From bae19c0aa75763da611ead5c22e2937047b6ff38 Mon Sep 17 00:00:00 2001
From: felmer <franz-josef.elmer@id.ethz.ch>
Date: Thu, 16 May 2019 08:02:38 +0200
Subject: [PATCH] SSDM-8127: interactive entity selector implemented. bug in
get_entity_for_identifier() of sample.py fixed
---
jupyter-openbis-extension/sample.py | 2 +-
.../static/downloadDialog.js | 20 +-
.../static/entitySearcher.js | 278 ++++++++++++++----
jupyter-openbis-extension/static/spinner.gif | Bin 0 -> 34357 bytes
jupyter-openbis-extension/static/state.js | 6 +-
.../static/uploadDialog.js | 29 +-
6 files changed, 241 insertions(+), 94 deletions(-)
create mode 100644 jupyter-openbis-extension/static/spinner.gif
diff --git a/jupyter-openbis-extension/sample.py b/jupyter-openbis-extension/sample.py
index 752dfe7..3b0bf54 100644
--- a/jupyter-openbis-extension/sample.py
+++ b/jupyter-openbis-extension/sample.py
@@ -5,8 +5,8 @@ from .connection import openbis_connections
from urllib.parse import parse_qs
-
def get_entity_for_identifier(conn, identifier):
+ entity = None
try:
entity = conn.openbis.get_sample(identifier)
except Exception as exc:
diff --git a/jupyter-openbis-extension/static/downloadDialog.js b/jupyter-openbis-extension/static/downloadDialog.js
index 304d4a7..b948043 100644
--- a/jupyter-openbis-extension/static/downloadDialog.js
+++ b/jupyter-openbis-extension/static/downloadDialog.js
@@ -1,10 +1,11 @@
define([
"base/js/dialog",
+ "jquery",
"./common",
"./state",
"./entitySearcher"
],
- function (dialog, common, state, entitySearcher) {
+ function (dialog, $, common, state, entitySearcher) {
var spinner = document.createElement("IMG")
spinner.className="openbis-feedback"
@@ -120,9 +121,9 @@ define([
return false
}
- currentEntityIdentifier = entityIdentifier.value
+ currentEntityIdentifier = entityIdentifier.firstChild.value
if (!currentEntityIdentifier) {
- alert('Please specify a Sample or Experiment identifier/permId')
+ alert('Please specify an Entity identifier/permId')
return false
}
var url = env.notebook.base_url
@@ -168,19 +169,11 @@ define([
var showDataSets = document.createElement("DIV")
var title = document.createElement("STRONG")
- title.textContent = "Sample or Experiment identifier/permId: "
+ title.textContent = "Entity identifier/permId: "
showDataSets.appendChild(title)
showDataSets.style.marginTop = '10px'
- // TODO Build and replace this component
- // var entityIdentifier = entitySearcher.getEntitySearcher(state)
-
- var entityIdentifier = document.createElement("INPUT")
- entityIdentifier.type = "text"
- entityIdentifier.name = "entityIdentifier"
- entityIdentifier.size = 40
- entityIdentifier.placeholder = "Sample or Experiment identifier/permId"
- entityIdentifier.value = state.entityIdentifier
+ var entityIdentifier = entitySearcher.getEntitySearcherForDownload(state)
var datasets_table = document.createElement("DIV")
var pagingContainer = document.createElement("DIV")
@@ -228,7 +221,6 @@ define([
download_dialog_box.appendChild(path)
function saveState() {
- state.entityIdentifier = entityIdentifier.value
state.directPermId = datasetPermId.value
state.workingDirectory = downloadPath.value
}
diff --git a/jupyter-openbis-extension/static/entitySearcher.js b/jupyter-openbis-extension/static/entitySearcher.js
index 1b74fb9..889db40 100644
--- a/jupyter-openbis-extension/static/entitySearcher.js
+++ b/jupyter-openbis-extension/static/entitySearcher.js
@@ -1,78 +1,240 @@
-define([],
- function () {
+define(["jquery", "./jquery-select2/js/select2.min"],
+ function($, select2) {
return {
- loadResorce(pathToResource, onLoad, jsOrCss) {
- var resource = null;
+ loadResource(pathToResource, jsOrCss, onLoad) {
+ var resource = null
- if(jsOrCss === 'js') {
- resource = document.createElement('script');
- resource.type = 'text/javascript';
- resource.src = pathToResource;
+ if (jsOrCss === 'js') {
+ resource = document.createElement('script')
+ resource.type = 'text/javascript'
+ resource.src = pathToResource
}
-
- if(jsOrCss === 'css') {
- resource = document.createElement('link');
- resource.type = 'text/css';
- resource.rel = 'stylesheet';
- resource.href = pathToResource;
+
+ if (jsOrCss === 'css') {
+ resource = document.createElement('link')
+ resource.type = 'text/css'
+ resource.rel = 'stylesheet'
+ resource.href = pathToResource
}
- resource.onload = onLoad;
- resource.onreadystatechange= function () {
- if (this.readyState == 'complete') {
- onLoad();
- }
+ resource.onload = onLoad
+ resource.onreadystatechange = function() {
+ if (this.readyState == 'complete') {
+ onLoad()
+ }
}
-
- var head = document.getElementsByTagName('head')[0];
- head.appendChild(resource);
+
+ var head = document.getElementsByTagName('head')[0]
+ head.appendChild(resource)
},
getRequireJSV3Config(baseURL) {
- return {
- baseUrl : baseURL + "/openbis/resources/api/v3",
- paths : {
- "stjs" : "lib/stjs/js/stjs",
- "underscore" : "lib/underscore/js/underscore",
- "moment" : "lib/moment/js/moment"
- },
- shim : {
- "stjs" : {
- exports : "stjs",
- deps : [ "underscore" ]
- },
- "underscore" : {
- exports : "_"
- }
- }
- }
- },
- getEntitySearcher(state) {
- var _this = this;
+ return {
+ baseUrl: baseURL + "/openbis/resources/api/v3",
+ paths: {
+ "stjs": "lib/stjs/js/stjs",
+ "underscore": "lib/underscore/js/underscore",
+ "moment": "lib/moment/js/moment"
+ },
+ shim: {
+ "stjs": {
+ exports: "stjs",
+ deps: ["underscore"]
+ },
+ "underscore": {
+ exports: "_"
+ }
+ }
+ }
+ },
+ getEntitySearcherForDownload(state) {
+ return this.getEntitySearcher(state, false)
+ },
+ getEntitySearcherForUpload(state) {
+ return this.getEntitySearcher(state, true)
+ },
+ getEntitySearcher(state, upload) {
+ var _this = this
var connection_name = state.connection.name
if (!connection_name) {
alert('Please choose a connection')
return false
}
- if(!state.openbisService) {
- var config = this.getRequireJSV3Config(state.connection.dto.url)
- require.config(config)
- require(['openbis'], function(openbis) {
- var apiUrl = state.connection.dto.url + "/openbis/openbis/rmi-application-server-v3.json"
- var v3 = new openbis(apiUrl)
- v3.login(state.connection.dto.username, state.connection.dto.password)
- .done(function(sessionToken) {
- state.openbisService = v3
- alert('openbis v3 service login succeed for ' + apiUrl +' : trusted-cross-origin-domains is set.')
- }).fail(function(result) {
- alert('openbis v3 service login failed for ' + apiUrl +' : trusted-cross-origin-domains is probably not set.')
- });
- });
+ var element = document.createElement("SPAN")
+ element.innerHTML = "<span style='color:orange;margin:5px'>loading...</span>"
+ if (!state.openbisService) {
+ require.config(this.getRequireJSV3Config(state.connection.dto.url))
+ require(["openbis", "as/dto/experiment/search/ExperimentSearchCriteria",
+ "as/dto/experiment/fetchoptions/ExperimentFetchOptions",
+ "as/dto/sample/search/SampleSearchCriteria",
+ "as/dto/sample/fetchoptions/SampleFetchOptions"], function(openbis) {
+ var apiUrl = state.connection.dto.url + "/openbis/openbis/rmi-application-server-v3.json"
+ var v3 = new openbis(apiUrl)
+ v3.login(state.connection.dto.username, state.connection.dto.password)
+ .done(function(sessionToken) {
+ state.openbisService = v3
+ _this.loadResource("/nbextensions/openbis/jquery-select2/css/select2.min.css", 'css', function() {
+ _this.createDropdown(element, state, upload)
+ })
+ }).fail(function(result) {
+ alert('openbis v3 service login failed for ' + apiUrl
+ + " : property 'trusted-cross-origin-domains' is probably not set in service.properties.")
+ })
+ })
+ } else {
+ _this.createDropdown(element, state, upload)
}
- var element = document.createElement("SPAN")
return element
+ },
+ createDropdown(container, state, upload) {
+ var _this = this
+ var $select = $("<select>", {class : 'form-control'})
+ $select.attr("multiple", "multiple")
+ $select.attr("required", "required")
+
+ container.innerHTML = null
+ $select.each(function() {
+ container.appendChild(this)
+ })
+ $select.select2({
+ width: upload ? '100%' : '80%',
+ maximumSelectionLength: 1,
+ minimumInputLength: 2,
+ placeholder : "Entity identifier/permId",
+ ajax: {
+ delay: 1000,
+ processResults: function (data) {
+ var results = []
+
+ for(var dIdx = 0; dIdx < data.length; dIdx++) {
+ var group = {
+ text: data[dIdx].type,
+ children : []
+ }
+
+ var entities = data[dIdx].objects
+ for (var eIdx = 0; eIdx < entities.length; eIdx++) {
+ group.children.push({
+ id : entities[eIdx].permId.permId,
+ text : _this.getDisplayName(entities[eIdx]),
+ data : {
+ id : entities[eIdx].permId.permId,
+ text : _this.getDisplayName(entities[eIdx]),
+ data : entities[eIdx]
+ }
+ })
+ }
+
+ if (entities.length > 0) {
+ results.push(group)
+ }
+ }
+
+ return {
+ "results": results,
+ "pagination": {
+ "more": false
+ }
+ }
+ },
+ transport: function (params, success, failure) {
+ var searchResults = []
+ _this.searchExperiments(state, params, function(result) {
+ searchResults.push(result)
+ _this.searchSamples(state, params, function(result) {
+ searchResults.push(result)
+ success(searchResults)
+ })
+ })
+ return {
+ abort : function () { /* Not implemented */ }
+ }
+ }
+ }
+ })
+ $select.on("select2:select", function() {
+ if (upload) {
+ state.uploadEntity = _this.getSelected($select)[0]
+ } else {
+ state.entity = _this.getSelected($select)[0]
+ }
+ })
+ if (upload && state.uploadEntity) {
+ _this.addSelected($select, state.uploadEntity)
+ } else if (upload == false && state.entity) {
+ _this.addSelected($select, state.entity)
+ }
+ },
+ searchExperiments(state, params, action) {
+ var ExperimentSearchCriteria = require("as/dto/experiment/search/ExperimentSearchCriteria")
+ var searchCriteria = new ExperimentSearchCriteria().withOrOperator()
+ searchCriteria.withCode().thatContains(params.data.q)
+ searchCriteria.withProperty("$NAME").thatContains(params.data.q)
+ var ExperimentFetchOptions = require("as/dto/experiment/fetchoptions/ExperimentFetchOptions")
+ var fetchOptions = new ExperimentFetchOptions()
+ fetchOptions.withProperties()
+ state.openbisService.searchExperiments(searchCriteria, fetchOptions).done(action)
+ },
+ searchSamples(state, params, action) {
+ var SampleSearchCriteria = require("as/dto/sample/search/SampleSearchCriteria")
+ var searchCriteria = new SampleSearchCriteria().withOrOperator()
+ searchCriteria.withCode().thatContains(params.data.q)
+ searchCriteria.withProperty("$NAME").thatContains(params.data.q)
+ var SampleFetchOptions = require("as/dto/sample/fetchoptions/SampleFetchOptions")
+ var fetchOptions = new SampleFetchOptions()
+ fetchOptions.withProperties()
+ state.openbisService.searchSamples(searchCriteria, fetchOptions).done(action)
+ },
+ getDisplayName(entity) {
+ var text = ""
+ var propertyReplacingCode = "$NAME"
+ if (entity.identifier && entity.identifier.identifier) {
+ text = entity.identifier.identifier
+ }
+ if (entity.properties && entity.properties[propertyReplacingCode]) {
+ text += " (" + entity.properties[propertyReplacingCode] + ")"
+ }
+ return text
+ },
+ getSelected($select) {
+ var selected = $select.select2('data')
+ var entities = []
+ for (var eIdx = 0; eIdx < selected.length; eIdx++) {
+ if (selected[eIdx].data) {
+ entities.push(selected[eIdx].data.data)
+ }
+ if (selected[eIdx].element.data) {
+ entities.push(selected[eIdx].element.data.data)
+ }
+ }
+ return entities
+ },
+ addSelected($select, v3entity) {
+ var text = this.getDisplayName(v3entity)
+ var id = null
+ if (v3entity.permId && v3entity.permId.permId) { //Only v3 objects supported
+ id = v3entity.permId.permId
+ } else {
+ throw {
+ name: "NonV3ObjectException",
+ message: "Object without v3 permId",
+ toString: function() {
+ return this.name + ": " + this.message
+ }
+ }
+ }
+
+ var data = {
+ id : id,
+ text : text,
+ data : v3entity
+ }
+
+ var newOption = new Option(text, id, true, true)
+ newOption.data = data
+ $select.append(newOption).trigger('change')
}
}
}
-)
\ No newline at end of file
+)
diff --git a/jupyter-openbis-extension/static/spinner.gif b/jupyter-openbis-extension/static/spinner.gif
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diff --git a/jupyter-openbis-extension/static/state.js b/jupyter-openbis-extension/static/state.js
index 2a0f35c..71ea8e2 100644
--- a/jupyter-openbis-extension/static/state.js
+++ b/jupyter-openbis-extension/static/state.js
@@ -12,7 +12,7 @@ define([],
// upload dialog
uploadDataSetType: null,
uploadDataSetTypes: {},
- uploadEntityIdentifier: '',
+ uploadEntity: null,
datasetCheckboxes: [],
fileCheckboxes: [],
selectedFiles: [],
@@ -20,11 +20,11 @@ define([],
// download dialog
selectedDatasets: new Set([]),
- entityIdentifier: '',
+ entity: null,
workingDirectory: '',
// openBIS v3 connection
- openBISV3 : null
+ openbisService : null
}
}
)
\ No newline at end of file
diff --git a/jupyter-openbis-extension/static/uploadDialog.js b/jupyter-openbis-extension/static/uploadDialog.js
index 0690d40..9f848ee 100644
--- a/jupyter-openbis-extension/static/uploadDialog.js
+++ b/jupyter-openbis-extension/static/uploadDialog.js
@@ -4,9 +4,9 @@ define([
"jquery",
"./state",
"./common",
+ "./entitySearcher"
],
- function (dialog, utils, $, state, common) {
-
+ function (dialog, utils, $, state, common, entitySearcher) {
var errorElements = { }
function createErrorElement(name) {
var element = document.createElement("STRONG")
@@ -23,10 +23,10 @@ define([
var spinner = document.createElement("IMG")
spinner.className="openbis-feedback"
spinner.src=""
- function showSpinner() {
- spinner.src="https://cdnjs.cloudflare.com/ajax/libs/slick-carousel/1.5.8/ajax-loader.gif"
+ function showSpinner(env) {
+ spinner.src = env.notebook.base_url + "nbextensions/openbis/spinner.gif"
}
- function hideSpinner() {
+ function hideSpinner(env) {
spinner.src=""
}
@@ -68,7 +68,7 @@ define([
response.json()
.then(function (data) {
var change_input_fields = function () {
- hideSpinner()
+ hideSpinner(env)
cleanErrors()
var oldType = state.uploadDataSetType
@@ -203,22 +203,16 @@ define([
getDatasetTypes(env, state.connection.name, dataset_types, input_fields)
var sample_title = document.createElement("STRONG")
- sample_title.textContent = "Sample or Experiment identifier/permId"
+ sample_title.textContent = "Entity"
var sample_error = createErrorElement('entityIdentifier')
- var entityIdentifier = document.createElement("INPUT")
- entityIdentifier.type = "text"
- entityIdentifier.name = 'entityIdentifier'
- entityIdentifier.placeholder = "Sample or Experiment identifier/permId"
- entityIdentifier.value = state.uploadEntityIdentifier
- entityIdentifier.size = "90"
- entityIdentifier.style.width="100%"
+ var entityIdentifier = entitySearcher.getEntitySearcherForUpload(state)
var ds_title = document.createElement("STRONG")
var dataSetListContainer = document.createElement("DIV")
if (env.notebook.metadata.datasets) {
- ds_title.textContent = "DataSets"
+ ds_title.textContent = "Parent DataSets"
dataSetListContainer.style.maxHeight="150px"
dataSetListContainer.style.overflow="auto"
get_dataset_list(env, dataSetListContainer)
@@ -256,7 +250,6 @@ define([
state.uploadDataSetTypes[state.uploadDataSetType][element.name] = element.value
}
}
- state.uploadEntityIdentifier = entityIdentifier.value
state.unselectedDatasets = state.datasetCheckboxes.filter(cb => !cb.checked).map(cb => cb.value)
state.selectedFiles = state.fileCheckboxes.filter(cb => cb.checked).map(cb => cb.value)
}
@@ -286,7 +279,7 @@ define([
"type": dataset_types.value,
"files": files,
"parents": state.datasetCheckboxes.filter(cb => cb.checked).map(cb => cb.value),
- "entityIdentifier": entityIdentifier.value,
+ "entityIdentifier": entityIdentifier.firstChild.value,
"props": props
}
@@ -333,7 +326,7 @@ define([
}
}
- showSpinner()
+ showSpinner(env)
cleanErrors()
utils.ajax(settings)
return false
--
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