{{$ctrl.treeError}}
diff --git a/client/client/app/components/ngbPathways/ngbInternalPathwaysTable/ngbInternalPathwaysTable.controller.js b/client/client/app/components/ngbPathways/ngbInternalPathwaysTable/ngbInternalPathwaysTable.controller.js
index 419d052cb..683909ce9 100644
--- a/client/client/app/components/ngbPathways/ngbInternalPathwaysTable/ngbInternalPathwaysTable.controller.js
+++ b/client/client/app/components/ngbPathways/ngbInternalPathwaysTable/ngbInternalPathwaysTable.controller.js
@@ -7,7 +7,6 @@ const RESIZE_DELAY = 300;
export default class ngbInternalPathwaysTableController extends baseController {
dispatcher;
isProgressShown = true;
- isEmptyResult = false;
errorMessageList = [];
debounce = (new Debounce()).debounce;
gridOptions = {
@@ -39,7 +38,7 @@ export default class ngbInternalPathwaysTableController extends baseController {
};
events = {
'pathways:internalPathways:page:change': this.loadData.bind(this),
- 'pathways:internalPathways:search': this.loadData.bind(this),
+ 'pathways:internalPathways:search': this.initialize.bind(this),
'read:show:pathways': this.loadData.bind(this)
};
@@ -87,10 +86,10 @@ export default class ngbInternalPathwaysTableController extends baseController {
}
});
await this.loadData();
+ this.isProgressShown = false;
}
async loadData() {
- this.isProgressShown = true;
try {
await this.ngbInternalPathwaysTableService.searchInternalPathways(this.ngbPathwaysService.currentSearch);
const dataLength = this.ngbInternalPathwaysTableService.internalPathways.length;
@@ -106,9 +105,7 @@ export default class ngbInternalPathwaysTableController extends baseController {
} else {
this.isEmptyResults = true;
}
- this.isProgressShown = false;
} catch (errorObj) {
- this.isProgressShown = false;
this.onError(errorObj.message);
}
this.$timeout(() => this.$scope.$apply());
@@ -121,7 +118,10 @@ export default class ngbInternalPathwaysTableController extends baseController {
rowClick(row, event) {
const entity = row.entity;
if (entity) {
- this.ngbPathwaysService.currentInternalPathwaysId = row.entity.xml;
+ this.ngbPathwaysService.currentInternalPathway = {
+ id: row.entity.id,
+ name: row.entity.name
+ };
this.changeState({state: 'INTERNAL_PATHWAYS_RESULT'});
} else {
event.stopImmediatePropagation();
@@ -136,7 +136,7 @@ export default class ngbInternalPathwaysTableController extends baseController {
const {columns} = this.gridApi.saveState.save();
const fieldTitleMap = (
o => Object.keys(o).reduce(
- (r, k) => Object.assign(r, { [o[k]]: k }), {}
+ (r, k) => Object.assign(r, {[o[k]]: k}), {}
)
)(this.ngbInternalPathwaysTableService.columnTitleMap);
const mapNameToField = function ({name}) {
diff --git a/client/client/app/components/ngbPathways/ngbInternalPathwaysTable/ngbInternalPathwaysTable.service.js b/client/client/app/components/ngbPathways/ngbInternalPathwaysTable/ngbInternalPathwaysTable.service.js
index cd7b91eaa..2bb558d67 100644
--- a/client/client/app/components/ngbPathways/ngbInternalPathwaysTable/ngbInternalPathwaysTable.service.js
+++ b/client/client/app/components/ngbPathways/ngbInternalPathwaysTable/ngbInternalPathwaysTable.service.js
@@ -1,5 +1,4 @@
import ClientPaginationService from '../../../shared/services/clientPaginationService';
-import {calculateColor} from '../../../shared/utils/calculateColor';
const DEFAULT_INTERNAL_PATHWAYS_COLUMNS = [
'name', 'description'
@@ -13,12 +12,9 @@ const INTERNAL_PATHWAYS_COLUMN_TITLES = {
description: 'Description'
};
const FIRST_PAGE = 1;
-const PAGE_SIZE = 15;
+const PAGE_SIZE = 11;
export default class ngbInternalPathwaysTableService extends ClientPaginationService {
-
- _internalPathwaysResult;
-
constructor(dispatcher, genomeDataService) {
super(dispatcher, FIRST_PAGE, PAGE_SIZE, 'pathways:internalPathways:page:change');
this.dispatcher = dispatcher;
@@ -60,30 +56,18 @@ export default class ngbInternalPathwaysTableService extends ClientPaginationSer
return new ngbInternalPathwaysTableService(dispatcher, genomeDataService);
}
- getInternalPathwaysResultById(id) {
- return this._internalPathwaysResult[id];
- }
-
- getInternalPathwaysById(id) {
- return this.internalPathways.filter(h => h.groupId === id)[0] || {};
- }
-
async searchInternalPathways(currentSearch) {
- const result = await this.loadInternalPathways(currentSearch);
- this._internalPathways = result.internalPathways;
- this._internalPathwaysResult = result.internalPathwaysResult;
+ this._internalPathways = await this.loadInternalPathways(currentSearch);
this.dispatcher.emitSimpleEvent('internalPathways:result:change');
}
async loadInternalPathways(currentSearch) {
- const emptyResult = {
- internalPathways: [],
- internalPathwaysResult: {}
- };
const filter = {
- query: currentSearch,
- page: this.currentPage,
- pageSize: this.pageSize
+ pagingInfo: {
+ pageSize: this.pageSize,
+ pageNum: this.currentPage
+ },
+ sortInfos: this.orderBy
};
const data = await this.genomeDataService.getInternalPathwaysLoad(filter);
if (data.error) {
@@ -91,58 +75,22 @@ export default class ngbInternalPathwaysTableService extends ClientPaginationSer
this.currentPage = FIRST_PAGE;
this._firstPage = FIRST_PAGE;
this._pageError = data.message;
- return emptyResult;
+ return [];
} else {
this._pageError = null;
}
this.totalPages = Math.ceil(data.totalCount / this.pageSize);
if (data && data.items) {
- return {
- internalPathways: this.getInternalPathwaysSearch(data.items),
- internalPathwaysResult: this.getInternalPathwaysResult(data.items)
- };
+ return data.items.map(this._formatServerToClient);
} else {
- return emptyResult;
+ return [];
}
}
- getInternalPathwaysSearch(data) {
- const result = [];
- data.forEach(value => result.push(this._formatServerToClient(value)));
- return result;
- }
-
- getInternalPathwaysResult(data) {
- return data;
- let maxHomologLength = 0;
- const result = {};
- if (data) {
- data.forEach(internalPathways => {
- maxHomologLength = 0;
- result[internalPathways.groupId] = [];
- internalPathways.genes.forEach((gene, key) => {
- result[internalPathways.groupId][key] = this._formatResultToClient(gene);
- if (maxHomologLength < result[internalPathways.groupId][key].aa) {
- maxHomologLength = result[internalPathways.groupId][key].aa;
- }
- });
- result[internalPathways.groupId].forEach((value, key) => {
- result[internalPathways.groupId][key].domainsObj = {
- domains: value.domains.map(d => ({...d, color: calculateColor(d.name)})),
- homologLength: value.aa,
- maxHomologLength: maxHomologLength,
- accession_id: value.accession_id
- };
- delete result[internalPathways.groupId][key].domains;
- });
- });
- }
- return result;
- }
-
getInternalPathwaysGridColumns() {
const result = [];
const columnsList = this.internalPathwaysColumns;
+ const headerCells = require('./ngbInternalPathwaysTable_header.tpl.html');
for (let i = 0; i < columnsList.length; i++) {
let sortDirection = 0;
let sortingPriority = 0;
@@ -162,8 +110,9 @@ export default class ngbInternalPathwaysTableService extends ClientPaginationSer
cellTemplate: `
{{row.entity.name}}
`,
enableHiding: false,
- enableColumnMenu: false,
+ enableSorting: true,
field: 'name',
+ headerCellTemplate: headerCells,
name: this.columnTitleMap[column]
};
break;
@@ -171,9 +120,9 @@ export default class ngbInternalPathwaysTableService extends ClientPaginationSer
default: {
columnSettings = {
enableHiding: false,
- enableColumnMenu: false,
field: column,
minWidth: 40,
+ headerCellTemplate: headerCells,
name: this.columnTitleMap[column],
width: '*'
};
@@ -194,52 +143,10 @@ export default class ngbInternalPathwaysTableService extends ClientPaginationSer
}
_formatServerToClient(internalPathways) {
- return internalPathways;
- const gene = new Set();
- const proteinFrequency = {};
- internalPathways.genes.forEach(g => {
- gene.add(g.symbol);
- if (proteinFrequency.hasOwnProperty(g.title)) {
- proteinFrequency[g.title] += 1;
- } else {
- proteinFrequency[g.title] = 1;
- }
- });
-
- const sortableProteinFrequency = [];
- for (const protein in proteinFrequency) {
- if (proteinFrequency.hasOwnProperty(protein)) {
- sortableProteinFrequency.push([protein, proteinFrequency[protein]]);
- }
- }
-
- sortableProteinFrequency.sort((b, a) => a[1] - b[1]);
-
- return {
- groupId: internalPathways.groupId,
- gene: [...gene].sort().join(', '),
- protein: sortableProteinFrequency[0] ? sortableProteinFrequency[0][0] : '',
- info: internalPathways.caption
- };
- }
-
- _formatResultToClient(result) {
return {
- geneId: result.geneId,
- name: result.symbol,
- species: result.speciesScientificName,
- accession_id: result.protAcc,
- protGi: result.protGi,
- aa: result.protLen,
- taxId: result.taxId,
- protein: result.title,
- domains: (result.domains || []).map(d => ({
- id: d.pssmId,
- start: d.begin,
- end: d.end,
- name: d.cddName
- }))
+ id: internalPathways.pathwayId,
+ name: internalPathways.prettyName || internalPathways.name,
+ description: internalPathways.pathwayDesc
};
}
-
}
diff --git a/client/client/app/components/ngbPathways/ngbInternalPathwaysTable/ngbInternalPathwaysTable_header.tpl.html b/client/client/app/components/ngbPathways/ngbInternalPathwaysTable/ngbInternalPathwaysTable_header.tpl.html
new file mode 100644
index 000000000..7f7c08195
--- /dev/null
+++ b/client/client/app/components/ngbPathways/ngbInternalPathwaysTable/ngbInternalPathwaysTable_header.tpl.html
@@ -0,0 +1,60 @@
+
diff --git a/client/client/app/components/ngbPathways/ngbPathways.service.js b/client/client/app/components/ngbPathways/ngbPathways.service.js
index 1004ccf1f..5572861ca 100644
--- a/client/client/app/components/ngbPathways/ngbPathways.service.js
+++ b/client/client/app/components/ngbPathways/ngbPathways.service.js
@@ -6,7 +6,7 @@ const PATHWAYS_STATES = {
export default class ngbPathwaysService {
pathwaysServiceMap = {};
- currentInternalPathwaysId;
+ currentInternalPathway;
constructor(dispatcher, projectContext,
ngbInternalPathwaysTableService, ngbInternalPathwaysResultService
diff --git a/client/client/app/components/ngbPathways/ngbPathwaysPanel.html b/client/client/app/components/ngbPathways/ngbPathwaysPanel.html
index c57b444e4..665618f66 100644
--- a/client/client/app/components/ngbPathways/ngbPathwaysPanel.html
+++ b/client/client/app/components/ngbPathways/ngbPathwaysPanel.html
@@ -1,17 +1,19 @@
-
-
-
+
+
@@ -39,12 +41,12 @@
ng-if="$ctrl.currentPathwaysState === $ctrl.pathwaysStates.KEGG">
+ class="blast-search-flex-column"
+ flex
+ ng-if="$ctrl.currentPathwaysState === $ctrl.pathwaysStates.INTERNAL_PATHWAYS">
+ class="blast-search-flex-column"
+ flex
+ ng-if="$ctrl.currentPathwaysState === $ctrl.pathwaysStates.INTERNAL_PATHWAYS_RESULT">
diff --git a/client/client/app/components/ngbPathways/ngbPathwaysPanel.scss b/client/client/app/components/ngbPathways/ngbPathwaysPanel.scss
index 9e3695cef..860bddb8d 100644
--- a/client/client/app/components/ngbPathways/ngbPathwaysPanel.scss
+++ b/client/client/app/components/ngbPathways/ngbPathwaysPanel.scss
@@ -2,11 +2,13 @@
color: rgb(51, 103, 214);
font-weight: bold;
cursor: pointer;
+
a {
color: inherit;
text-decoration: none;
}
}
+
.pathways-search-result {
padding: 5px 2px;
@@ -17,6 +19,32 @@
font-size: 18px;
}
}
+
.pathways-no-feature {
font-weight: bold;
}
+
+.pathways-search-container {
+ width: 100%;
+ display: flex;
+ margin-top: 10px;
+
+ .pathways-search-input {
+ font-size: 14px;
+ margin: 5px 0 10px 6px;
+
+ .pathways-search-input-label {
+ padding-bottom: 2px;
+ }
+ }
+ .pathways-search-button {
+ margin: 6px 2px 6px 10px;
+ line-height: 32px;
+ min-height: 32px;
+ height: 32px;
+ }
+}
+
+.pathways-search-input .md-errors-spacer {
+ min-height: 0;
+}
diff --git a/client/client/dataServices/data-service.js b/client/client/dataServices/data-service.js
index fc6680b36..67dae878c 100644
--- a/client/client/dataServices/data-service.js
+++ b/client/client/dataServices/data-service.js
@@ -1,9 +1,6 @@
-import {
- SessionExpirationBehavior,
- SessionExpirationBehaviorStorageKey
-} from './utils/session-expiration-behavior';
import BluebirdPromise from 'bluebird';
import ngbConstants from '../constants';
+import {SessionExpirationBehavior, SessionExpirationBehaviorStorageKey} from './utils/session-expiration-behavior';
const AUTH_ERROR_CODE = 401;
const ERROR_CODE_RANGE_START = 400;
@@ -101,6 +98,20 @@ export class DataService {
});
}
+ getRawFile(method, url, data, ...rest) {
+ return $http(method, this._serverUrl + url, data, ...rest)
+ .then((xhr) => {
+ if (xhr.status === AUTH_ERROR_CODE) {
+ this.handleAuthenticationError();
+ return Promise.reject(xhr.response);
+ }
+ if (xhr.status >= ERROR_CODE_RANGE_START) {
+ return Promise.reject(xhr.response);
+ }
+ return xhr.responseText;
+ });
+ }
+
getFullUrl(url) {
return this._serverUrl + url;
}
diff --git a/client/client/dataServices/genome/genome-data-service.js b/client/client/dataServices/genome/genome-data-service.js
index 50675912c..198101ddc 100644
--- a/client/client/dataServices/genome/genome-data-service.js
+++ b/client/client/dataServices/genome/genome-data-service.js
@@ -238,14 +238,28 @@ export class GenomeDataService extends DataService {
}
getInternalPathwaysLoad(filter) {
- return this._internalPathways;
+ // return this._internalPathways;
return new Promise((resolve, reject) => {
- this.post('homolog/search', filter)
+ this.post('pathways', filter)
.then((data) => {
if (data) {
resolve(data);
} else {
- reject(new Error('No orthologs or paralogs received'));
+ reject(new Error('No pathways received'));
+ }
+ })
+ .catch(reject);
+ });
+ }
+
+ loadPathwayFileById(id) {
+ return new Promise((resolve, reject) => {
+ this.getRawFile('get', `pathway/content/${id}`, null, {customResponseType: 'text'})
+ .then((data) => {
+ if (data) {
+ resolve(data);
+ } else {
+ reject(new Error('No pathway info received'));
}
})
.catch(reject);