From b95b5d911056dd875443c17ff79be3f94f84b75d Mon Sep 17 00:00:00 2001
From: juanf <juanf>
Date: Wed, 13 Aug 2014 14:44:40 +0000
Subject: [PATCH] ELN Refactoring - Refactored Sample Form (Ongoing work)
SVN: 32184
---
.../newbrowser/html/js/config/Profile.js | 8 +
.../views/SampleForm/SampleFormController.js | 216 +++++++++++++++++-
.../js/views/SampleForm/SampleFormView.js | 6 +-
3 files changed, 226 insertions(+), 4 deletions(-)
diff --git a/plasmid/source/core-plugins/newbrowser/1/as/webapps/newbrowser/html/js/config/Profile.js b/plasmid/source/core-plugins/newbrowser/1/as/webapps/newbrowser/html/js/config/Profile.js
index db44631bd0f..fd9fc24cdaa 100644
--- a/plasmid/source/core-plugins/newbrowser/1/as/webapps/newbrowser/html/js/config/Profile.js
+++ b/plasmid/source/core-plugins/newbrowser/1/as/webapps/newbrowser/html/js/config/Profile.js
@@ -69,6 +69,14 @@ $.extend(DefaultProfile.prototype, {
"isEnabled" : false
};
+ this.getDefaultDataStoreCode = function() {
+ var dataStoreCode = null;
+ if(this.allDataStores.length > 0) {
+ var dataStoreCode = this.allDataStores[0].code
+ }
+ return dataStoreCode;
+ }
+
this.getDefaultDataStoreURL = function() {
var dataStoreURL = null;
if(this.allDataStores.length > 0) {
diff --git a/plasmid/source/core-plugins/newbrowser/1/as/webapps/newbrowser/html/js/views/SampleForm/SampleFormController.js b/plasmid/source/core-plugins/newbrowser/1/as/webapps/newbrowser/html/js/views/SampleForm/SampleFormController.js
index ee3e7c9534a..988cef9ff7b 100644
--- a/plasmid/source/core-plugins/newbrowser/1/as/webapps/newbrowser/html/js/views/SampleForm/SampleFormController.js
+++ b/plasmid/source/core-plugins/newbrowser/1/as/webapps/newbrowser/html/js/views/SampleForm/SampleFormController.js
@@ -31,7 +31,221 @@ function SampleFormController(mainController, mode, sample) {
return this._sampleFormModel.isFormLoaded;
}
- this.createUpdateSample = function() {
+ this.createUpdateCopySample = function(isCopyWithNewCode, linkParentsOnCopy, copyChildrenOnCopy) {
+ Util.blockUI();
+ var _this = this;
+ //
+ // Parents/Children Links
+ //
+ if(!this._sampleFormModel.sampleLinksParents.isValid()) {
+ Util.showError("Missing Parents.");
+ return;
+ }
+ var sampleParentsFinal = this._sampleFormModel.sampleLinksParents.getSamplesIdentifiers();
+
+ if(!this._sampleFormModel.sampleLinksChildren.isValid()) {
+ Util.showError("Missing Children.");
+ return;
+ }
+ var sampleChildrenFinal = this._sampleFormModel.sampleLinksChildren.getSamplesIdentifiers();
+ var sampleChildrenRemovedFinal = this._sampleFormModel.sampleLinksChildren.getSamplesRemovedIdentifiers();
+
+ //
+ // Check that the same sample is not a parent and a child at the same time
+ //
+ var intersect_safe = function(a, b) {
+ var ai=0, bi=0;
+ var result = new Array();
+
+ while( ai < a.length && bi < b.length )
+ {
+ if (a[ai] < b[bi] ){ ai++; }
+ else if (a[ai] > b[bi] ){ bi++; }
+ else /* they're equal */
+ {
+ result.push(a[ai]);
+ ai++;
+ bi++;
+ }
+ }
+
+ return result;
+ }
+
+ sampleParentsFinal.sort();
+ sampleChildrenFinal.sort();
+ var intersection = intersect_safe(sampleParentsFinal, sampleChildrenFinal);
+ if(intersection.length > 0) {
+ Util.showError("The same entity can't be a parent and a child, please check: " + intersection);
+ return;
+ }
+
+ //
+ //Identification Info
+ //
+ var sampleCode = this._sampleFormModel.sample.code;
+ var properties = this._sampleFormModel.sample.properties;
+
+ var sampleSpace = this._sampleFormModel.sample.spaceCode; //ELN Sub Experiments will have a space by default but not common Samples
+ if(!sampleSpace) { //Common Samples have maybe a default space to be attached to
+ sampleSpace = profile.getSpaceForSampleType(this.sampleTypeCode);
+ }
+
+ var experimentIdentifier = this._sampleFormModel.sample.experimentIdentifierOrNull; //ELN Sub Experiments will have a experiment by default but not common Samples
+ if(!experimentIdentifier) { //Common Samples have maybe a default experiment to be attached to
+ experimentIdentifier = profile.getExperimentIdentifierForSample(
+ this._sampleFormModel.sample.sampleTypeCode,
+ this._sampleFormModel.sample.code,
+ properties);
+ }
+
+ var sampleProject = null;
+ var sampleExperiment = null;
+
+ if(experimentIdentifier) { //If there is a experiment detected, the sample should be attached to the experiment completely.
+ sampleSpace = experimentIdentifier.split("/")[1];
+ sampleProject = experimentIdentifier.split("/")[2];
+ sampleExperiment = experimentIdentifier.split("/")[3];
+ }
+
+ //Children to create
+ var samplesToCreate = [];
+ this._sampleFormModel.sampleLinksChildren.getSamples().forEach(function(child) {
+ if(child.newSample) {
+ child.properties = {};
+ if(profile.storagesConfiguration["isEnabled"]) {
+ child.properties[_this.profile.storagesConfiguration["STORAGE_PROPERTIES"][0]["NAME_PROPERTY"]] = $("#childrenStorageSelector").val();
+ child.properties[_this.profile.storagesConfiguration["STORAGE_PROPERTIES"][0]["ROW_PROPERTY"]] = 1;
+ child.properties[_this.profile.storagesConfiguration["STORAGE_PROPERTIES"][0]["COLUMN_PROPERTY"]] = 1;
+ child.properties[_this.profile.storagesConfiguration["STORAGE_PROPERTIES"][0]["BOX_PROPERTY"]] = $("#sampleSpaceProject").val().replace(/\//g,'\/') + "_" + $("#sampleCode").val() + "_EXP_RESULTS";
+ child.properties[_this.profile.storagesConfiguration["STORAGE_PROPERTIES"][0]["USER_PROPERTY"]] = _this.serverFacade.openbisServer.getSession().split("-")[0];
+ }
+ samplesToCreate.push(child);
+ }
+ });
+
+ //Method
+ var method = "";
+ if(this._sampleFormModel.mode === FormMode.CREATE) {
+ method = "insertSample";
+ } else if(this._sampleFormModel.mode === FormMode.EDIT) {
+ method = "updateSample";
+ }
+
+ var parameters = {
+ //API Method
+ "method" : method,
+ //Identification Info
+ "sampleSpace" : sampleSpace,
+ "sampleProject" : sampleProject,
+ "sampleExperiment" : sampleExperiment,
+ "sampleCode" : sampleCode,
+ "sampleType" : this._sampleFormModel.sample.sampleTypeCode,
+ //Other Properties
+ "sampleProperties" : properties,
+ //Parent links
+ "sampleParents": sampleParentsFinal,
+ //Children links
+ "sampleChildren": sampleChildrenFinal,
+ "sampleChildrenNew": samplesToCreate,
+ "sampleChildrenRemoved": sampleChildrenRemovedFinal
+ };
+
+ //
+ // Copy override - This part modifies what is done for a create/update and adds a couple of extra parameters needed to copy to the bench correctly
+ //
+ if(isCopyWithNewCode) {
+ parameters["method"] = "copySample";
+ parameters["sampleCode"] = isCopyWithNewCode;
+ if(!linkParentsOnCopy) {
+ parameters["sampleParents"] = [];
+ }
+ if(!copyChildrenOnCopy) {
+ parameters["sampleChildren"] = [];
+ } else if(profile.storagesConfiguration["isEnabled"]) {
+ //1. All properties belonging to benches, to not to copy
+ parameters["notCopyProperties"] = [];
+ parameters["defaultBenchPropertyList"] = [];
+ for(var i = 0; i < profile.storagesConfiguration["STORAGE_PROPERTIES"].length; i++) {
+ var storagePropertyGroup = profile.storagesConfiguration["STORAGE_PROPERTIES"][i];
+ var listToUse = "notCopyProperties";
+ if(i === 0) {
+ listToUse = "defaultBenchPropertyList";
+ }
+ parameters[listToUse].push(storagePropertyGroup["NAME_PROPERTY"]);
+ parameters[listToUse].push(storagePropertyGroup["ROW_PROPERTY"]);
+ parameters[listToUse].push(storagePropertyGroup["COLUMN_PROPERTY"]);
+ parameters[listToUse].push(storagePropertyGroup["BOX_PROPERTY"]);
+ parameters[listToUse].push(storagePropertyGroup["USER_PROPERTY"]);
+ }
+
+ //2. Default Bench properties
+ var defaultStoragePropertyGroup = profile.storagesConfiguration["STORAGE_PROPERTIES"][0];
+ parameters["defaultBenchProperties"] = {};
+ var $benchDropdown = FormUtil.getDefaultBenchDropDown();
+ var defaultBench = $benchDropdown.children()[1].value;
+ parameters["defaultBenchProperties"][defaultStoragePropertyGroup["NAME_PROPERTY"]] = defaultBench;
+ parameters["defaultBenchProperties"][defaultStoragePropertyGroup["ROW_PROPERTY"]] = 1;
+ parameters["defaultBenchProperties"][defaultStoragePropertyGroup["COLUMN_PROPERTY"]] = 1;
+ parameters["defaultBenchProperties"][defaultStoragePropertyGroup["BOX_PROPERTY"]] = $("#sampleSpaceProject").val().replace(/\//g,'\/') + "_" + isCopyWithNewCode + "_EXP_RESULTS";
+ parameters["defaultBenchProperties"][defaultStoragePropertyGroup["USER_PROPERTY"]] = mainController.serverFacade.openbisServer.getSession().split("-")[0];
+ }
+ parameters["sampleChildrenNew"] = [];
+ parameters["sampleChildrenRemoved"] = [];
+ }
+
+ //
+ // Sending the request to the server
+ //
+ if(profile.getDefaultDataStoreCode()) {
+ window.mainController.serverFacade.createReportFromAggregationService(profile.getDefaultDataStoreCode(), parameters, function(response) {
+ _this._createUpdateCopySampleCallback(_this, isCopyWithNewCode, response);
+ });
+ } else {
+ Util.showError("No DSS available.", function() {Util.unblockUI();});
+ }
+
+ return false;
+ }
+
+ this._createUpdateCopySampleCallback = function(_this, isCopyWithNewCode, response) {
+ if(response.error) { //Error Case 1
+ Util.showError(response.error.message, function() {Util.unblockUI();});
+ } else if (response.result.columns[1].title === "Error") { //Error Case 2
+ var stacktrace = response.result.rows[0][1].value;
+ Util.showStacktraceAsError(stacktrace);
+ } else if (response.result.columns[0].title === "STATUS" && response.result.rows[0][0].value === "OK") { //Success Case
+ var sampleType = profile.getSampleTypeForSampleTypeCode(_this._sampleFormModel.sample.sampleTypeCode);
+ var sampleTypeDisplayName = sampleType.description;
+ if(!sampleTypeDisplayName) {
+ sampleTypeDisplayName = _this._sampleFormModel.sample.sampleTypeCode;
+ }
+
+ var message = "";
+ if(isCopyWithNewCode) {
+ message = "Copied with new code: " + isCopyWithNewCode + ".";
+ } else if(_this._sampleFormModel.mode === FormMode.CREATE) {
+ message = "Created.";
+ } else if(_this._sampleFormModel.mode === FormMode.EDIT) {
+ message = "Updated.";
+ }
+
+ var callbackOk = function() {
+ Util.unblockUI();
+ if((isCopyWithNewCode || _this._sampleFormModel.mode === FormMode.CREATE) && _this._sampleFormModel.sample.experimentIdentifierOrNull) {
+ window.mainController.sideMenu.refreshSubExperiment(_this._sampleFormModel.sample.experimentIdentifierOrNull);
+ }
+// TO-DO: The Sample is not necessarily searchable after creation since the index runs asynchronously
+// localReference.serverFacade.searchWithType(localReference.sampleTypeCode, $("#sampleCode")[0].value, function(data) {
+// mainController.changeView('showViewSamplePageFromPermId',data[0].permId);
+// });
+ }
+
+ Util.showSuccess(sampleTypeDisplayName + " " + message, callbackOk);
+ _this._sampleFormModel.isFormDirty = false;
+ } else { //This should never happen
+ Util.showError("Unknown Error.", function() {Util.unblockUI();});
+ }
}
}
\ No newline at end of file
diff --git a/plasmid/source/core-plugins/newbrowser/1/as/webapps/newbrowser/html/js/views/SampleForm/SampleFormView.js b/plasmid/source/core-plugins/newbrowser/1/as/webapps/newbrowser/html/js/views/SampleForm/SampleFormView.js
index 5dc2d7b5ead..466d56632c0 100644
--- a/plasmid/source/core-plugins/newbrowser/1/as/webapps/newbrowser/html/js/views/SampleForm/SampleFormView.js
+++ b/plasmid/source/core-plugins/newbrowser/1/as/webapps/newbrowser/html/js/views/SampleForm/SampleFormView.js
@@ -123,7 +123,7 @@ function SampleFormView(sampleFormController, sampleFormModel) {
$formColumn.append(FormUtil.getFieldForComponentWithLabel(spacesDropDown, "Space"));
spacesDropDown.change(function(event){
var spacesDropDown = $(this);
- _this._sampleFormModel.sample.space = spacesDropDown.val();
+ _this._sampleFormModel.sample.spaceCode = spacesDropDown.val();
_this._sampleFormModel.isFormDirty = true;
});
} else {
@@ -297,7 +297,7 @@ function SampleFormView(sampleFormController, sampleFormModel) {
if(this._sampleFormModel.mode !== FormMode.VIEW) {
var $updateBtn = $("<a>", { "class" : "btn btn-primary"}).append(title);
$updateBtn.click(function() {
- _this._sampleFormController.createUpdateSample();
+ _this._sampleFormController.createUpdateCopySample();
});
$formColumn.append($updateBtn);
@@ -397,7 +397,7 @@ function SampleFormView(sampleFormController, sampleFormModel) {
var isValid = newSampleCodeForCopy[0].checkValidity();
if(isValid) {
var newSampleCodeForCopyValue = newSampleCodeForCopy.val();
- _this._sampleFormController.createUpdateSample(newSampleCodeForCopyValue, linkParentsOnCopy, copyChildrenOnCopy);
+ _this._sampleFormController.createUpdateCopySample(newSampleCodeForCopyValue, linkParentsOnCopy, copyChildrenOnCopy);
Util.unblockUI();
} else {
Util.showError("Invalid code.", function() {}, true);
--
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