
+ $inputGroup.css("margin-top", "3px");
+ $container.append($inputGroup);
+ $dropdown.select2({ width : "100%", theme : "bootstrap", minimumResultsForSearch: 10 });
+ if (selectAction) {
+ $dropdown.on('select2:select', function (e) {
+ selectAction(e.params.data.id);
+ });
+ }
+ $inputGroup.getValue = function() {
+ return $dropdown.val();
+ }
+ return $inputGroup;
+ }
+
+ this.getDropdown = function(options, value) {
+ var $input = $("<select>", { class : "form-control", type : "text" });
+ $input.append($("<option>", { "disabled" : true, "selected" : true, "value" : true }).text(" -- select an option -- "));
+ for (option of options) {
+ var $option = $("<option>");
+ $option.text(option.label);
+ $option.attr("value", option.value);
+ $input.append($option);
+ }
+ if (value) {
+ $input.val(value);
+ }
+ return $input;
+ }
+
+ this.getInputGroup = function($input, label) {
+ var $inputGroup = $("<div>", { class : "input-group" });
+ $inputGroup.append($("<span>", { class : "input-group-addon" }).text(label).css({ 'min-width' : '150px' }));
+ $inputGroup.append($input);
+ return $inputGroup;
+ }
+
+ this.getButton = function($html, action, size, icon) {
+ var buttonSize = size ? size : 'md';
+ var $button = $('<button>', {
+ type : 'button',
+ class : 'btn btn-default btn-' + buttonSize,
+ 'aria-label' : 'Left Align'
+ });
+ if(icon) {
+ var $icon = $('<span>', { class : 'glyphicon ' + icon });
+ $icon.css("margin-right", "0.5rem");
+ $button.append($icon);
+ }
+ if($html) {
+ $button.append($("<span>").text($html));
+ }
+ if(action) {
+ $button.click(action);
+ }
+ return $button;
+ }
+
+ this.getFieldset = function(legendText) {
+ var $fieldset = $('<fieldset>');
+ if (legendText) {
+ var $legend = $('<legend>', { class : 'section-legend' }).append(legendText)
+ $fieldset.append($legend);
+ }
+ return $fieldset;
+ }
+
+ this.getLoader = function() {
+ return $('<div>').attr('class', 'loader col-centered');
+ }
+
+ // blocks given $component or whole screen of none given
+ this.startLoading = function($component) {
+ var params = {
+ message : this.getLoader(),
+ css: {
+ border: 'none',
+ padding: '15px',
+ backgroundColor: 'transparent',
+ },
+ overlayCSS: {
+ opacity : 0.1,
+ }
+ };
+ if ($component) {
+ $component.block(params);
+ } else {
+ $.blockUI(params);
+ }
+ }
+
+ // unblocks given $component or whole screen of none given
+ this.stopLoading = function($component) {
+ if ($component) {
+ $component.unblock();
+ } else {
+ $.unblockUI();
+ }
+ }
+}
\ No newline at end of file
diff --git a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/plugins/bbb-hub/plugin.js b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/plugins/bbb-hub/plugin.js
new file mode 100644
index 0000000000000000000000000000000000000000..b6803e35362dff0ecd780bb4c5a171bc4d21425d
--- /dev/null
+++ b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/plugins/bbb-hub/plugin.js
@@ -0,0 +1,37 @@
+function BBBHubTechnology() {
+ this.init();
+}
+
+$.extend(BBBHubTechnology.prototype, ELNLIMSPlugin.prototype, {
+ // This code is copy of openBis plugin. It was taken from here:
+ // https://sissource.ethz.ch/sis/bbb-hub/tree/master/openbis/core-plugins/bbb-hub/1/as/webapps/snakemake/html/js
+ // Now it is a ELN plugin.
+
+ init: function() {
+ loadJSResorce("./plugins/bbb-hub/UiComponents.js");
+ loadJSResorce("./plugins/bbb-hub/BBBServerFacade.js");
+ loadJSResorce("./plugins/bbb-hub/snakemake-table.js");
+ loadJSResorce("./plugins/bbb-hub/snakemake-trigger.js");
+ },
+
+ experimentFormTop : function($container, model) {
+ BBBServerFacade.getExperiment($container, model);
+ },
+
+ experimentFormBottom : function($container, model) {
+ },
+
+ getExtraUtilities : function() {
+ return [{
+ icon : "fa fa-table",
+ uniqueViewName : "BBB_VIEW_NAME_TEST",
+ label : "Snakemake",
+ paintView : function($header, $content) {
+ $header.append($("<h1>").append("Public Index Page"));
+ BBBServerFacade.getExperiments($content);
+ }
+ }];
+ }
+});
+
+profile.plugins.push(new BBBHubTechnology());
\ No newline at end of file
diff --git a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/plugins/bbb-hub/snakemake-table.js b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/plugins/bbb-hub/snakemake-table.js
new file mode 100644
index 0000000000000000000000000000000000000000..a6add5714f1bd889e0379b02921fe668b826fe0a
--- /dev/null
+++ b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/plugins/bbb-hub/snakemake-table.js
@@ -0,0 +1,169 @@
+var SnakemakeTable = new function() {
+
+ this.paintTable = function(container, experiments, roles) {
+ var columns = [];
+
+ columns.push({
+ label : 'Code',
+ property : 'code',
+ isExportable: false,
+ sortable : true
+ });
+
+ columns.push({
+ label : 'Description',
+ property : 'description',
+ isExportable: false,
+ sortable : true
+ });
+
+ columns.push({
+ label : 'Group',
+ property : 'group',
+ isExportable: false,
+ sortable : true
+ });
+
+ columns.push({
+ label : 'E-mail',
+ property : 'email',
+ isExportable: false,
+ sortable : true
+ });
+
+ columns.push({
+ label : 'Special access',
+ property : 'specialAccess',
+ isExportable: false,
+ sortable : true
+ });
+
+ var getDataList = function(callback) {
+ var entities = [];
+
+ var rolesMap = SnakemakeTable.rolesMap(roles);
+
+ var dataList = [];
+
+ for (i = 0; i < experiments.length; i++) {
+ if (experiments[i].type === undefined || experiments[i].type.code !== "BBB") {
+ continue;
+ }
+
+ var desc = experiments[i].properties["BBB.DESCRIPTION"];
+ var group = experiments[i].properties["BBB.GROUP"];
+ var registrator = experiments[i].registrator;
+ var projectCode = experiments[i].project.code;
+ var spaceCode = experiments[i].project.space.code;
+
+ var model = { 'code' : experiments[i].code,
+ 'description' : desc === undefined ? "" : desc,
+ 'group' : group === undefined ? "" : group,
+ 'email' : registrator === null ? "" : registrator.email,
+ 'specialAccess' : SnakemakeTable.getSpecialAccess(rolesMap, projectCode, spaceCode)
+ };
+
+ dataList.push(model);
+ }
+ callback(dataList);
+ };
+
+ var dataGridController = new DataGridController(null, columns, [], null, getDataList, null, true, "ENTITY_TABLE_BBB", null, 90);
+ dataGridController.init(container);
+ }
+
+ this.prepareData = function(experiments, roles) {
+ var data = [];
+
+ var rolesMap = SnakemakeTable.rolesMap(roles);
+
+ for (i = 0; i < experiments.length; i++) {
+ var row = [];
+
+ if (experiments[i].type === undefined || experiments[i].type.code !== "BBB") {
+ continue;
+ }
+
+ var desc = experiments[i].properties["BBB.DESCRIPTION"];
+ var group = experiments[i].properties["BBB.GROUP"];
+ var registrator = experiments[i].registrator;
+ var projectCode = experiments[i].project.code;
+ var spaceCode = experiments[i].project.space.code;
+
+ row.push(experiments[i].code);
+ row.push(desc === undefined ? "" : desc);
+ row.push(group === undefined ? "" : group);
+ row.push(registrator === null ? "" : registrator.email);
+ row.push(SnakemakeTable.getSpecialAccess(rolesMap, projectCode, spaceCode));
+
+ data.push(row);
+ }
+
+ return data;
+ }
+
+ this.getSpecialAccess = function(rolesMap, projectCode, spaceCode) {
+ var projectUsers = rolesMap["projects"][projectCode] === undefined ? "" : rolesMap["projects"][projectCode]["users"].join(", ");
+ var projectGroups = rolesMap["projects"][projectCode] === undefined ? "" : rolesMap["projects"][projectCode]["groups"].join(", ");
+
+ var spaceUsers = rolesMap["space"][spaceCode] === undefined ? "" : rolesMap["space"][spaceCode]["users"].join(", ");
+ var spaceGroups = rolesMap["space"][spaceCode] === undefined ? "" : rolesMap["space"][spaceCode]["groups"].join(", ");
+
+ var users = projectUsers + (projectUsers !== "" && spaceUsers !== "" ? ", " : "") + spaceUsers;
+ var groups = projectGroups + (projectGroups !== "" && spaceGroups !== "" ? ", " : "") + spaceGroups;
+
+ var access = "";
+ if (users !== "") {
+ access += "<span style='font-weight:bold'>Users: </span>" + users;
+ }
+
+ if (groups !== "") {
+ if (access !== "") {
+ access += "<br/>";
+ }
+ access += "<span style='font-weight:bold'>Groups: </span>" + groups;
+ }
+
+ return access;
+ }
+
+ this.rolesMap = function(roles) {
+ var rolesMap = new Map();
+
+ var projects = new Map();
+ var spaces = new Map();
+
+ rolesMap["projects"] = projects;
+ rolesMap["space"] = spaces;
+
+ for (i = 0; i < roles.length; i++) {
+ var user = roles[i].user == null ? null : roles[i].user.userId;
+ var group = roles[i].authorizationGroup == null ? null : roles[i].authorizationGroup.code;
+
+ if (roles[i].project !== null) {
+ var value = projects[roles[i].project.code];
+ projects[roles[i].project.code] = SnakemakeTable.appendValue(value, user, group);
+ } else {
+ var value = spaces[roles[i].space.code];
+ spaces[roles[i].space.code] = SnakemakeTable.appendValue(value, user, group);
+ }
+ }
+
+ return rolesMap;
+ }
+
+ this.appendValue = function(value, user, group) {
+ if (value === undefined) {
+ value = new Map();
+ value["users"] = new Array();
+ value["groups"] = new Array();
+ }
+
+ if (user !== null) {
+ value["users"].push(user);
+ } else {
+ value["groups"].push(group);
+ }
+ return value;
+ }
+}
\ No newline at end of file
diff --git a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/plugins/bbb-hub/snakemake-trigger.js b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/plugins/bbb-hub/snakemake-trigger.js
new file mode 100644
index 0000000000000000000000000000000000000000..a3756fdfc4a20c0d1432b9973209524ad2dbe27b
--- /dev/null
+++ b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/plugins/bbb-hub/snakemake-trigger.js
@@ -0,0 +1,161 @@
+var SnakemakeTrigger = new function() {
+
+ var groups;
+ var propTypeCodeToLabelMap = {};
+ var dataSetPaths;
+ var $formContainerAll;
+ var $formContainerGroups;
+ var $dropdownGroupBy;
+ var $dropdownGroup1;
+ var $dropdownGroup2;
+ var $button;
+ var $model;
+
+ this.paintTriggerContainers = function($container, model, experiment) {
+ $model = model;
+ SnakemakeTrigger.paintFormContainers($container);
+ SnakemakeTrigger.paintProcessAll();
+ SnakemakeTrigger.paintGroupBy(experiment);
+ SnakemakeTrigger.paintGroupValues();
+ groups = SnakemakeTrigger.getGroups(experiment);
+ files = SnakemakeTrigger.getFiles(experiment);
+ }
+
+ this.paintFormContainers = function($container) {
+ var $fieldsetAll = UiComponents.getFieldset("Process all comparisons");
+ var $fieldsetGroups = UiComponents.getFieldset("Pick groups to compare");
+ $formContainerAll = $('<div>').addClass('form-group');
+ $formContainerGroups = $('<div>').addClass('form-group');
+ $fieldsetAll.append($formContainerAll);
+ $fieldsetGroups.append($formContainerGroups);
+ $container.append($fieldsetAll).append($fieldsetGroups);
+ }
+
+ this.paintProcessAll = function() {
+ var $buttonAll = UiComponents.getButton("Start processing", SnakemakeTrigger.startProcessingAll);
+ $formContainerAll.append($buttonAll);
+ }
+
+ this.paintGroupBy = function(experiment) {
+ var groupByOptions = [];
+ if (experiment.samples.length > 0) {
+ var sample = experiment.samples[0];
+ for (var i = 0; i < sample.type.propertyAssignments.length; i++) {
+ var propertyAssignment = sample.type.propertyAssignments[i];
+ groupByOptions.push({
+ label: propertyAssignment.propertyType.label,
+ value: propertyAssignment.propertyType.code,
+ });
+ propTypeCodeToLabelMap[propertyAssignment.propertyType.code] = propertyAssignment.propertyType.label;
+ }
+ }
+
+ $dropdownGroupBy = UiComponents.addDropdown("Group by", groupByOptions, $formContainerGroups, SnakemakeTrigger.paintGroupValues);
+ }
+
+ this.paintGroupValues = function(propertyType) {
+ if (propertyType) {
+ var groupOptions = groups[propertyType].map(function(value) { return {
+ label: value,
+ value: value,
+ }});
+ } else {
+ var groupOptions = [];
+ }
+
+ if ($dropdownGroup1) {
+ $dropdownGroup1.remove();
+ }
+ if ($dropdownGroup2) {
+ $dropdownGroup2.remove();
+ }
+ if ($button) {
+ $button.remove();
+ }
+
+ $dropdownGroup1 = UiComponents.addDropdown("Group 1", groupOptions, $formContainerGroups);
+ $dropdownGroup2 = UiComponents.addDropdown("Group 2", groupOptions, $formContainerGroups);
+
+ $button = UiComponents.getButton("Start processing", SnakemakeTrigger.startProcessing);
+ $button.css("margin-top", "20px");
+ $formContainerGroups.append($button);
+ }
+
+ this.getGroups = function(experiment) {
+ var groups = {};
+ for (var i = 0; i < experiment.samples.length; i++) {
+ var sample = experiment.samples[i];
+ // collect groups
+ for (var propertyKey in sample.properties) {
+ if (sample.properties.hasOwnProperty(propertyKey)) {
+ var propertyValue = sample.properties[propertyKey];
+ if (groups.hasOwnProperty(propertyKey) == false) {
+ groups[propertyKey] = [];
+ }
+ if (groups[propertyKey].indexOf(propertyValue) == -1) {
+ groups[propertyKey].push(propertyValue);
+ }
+ }
+ }
+ }
+ return groups;
+ }
+
+ this.getFiles = function(experiment) {
+ dataSetPaths = [];
+ for (var i = 0; i < experiment.dataSets.length; i++) {
+ var dataSet = experiment.dataSets[i];
+ if (dataSet.type.code == "FASTQ" || dataSet.type.code == "METADATA") {
+ var path = dataSet.physicalData.shareId + "/" + dataSet.physicalData.location;
+ dataSetPaths.push(path);
+ }
+ }
+ }
+
+ this.startProcessingAll = function() {
+ UiComponents.startLoading();
+ var jsonrpc = {
+ "method": "start_processing_all",
+ "params": {
+ "data_set_paths": dataSetPaths
+ }
+ };
+ BBBServerFacade.callCustomASService(jsonrpc, $model, function(result) {
+ UiComponents.stopLoading();
+ if (result.success) {
+ alert("Processing started.");
+ } else {
+ alert("Error: " + result.data);
+ }
+ });
+ }
+
+ this.startProcessing = function() {
+ var groupSelection = {
+ groupBy: propTypeCodeToLabelMap[$dropdownGroupBy.getValue()],
+ group1: $dropdownGroup1.getValue(),
+ group2: $dropdownGroup2.getValue(),
+ }
+ if (!groupSelection.groupBy || !groupSelection.group1 || !groupSelection.group2) {
+ alert("Select both groups first.");
+ return;
+ }
+ UiComponents.startLoading();
+
+ var jsonrpc = {
+ "method": "start_processing",
+ "params": {
+ "group_selection": groupSelection,
+ "data_set_paths": dataSetPaths
+ }
+ };
+ BBBServerFacade.callCustomASService(jsonrpc, $model, function(result) {
+ UiComponents.stopLoading();
+ if (result.success) {
+ alert("Processing started.");
+ } else {
+ alert("Error: " + result.data);
+ }
+ });
+ }
+}
\ No newline at end of file
diff --git a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/plugins/generic/plugin.js b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/plugins/generic/plugin.js
index 1540f3564172c0775d4705c8fe0bca07cd1789f9..6126b9586ff14e8b11e06b9df424cb7450244539 100644
--- a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/plugins/generic/plugin.js
+++ b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/plugins/generic/plugin.js
@@ -19,6 +19,7 @@ $.extend(GenericTechnology.prototype, ELNLIMSPlugin.prototype, {
},
"STORAGE_POSITION" : {
"SHOW" : false,
+ "SHOW_ON_NAV" : false,
"SAMPLE_CHILDREN_DISABLED" : true
},
"REQUEST" : {
diff --git a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/dss/reporting-plugins/exports-api/exportsApi.py b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/dss/reporting-plugins/exports-api/exportsApi.py
index 5b2123c18abba4161fdb550f1d251723a0f50e0a..42682ce0df74fa840b961310fcbfc8379efc80a9 100644
--- a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/dss/reporting-plugins/exports-api/exportsApi.py
+++ b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/dss/reporting-plugins/exports-api/exportsApi.py
@@ -21,14 +21,13 @@ import jarray
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 java.io import File
+from java.io import File, BufferedInputStream
from java.io import FileInputStream
from java.io import FileOutputStream
from java.lang import String
from java.lang import StringBuilder
from java.util import ArrayList
-from java.util.zip import ZipEntry, Deflater
-from java.util.zip import ZipOutputStream
+from java.util.zip import ZipEntry, Deflater, ZipOutputStream, CRC32
from org.apache.commons.io import FileUtils
# Java Core
from org.apache.commons.io import IOUtils
@@ -263,7 +262,7 @@ def cleanUp(tempDirPath, tempZipFilePath):
FileUtils.forceDelete(File(tempZipFilePath));
-def generateFilesInZip(zos, entities, includeRoot, sessionToken, tempDirPath):
+def generateFilesInZip(zos, entities, includeRoot, sessionToken, tempDirPath, deflated=True):
# Services used during the export process
v3 = ServiceProvider.getV3ApplicationService();
v3d = ServiceProvider.getApplicationContext().getBean(V3_DSS_BEAN);
@@ -364,7 +363,7 @@ def generateFilesInZip(zos, entities, includeRoot, sessionToken, tempDirPath):
rawFile = File(tempDirPath + filePath + ".json");
rawFile.getParentFile().mkdirs();
IOUtils.copyLarge(rawFileInputStream, FileOutputStream(rawFile));
- addToZipFile(filePath, rawFile, zos);
+ addToZipFile(filePath, rawFile, zos, deflated=deflated);
emptyZip = False
# To avoid empty directories on the zip file, it makes the first found entity the base directory
@@ -382,20 +381,20 @@ def generateFilesInZip(zos, entities, includeRoot, sessionToken, tempDirPath):
if entityObj is not None and entityFilePath is not None:
# JSON
entityJson = String(objectMapper.writeValueAsString(entityObj));
- fileMetadatum = addFile(tempDirPath, entityFilePath, "json", entityJson.getBytes(), zos);
+ fileMetadatum = addFile(tempDirPath, entityFilePath, "json", entityJson.getBytes(), zos, deflated=deflated);
fileMetadata.append(fileMetadatum)
emptyZip = False
# TEXT
entityTXT = String(getTXT(entityObj, v3, sessionToken, False));
- fileMetadatum = addFile(tempDirPath, entityFilePath, "txt", entityTXT.getBytes(), zos);
+ fileMetadatum = addFile(tempDirPath, entityFilePath, "txt", entityTXT.getBytes(), zos, deflated=deflated);
fileMetadata.append(fileMetadatum)
# DOCX
entityDOCX = getDOCX(entityObj, v3, sessionToken, False);
- fileMetadatum = addFile(tempDirPath, entityFilePath, "docx", entityDOCX, zos);
+ fileMetadatum = addFile(tempDirPath, entityFilePath, "docx", entityDOCX, zos, deflated=deflated);
fileMetadata.append(fileMetadatum)
# HTML
entityHTML = getDOCX(entityObj, v3, sessionToken, True);
- fileMetadatum = addFile(tempDirPath, entityFilePath, "html", entityHTML, zos);
+ fileMetadatum = addFile(tempDirPath, entityFilePath, "html", entityHTML, zos, deflated=deflated);
fileMetadata.append(fileMetadatum)
operationLog.info("--> Entity type: " + type + " permId: " + permId + " post html.");
if emptyZip:
@@ -651,12 +650,12 @@ def objToStrArray(objArray):
return result
-def addFile(tempDirPath, entityFilePath, extension, fileContent, zos):
+def addFile(tempDirPath, entityFilePath, extension, fileContent, zos, deflated=True):
entityFileNameWithExtension = entityFilePath + "." + extension
entityFile = File(tempDirPath + entityFileNameWithExtension);
entityFile.getParentFile().mkdirs();
IOUtils.write(fileContent, FileOutputStream(entityFile));
- addToZipFile(entityFileNameWithExtension, entityFile, zos);
+ addToZipFile(entityFileNameWithExtension, entityFile, zos, deflated=deflated);
FileUtils.forceDelete(entityFile);
extensionToMimeType = {
@@ -685,19 +684,45 @@ def getFilePath(spaceCode, projCode, expCode, sampCode, dataCode):
fileName += "/" + 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);
+def addToZipFile(path, file, zos, deflated=True):
+ zipEntry = ZipEntry(path[1:]) # Making paths relative to make them compatible with Windows zip implementation
+ if not deflated:
+ zipEntry.setMethod(ZipOutputStream.STORED)
+ zipEntry.setSize(file.length())
+ zipEntry.setCompressedSize(-1)
+ crc = getFileCRC(file)
+ zipEntry.setCrc(crc)
+ else:
+ zipEntry.setMethod(ZipOutputStream.DEFLATED)
+
+ zos.putNextEntry(zipEntry)
- bytes = jarray.zeros(1024, "b");
- length = fis.read(bytes);
- while length >= 0:
- zos.write(bytes, 0, length);
- length = fis.read(bytes);
+ try:
+ bis = BufferedInputStream(FileInputStream(file))
+ bytes = jarray.zeros(1024, "b")
+ length = bis.read(bytes)
+ while length >= 0:
+ zos.write(bytes, 0, length)
+ length = bis.read(bytes)
+ finally:
+ zos.closeEntry()
+ if bis is not None:
+ bis.close()
- zos.closeEntry();
- fis.close();
+def getFileCRC(file):
+ bis = None
+ crc = CRC32()
+ try:
+ bis = BufferedInputStream(FileInputStream(file))
+ b = jarray.zeros(1024, "b")
+ length = bis.read(b)
+ while length != -1:
+ crc.update(b, 0, length)
+ length = bis.read(b)
+ finally:
+ if bis is not None:
+ bis.close()
+ return crc.getValue()
def getConfigurationProperty(transaction, propertyName):
threadProperties = transaction.getGlobalState().getThreadParameters().getThreadProperties();
@@ -719,9 +744,10 @@ def generateZipFile(entities, params, tempDirPath, tempZipFilePath, deflated=Tru
fos = FileOutputStream(tempZipFilePath)
zos = ZipOutputStream(fos)
if not deflated:
+ zos.setMethod(ZipOutputStream.STORED)
zos.setLevel(Deflater.NO_COMPRESSION)
- fileMetadata = generateFilesInZip(zos, entities, includeRoot, sessionToken, tempDirPath)
+ fileMetadata = generateFilesInZip(zos, entities, includeRoot, sessionToken, tempDirPath, deflated=deflated)
finally:
if zos is not None:
zos.close()
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
index e7ec266b7609e990e4a8992e5563e7457dc9d623..2c48c58426a2dd243546ee575f825c3ae7296423 100644
--- 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
@@ -228,9 +228,10 @@ def generateExternalZipFile(params, exportDirPath, contentZipFilePath, contentZi
fos = FileOutputStream(exportZipFileName)
zos = ZipOutputStream(fos)
if not deflated:
+ zos.setMethod(ZipOutputStream.STORED)
zos.setLevel(Deflater.NO_COMPRESSION)
- addToZipFile(' ' + contentZipFileName, File(contentZipFilePath), zos)
+ addToZipFile(' ' + contentZipFileName, File(contentZipFilePath), zos, deflated)
generateXML(zipOutputStream=zos, fileMetadata=fileMetadata, exportDirPath=exportDirPath,
userInformation=userInformation, entities=entities, params=params)
diff --git a/openbis_standard_technologies/dist/tarball/installer/data/doc/getting-started-with-openBIS.html b/openbis_standard_technologies/dist/tarball/installer/data/doc/getting-started-with-openBIS.html
index 279e4d88889bff95117328a2e2d69a42cac095d5..087d6e1a246b4999a231532fe4e89b5a1a6ce6b3 100644
--- a/openbis_standard_technologies/dist/tarball/installer/data/doc/getting-started-with-openBIS.html
+++ b/openbis_standard_technologies/dist/tarball/installer/data/doc/getting-started-with-openBIS.html
@@ -145,9 +145,12 @@
<ol>
<li>Log in to <a href="https://${HOSTNAME}:8443/openbis/webapp/eln-lims">ELN/LIMS</a> interface as admin.</li>
- <li>Using the navigation tree on the left hand-side go to LAB NOTEBOOK -> DEFAULT_LAB_NOTEBOOK -> DEFAULT_PROJECT -> DEFAULT_EXPERIMENT. </li>
- <li>Click on the plus sign on the toolbar and create a new EXPERIMENTAL_STEP.</li>
- <li>After creating it, a new component will appear on the right hand-side. Select "ELN Preview Image" from the dropdown and drop an image file in the Files Uploader.</li>
+ <li>Using the navigation tree on the left hand-side go to <em>Lab Notebook</em> -> <em>Others</em>
+ -> <em>Default Lab Notebook</em> -> <em>Default Project</em> -> <em>Default Experiment</em></li>
+ <li>Click on the Upload plus sign on the toolbar and create a new <em>Experimental Step</em>.</li>
+ <li>Click on the Upload button.</li>
+ <li>Choose <em>Eln Preview</em> as Data Set Type and drop an image file in the Files Uploader section.</li>
+ <li>Click the Save button.</li>
<li>Now you have a basic lab notebook with an experiment, experimental step and one image used as preview.</li>
</ol>
diff --git a/pybis/src/python/CHANGELOG.md b/pybis/src/python/CHANGELOG.md
index 8d7c4903179742ece72e4492062d01caf1335b7e..ddc9cefd6540d09e80d603c682be4513a9200b1a 100644
--- a/pybis/src/python/CHANGELOG.md
+++ b/pybis/src/python/CHANGELOG.md
@@ -1,3 +1,7 @@
+## Changes with pybis-1.11.1
+
+- added automatically accepting host key, otherwise mount() will hang the first time
+
## Changes with pybis-1.11.0
* implemented mount() and unmount() methods to mount openBIS dataStore server via SSHFS and FUSE
diff --git a/pybis/src/python/pybis/__init__.py b/pybis/src/python/pybis/__init__.py
index 264495435a19d4dd8c4c63f97115a4d484de6994..b0e578dcb1db65cd510e7b661f80be5f42689c29 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__ = '1.11.0'
+__version__ = '1.11.1'
from . import pybis
from .pybis import Openbis
diff --git a/pybis/src/python/pybis/pybis.py b/pybis/src/python/pybis/pybis.py
index 9354ad34bf216f2c68131cbad83f006277627454..4729f9e0d3c8beed22bcb9468c4baa0483e2204f 100644
--- a/pybis/src/python/pybis/pybis.py
+++ b/pybis/src/python/pybis/pybis.py
@@ -1106,8 +1106,8 @@ class Openbis:
os_options = {
- "darwin": "-oauto_cache,reconnect,defer_permissions,noappledouble,negative_vncache,volname={}".format(hostname),
- "linux": "-oauto_cache,reconnect",
+ "darwin": "-oauto_cache,reconnect,defer_permissions,noappledouble,negative_vncache,volname={} -oStrictHostKeyChecking=no ".format(hostname),
+ "linux": "-oauto_cache,reconnect -oStrictHostKeyChecking=no",
}
if volname is None:
diff --git a/pybis/src/python/setup.py b/pybis/src/python/setup.py
index 43b0dc555b95a310ca05be6d47fc51986ab007e0..08a6e22b1766a31aa4cf8219855a2d1023e9b372 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= '1.11.0',
+ version= '1.11.1',
author='Swen Vermeul • ID SIS • ETH Zürich',
author_email='swen@ethz.ch',
description='openBIS connection and interaction, optimized for using with Jupyter',