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Merge pull request #6134 from jmchilton/rule_fixes_8

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Improve data initialization of rule builder for long term support.
This commit is contained in:
Dannon
2018-05-15 07:30:56 -04:00
committed by GitHub
parent 076e1ddaec 788ed8aa43
commit 3d6443b58b
4 changed files with 65 additions and 16 deletions
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client/galaxy/scripts/components/RuleCollectionBuilder.vue
+39 -9
View File
@@ -285,7 +285,7 @@
</button>
<div class="dropdown-menu" role="menu">
<rule-target-component :builder="this" rule-type="add_column_basename" />
<rule-target-component :builder="this" rule-type="add_column_metadata" v-if="elementsType == 'collection_contents'"/>
<rule-target-component :builder="this" rule-type="add_column_metadata" v-if="metadataOptions"/>
<rule-target-component :builder="this" rule-type="add_column_regex" />
<rule-target-component :builder="this" rule-type="add_column_concatenate" />
<rule-target-component :builder="this" rule-type="add_column_rownum" />
@@ -833,6 +833,27 @@ export default {
value: "identifier0"
});
}
} else if (this.elementsType == "datasets") {
rules.push(
{
type: "add_column_metadata",
value: "hid"
},
{
type: "add_column_metadata",
value: "name"
}
);
} else if (this.elementsType == "library_datasets") {
rules.push({
type: "add_column_metadata",
value: "name"
});
} else if (this.elementsType == "ftp") {
rules.push({
type: "add_column_metadata",
value: "path"
});
}
}
return {
@@ -1061,14 +1082,14 @@ export default {
},
hotData() {
let data, sources, columns;
if (this.elementsType == "datasets") {
data = this.initialElements.map(el => [el["hid"], el["name"]]);
if (
this.elementsType == "datasets" ||
this.elementsType == "library_datasets" ||
this.elementsType == "ftp"
) {
data = this.initialElements.map(el => []);
sources = this.initialElements.slice();
columns = ["new", "new"];
} else if (this.elementsType == "library_datasets") {
data = this.initialElements.map(el => [el["name"]]);
sources = this.initialElements.slice();
columns = ["new"];
columns = [];
} else if (this.elementsType == "collection_contents") {
const collection = this.initialElements;
if (collection) {
@@ -1134,7 +1155,7 @@ export default {
return asDict;
},
metadataOptions() {
const metadataOptions = {};
let metadataOptions = {};
if (this.elementsType == "collection_contents") {
let collectionType;
if (this.initialElements) {
@@ -1153,6 +1174,15 @@ export default {
metadataOptions["identifier" + index] = _l("Paired Identifier");
}
}
} else if ( this.elementsType == "ftp" ) {
metadataOptions["path"] = _l("Path");
} else if ( this.elementsType == "library_datasets" ) {
metadataOptions["name"] = _l("Name");
} else if ( this.elementsType == "datasets" ) {
metadataOptions["hid"] = _l("History ID (hid)");
metadataOptions["name"] = _l("Name");
} else {
metadataOptions = null;
}
return metadataOptions;
},
client/galaxy/scripts/mvc/collection/list-collection-creator.js
+4
View File
@@ -1138,6 +1138,10 @@ function createCollectionViaRules(selection, defaultHideSourceItems) {
elements = selection.toJSON();
elementsType = "datasets";
importType = "collections";
} else if (selection.elements) {
elementsType = selection.selectionType;
importType = selection.dataType || "collections";
elements = selection.elements;
} else {
const hasNonWhitespaceChars = RegExp(/[^\s]/);
// Have pasted data, data from a history dataset, or FTP list.
client/galaxy/scripts/mvc/rules/rule-definitions.js
+16 -5
View File
@@ -166,11 +166,22 @@ const RULES = {
},
apply: (rule, data, sources, columns) => {
const ruleValue = rule.value;
const identifierIndex = parseInt(ruleValue.substring("identifier".length));
function newRow(row, index) {
const newRow = row.slice();
newRow.push(sources[index]["identifiers"][identifierIndex]);
return newRow;
let newRow;
if (ruleValue.startsWith("identifier")) {
const identifierIndex = parseInt(ruleValue.substring("identifier".length));
newRow = (row, index) => {
const newRow = row.slice();
newRow.push(sources[index]["identifiers"][identifierIndex]);
return newRow;
};
} else if (ruleValue == "hid" || ruleValue == "name" || ruleValue == "path") {
newRow = (row, index) => {
const newRow = row.slice();
newRow.push(sources[index][ruleValue]);
return newRow;
};
} else {
return { error: `Unknown metadata type [${ruleValue}}]` };
}
data = data.map(newRow);
columns.push(NEW_COLUMN);
client/galaxy/scripts/mvc/upload/collection/rules-input-view.js
+6 -2
View File
@@ -8,6 +8,7 @@ export default Backbone.View.extend({
initialize: function(app) {
this.app = app;
this.options = app.options;
this.ftpFiles = [];
this.ftpUploadSite = app.currentFtp();
this.setElement(this._template());
this.btnBuild = new Ui.Button({
@@ -100,6 +101,7 @@ export default Backbone.View.extend({
} else if (selectionType == "ftp") {
UploadUtils.getRemoteFiles(ftp_files => {
this._setPreview(ftp_files.map(file => file["path"]).join("\n"));
this.ftpFiles = ftp_files;
});
}
this._updateScreen();
@@ -137,13 +139,15 @@ export default Backbone.View.extend({
_buildSelection: function(content) {
const selectionType = this.selectionType;
const selection = { content: content };
const selection = {};
if (selectionType == "dataset" || selectionType == "paste") {
selection.selectionType = "raw";
selection.content = content;
} else if (selectionType == "ftp") {
selection.selectionType = "ftp";
selection.elements = this.ftpFiles;
selection.ftpUploadSite = this.ftpUploadSite;
}
selection.ftpUploadSite = this.ftpUploadSite;
selection.dataType = this.dataType;
Galaxy.currHistoryPanel.buildCollection("rules", selection, true);
this.app.modal.hide();