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Fran McDadeFran McDade
Fran McDade
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Fran McDade
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Hyperlink Analysis Protocol to corresponding Pipelines page in the portal. Second pass. Resolves #950.
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-115
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+158
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‎spa/src/app/files/analysis-protocol-pipeline-linker/analysis-protocol-pipeline-linker.component.html‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -1,4 +1,4 @@
1-
<ng-container *ngFor="let analysisProtocol of getAnalysisProtocols(); last as lastAnalysisProtocol">
1+
<ng-container *ngFor="let analysisProtocol of listAnalysisProtocols(); last as lastAnalysisProtocol">
22
<ng-container [ngSwitch]="isAnalysisProtocolLinked(analysisProtocol)">
33
<a href="{{getPipelineLink(analysisProtocol)}}" rel="noopener noreferrer" target="_blank" *ngSwitchDefault>{{analysisProtocol}}<span class="comma" *ngIf="!lastAnalysisProtocol">, </span></a>
44
<span *ngSwitchCase="false">{{analysisProtocol}}<span class="comma" *ngIf="!lastAnalysisProtocol">, </span></span>

‎spa/src/app/files/analysis-protocol-pipeline-linker/analysis-protocol-pipeline-linker.component.spec.ts‎

Lines changed: 103 additions & 75 deletions
Original file line numberDiff line numberDiff line change
@@ -24,6 +24,16 @@ describe("AnalysisProtocolPipelineLinkerComponent", () => {
2424
// Create response for testConfig.getPortalUrl()
2525
testConfig.getPortalURL.and.returnValue("https://test.com");
2626

27+
// Local values
28+
const LOCAL_VALUE_PIPELINE_LINKS_BY_ANALYSIS_PROTOCOL_KEY = {
29+
"smartseq2": "/pipelines/smart-seq2-workflow",
30+
"optimus": "/pipelines/optimus-workflow"
31+
};
32+
33+
// Index values
34+
const INDEX_OF_PIPELINE_LINKS_BY_ANALYSIS_PROTOCOL_KEY_OPTIMUS = 1;
35+
const INDEX_OF_PIPELINE_LINKS_BY_ANALYSIS_PROTOCOL_KEY_SMARTSEQ2 = 0;
36+
2737
// Template values
2838
const TEMPLATE_VALUE_DATA_PORTAL_LINK_SMARTSEQ2 = "/pipelines/smart-seq2-workflow";
2939
const TEMPLATE_VALUE_DATA_PORTAL_LINK_OPTIMUS = "/pipelines/optimus-workflow";
@@ -67,114 +77,145 @@ describe("AnalysisProtocolPipelineLinkerComponent", () => {
6777
});
6878

6979
/**
70-
* Confirm get analysis protocols returns a concatenated string array when multiple workflow values.
80+
* Confirm get pipeline link returns corresponding data portal optimus link when analysis protocol includes "optimus".
7181
*/
72-
it("should get analysis protocols returns a concatenated string array when multiple workflow values", () => {
82+
it(`should get pipeline link returns corresponding data portal optimus link when analysis protocol includes "optimus"`, () => {
7383

74-
component.workflow = INPUT_VALUE_WORKFLOW_MULTIPLE_MIXED_VALUES;
75-
fixture.detectChanges();
84+
// Confirm link is for data portal optimus
85+
const pipelineLink = component.getPipelineLink(TEST_VALUE_OPTIMUS);
86+
expect(pipelineLink).toEqual(`${testConfig.getPortalURL()}${TEMPLATE_VALUE_DATA_PORTAL_LINK_OPTIMUS}`);
87+
});
7688

77-
// Confirm get analysis protocols returns a concatenated string array
78-
const getAnalysisProtocols = component.getAnalysisProtocols();
79-
expect(getAnalysisProtocols).toEqual(TEST_VALUE_ANALYSIS_PROTOCOLS_MULTIPLE_MIXED_VALUES);
89+
/**
90+
* Confirm get pipeline link returns corresponding data portal smartseq2 link when analysis protocol includes "smartseq2".
91+
*/
92+
it(`should get pipeline link returns corresponding data portal smartseq2 link when analysis protocol includes "smartseq2"`, () => {
93+
94+
// Confirm link is for data portal smartseq2
95+
const pipelineLink = component.getPipelineLink(TEST_VALUE_SMARTSEQ2);
96+
expect(pipelineLink).toEqual(`${testConfig.getPortalURL()}${TEMPLATE_VALUE_DATA_PORTAL_LINK_SMARTSEQ2}`);
8097
});
8198

8299
/**
83-
* Confirm get analysis protocols returns a string array when single workflow values.
100+
* Confirm get pipeline link returns the root base path when there is no corresponding pipeline.
84101
*/
85-
it("should get analysis protocols returns a string array when single workflow values", () => {
102+
it("should get pipeline link returns the root base path when there is no corresponding pipeline", () => {
86103

87-
component.workflow = INPUT_VALUE_WORKFLOW_SINGLE_OPTIMUS_VALUE;
88-
fixture.detectChanges();
104+
// Confirm no link is returned
105+
const pipelineLink = component.getPipelineLink(TEST_VALUE_CELL_RANGER);
106+
expect(pipelineLink).toEqual("/");
107+
});
89108

90-
// Confirm get analysis protocols returns a string array
91-
const getAnalysisProtocols = component.getAnalysisProtocols();
92-
expect(getAnalysisProtocols).toEqual([TEST_VALUE_OPTIMUS]);
109+
/**
110+
* Confirm is analysis protocol linked returns true when analysis protocol includes "optimus".
111+
*/
112+
it(`should is analysis protocol linked returns true when analysis protocol includes "optimus"`, () => {
113+
114+
// Confirm true is returned
115+
const analysisProtocolLinked = component.isAnalysisProtocolLinked(TEST_VALUE_OPTIMUS);
116+
expect(analysisProtocolLinked).toEqual(true);
93117
});
94118

95119
/**
96-
* Confirm get analysis protocols returns an empty array when empty workflow values.
120+
* Confirm is analysis protocol linked returns true when analysis protocol includes "smartseq2".
97121
*/
98-
it("should get analysis protocols returns an empty array when empty workflow values", () => {
122+
it(`should is analysis protocol linked returns true when analysis protocol includes "smartseq2"`, () => {
99123

100-
component.workflow = "";
101-
fixture.detectChanges();
124+
// Confirm true is returned
125+
const analysisProtocolLinked = component.isAnalysisProtocolLinked(TEST_VALUE_SMARTSEQ2);
126+
expect(analysisProtocolLinked).toEqual(true);
127+
});
102128

103-
// Confirm get analysis protocols returns a concatenated string array
104-
const getAnalysisProtocols = component.getAnalysisProtocols();
105-
expect(getAnalysisProtocols).toEqual([]);
129+
/**
130+
* Confirm is analysis protocol linked returns false when analysis protocol neither includes "smartseq2" nor "optimus".
131+
*/
132+
it(`should is analysis protocol linked returns true when analysis protocol neither includes "smartseq2" nor "optimus"`, () => {
133+
134+
// Confirm true is returned
135+
const analysisProtocolLinked = component.isAnalysisProtocolLinked(TEST_VALUE_CELL_RANGER);
136+
expect(analysisProtocolLinked).toEqual(false);
106137
});
138+
107139
/**
108-
* Confirm get analysis protocols returns a string array when single workflow values.
140+
* Confirm list analysis protocols returns a concatenated string array when multiple workflow values.
109141
*/
110-
it("should get analysis protocols returns a string array when single workflow values", () => {
142+
it("should list analysis protocols returns a concatenated string array when multiple workflow values", () => {
111143

112-
component.workflow = INPUT_VALUE_WORKFLOW_SINGLE_OPTIMUS_VALUE;
144+
component.workflow = INPUT_VALUE_WORKFLOW_MULTIPLE_MIXED_VALUES;
113145
fixture.detectChanges();
114146

115-
// Confirm get analysis protocols returns a string array
116-
const getAnalysisProtocols = component.getAnalysisProtocols();
117-
expect(getAnalysisProtocols).toEqual([TEST_VALUE_OPTIMUS]);
147+
// Confirm get analysis protocols returns a concatenated string array
148+
const analysisProtocols = component.listAnalysisProtocols();
149+
expect(analysisProtocols).toEqual(TEST_VALUE_ANALYSIS_PROTOCOLS_MULTIPLE_MIXED_VALUES);
118150
});
119151

120152
/**
121-
* Confirm get pipeline link returns corresponding data portal optimus link when analysis protocol includes "optimus".
153+
* Confirm list analysis protocols returns a string array when single workflow values.
122154
*/
123-
it(`should get pipeline link returns corresponding data portal optimus link when analysis protocol includes "optimus"`, () => {
155+
it("should list analysis protocols returns a string array when single workflow values", () => {
124156

125-
// Confirm link is for data portal optimus
126-
const getPipelineLink = component.getPipelineLink(TEST_VALUE_OPTIMUS);
127-
expect(getPipelineLink).toEqual(testConfig.getPortalURL() + TEMPLATE_VALUE_DATA_PORTAL_LINK_OPTIMUS);
157+
component.workflow = INPUT_VALUE_WORKFLOW_SINGLE_OPTIMUS_VALUE;
158+
fixture.detectChanges();
159+
160+
// Confirm get analysis protocols returns a string array
161+
const analysisProtocols = component.listAnalysisProtocols();
162+
expect(analysisProtocols).toEqual([TEST_VALUE_OPTIMUS]);
128163
});
129164

130165
/**
131-
* Confirm get pipeline link returns corresponding data portal smartseq2 link when analysis protocol includes "smartseq2".
166+
* Confirm list analysis protocols returns an empty array when empty workflow values.
132167
*/
133-
it(`should get pipeline link returns corresponding data portal smartseq2 link when analysis protocol includes "smartseq2"`, () => {
168+
it("should list analysis protocols returns an empty array when empty workflow values", () => {
134169

135-
// Confirm link is for data portal smartseq2
136-
const getPipelineLink = component.getPipelineLink(TEST_VALUE_SMARTSEQ2);
137-
expect(getPipelineLink).toEqual(testConfig.getPortalURL() + TEMPLATE_VALUE_DATA_PORTAL_LINK_SMARTSEQ2);
170+
component.workflow = "";
171+
fixture.detectChanges();
172+
173+
// Confirm get analysis protocols returns a concatenated string array
174+
const analysisProtocols = component.listAnalysisProtocols();
175+
expect(analysisProtocols).toEqual([]);
138176
});
139177

140178
/**
141-
* Confirm get pipeline link returns the root base path when there is no corresponding pipeline.
179+
* Confirm list analysis protocols returns a string array when single workflow values.
142180
*/
143-
it("should get pipeline link returns the root base path when there is no corresponding pipeline", () => {
181+
it("should list analysis protocols returns a string array when single workflow values", () => {
144182

145-
// Confirm no link is returned
146-
const getPipelineLink = component.getPipelineLink(TEST_VALUE_CELL_RANGER);
147-
expect(getPipelineLink).toEqual("/");
183+
component.workflow = INPUT_VALUE_WORKFLOW_SINGLE_OPTIMUS_VALUE;
184+
fixture.detectChanges();
185+
186+
// Confirm get analysis protocols returns a string array
187+
const analysisProtocols = component.listAnalysisProtocols();
188+
expect(analysisProtocols).toEqual([TEST_VALUE_OPTIMUS]);
148189
});
149190

150191
/**
151-
* Confirm is analysis protocol linked returns true when analysis protocol includes "optimus".
192+
* Confirm find analysis protocol key returns "optimus" when analysis protocol includes "optimus".
152193
*/
153-
it(`should is analysis protocol linked returns true when analysis protocol includes "optimus"`, () => {
194+
it(`should find analysis protocol key return "optimus" when analysis protocol includes "optimus"`, () => {
154195

155-
// Confirm true is returned
156-
const isAnalysisProtocolLinked = component.isAnalysisProtocolLinked(TEST_VALUE_OPTIMUS);
157-
expect(isAnalysisProtocolLinked).toEqual(true);
196+
// Confirm key returned is "optimus"
197+
const analysisProtocolKey = component["findAnalysisProtocolKey"](LOCAL_VALUE_PIPELINE_LINKS_BY_ANALYSIS_PROTOCOL_KEY, TEST_VALUE_OPTIMUS);
198+
expect(analysisProtocolKey).toEqual(Object.keys(LOCAL_VALUE_PIPELINE_LINKS_BY_ANALYSIS_PROTOCOL_KEY)[INDEX_OF_PIPELINE_LINKS_BY_ANALYSIS_PROTOCOL_KEY_OPTIMUS]);
158199
});
159200

160201
/**
161-
* Confirm is analysis protocol linked returns true when analysis protocol includes "smartseq2".
202+
* Confirm find analysis protocol key returns "smartseq2" when analysis protocol includes "smartseq2".
162203
*/
163-
it(`should is analysis protocol linked returns true when analysis protocol includes "smartseq2"`, () => {
204+
it(`should find analysis protocol key return "smartseq2" when analysis protocol includes "smartseq2"`, () => {
164205

165-
// Confirm true is returned
166-
const isAnalysisProtocolLinked = component.isAnalysisProtocolLinked(TEST_VALUE_SMARTSEQ2);
167-
expect(isAnalysisProtocolLinked).toEqual(true);
206+
// Confirm key returned is "smartseq2"
207+
const analysisProtocolKey = component["findAnalysisProtocolKey"](LOCAL_VALUE_PIPELINE_LINKS_BY_ANALYSIS_PROTOCOL_KEY, TEST_VALUE_SMARTSEQ2);
208+
expect(analysisProtocolKey).toEqual(Object.keys(LOCAL_VALUE_PIPELINE_LINKS_BY_ANALYSIS_PROTOCOL_KEY)[INDEX_OF_PIPELINE_LINKS_BY_ANALYSIS_PROTOCOL_KEY_SMARTSEQ2]);
168209
});
169210

170211
/**
171-
* Confirm is analysis protocol linked returns false when analysis protocol neither includes "smartseq2" nor "optimus".
212+
* Confirm find analysis protocol key returns undefined when analysis protocol is neither includes "smartseq2" nor "optimus".
172213
*/
173-
it(`should is analysis protocol linked returns true when analysis protocol neither includes "smartseq2" nor "optimus"`, () => {
214+
it(`should find analysis protocol key return undefined when analysis protocol is neither includes "smartseq2" nor "optimus"`, () => {
174215

175-
// Confirm true is returned
176-
const isAnalysisProtocolLinked = component.isAnalysisProtocolLinked(TEST_VALUE_CELL_RANGER);
177-
expect(isAnalysisProtocolLinked).toEqual(false);
216+
// Confirm key returned is undefined
217+
const analysisProtocolKey = component["findAnalysisProtocolKey"](LOCAL_VALUE_PIPELINE_LINKS_BY_ANALYSIS_PROTOCOL_KEY, TEST_VALUE_CELL_RANGER);
218+
expect(analysisProtocolKey).toBeUndefined();
178219
});
179220

180221
/**
@@ -206,30 +247,17 @@ describe("AnalysisProtocolPipelineLinkerComponent", () => {
206247
});
207248

208249
/**
209-
* Confirm all linked analysis protocols are displayed, when multiple mixed workflow.
250+
* Confirm all analysis protocols are displayed, when multiple mixed workflow.
210251
*/
211-
it("should display all linked analysis protocols when multiple mixed workflow", () => {
252+
it("should display all analysis protocols when multiple mixed workflow", () => {
212253

213254
// Set up initial component state
214255
component.workflow = INPUT_VALUE_WORKFLOW_MULTIPLE_MIXED_VALUES;
215256

216257
fixture.detectChanges();
217258

218-
// Confirm linked protocols are displayed
259+
// Confirm all protocols are displayed
219260
expect(getAnalysisProtocolsDisplayed("a").length).toEqual(2);
220-
});
221-
222-
/**
223-
* Confirm all unlinked analysis protocols are displayed, when multiple mixed workflow.
224-
*/
225-
it("should display all unlinked analysis protocols when multiple mixed workflow", () => {
226-
227-
// Set up initial component state
228-
component.workflow = INPUT_VALUE_WORKFLOW_MULTIPLE_MIXED_VALUES;
229-
230-
fixture.detectChanges();
231-
232-
// Confirm unlinked protocols are displayed
233261
expect(getAnalysisProtocolsDisplayed("span").length).toEqual(1);
234262
});
235263

@@ -261,7 +289,7 @@ describe("AnalysisProtocolPipelineLinkerComponent", () => {
261289
const analysisPortalDEs = getAnalysisProtocolsDisplayed("a");
262290

263291
// Confirm href link
264-
expect(getHrefValue(analysisPortalDEs[0])).toEqual(testConfig.getPortalURL() + TEMPLATE_VALUE_DATA_PORTAL_LINK_OPTIMUS);
292+
expect(getHrefValue(analysisPortalDEs[0])).toEqual(`${testConfig.getPortalURL()}${TEMPLATE_VALUE_DATA_PORTAL_LINK_OPTIMUS}`);
265293
});
266294

267295
/**
@@ -277,7 +305,7 @@ describe("AnalysisProtocolPipelineLinkerComponent", () => {
277305
const analysisPortalDEs = getAnalysisProtocolsDisplayed("a");
278306

279307
// Confirm href link
280-
expect(getHrefValue(analysisPortalDEs[0])).toEqual(testConfig.getPortalURL() + TEMPLATE_VALUE_DATA_PORTAL_LINK_SMARTSEQ2);
308+
expect(getHrefValue(analysisPortalDEs[0])).toEqual(`${testConfig.getPortalURL()}${TEMPLATE_VALUE_DATA_PORTAL_LINK_SMARTSEQ2}`);
281309
});
282310

283311
/**

‎spa/src/app/files/analysis-protocol-pipeline-linker/analysis-protocol-pipeline-linker.component.ts‎

Lines changed: 31 additions & 22 deletions
Original file line numberDiff line numberDiff line change
@@ -40,21 +40,6 @@ export class AnalysisProtocolPipelineLinkerComponent {
4040
this.portalURL = this.configService.getPortalURL();
4141
}
4242

43-
/**
44-
* Returns concatenated string array of workflow values.
45-
*
46-
* @returns {string[]}
47-
*/
48-
public getAnalysisProtocols(): string[] {
49-
50-
if ( !this.workflow ) {
51-
52-
return [];
53-
}
54-
55-
return this.workflow.split(", ");
56-
}
57-
5843
/**
5944
* Returns corresponding Data Portal pipeline link for the specified analysis protocol.
6045
*
@@ -63,10 +48,7 @@ export class AnalysisProtocolPipelineLinkerComponent {
6348
*/
6449
public getPipelineLink(analysisProtocol: string): string {
6550

66-
const analysisProtocolKey = Object.keys(this.pipelineLinksByAnalysisProtocolKey).filter(key => {
67-
68-
return analysisProtocol.includes(key);
69-
}).toString();
51+
const analysisProtocolKey = this.findAnalysisProtocolKey(this.pipelineLinksByAnalysisProtocolKey, analysisProtocol);
7052

7153
if ( !analysisProtocolKey ) {
7254

@@ -75,7 +57,7 @@ export class AnalysisProtocolPipelineLinkerComponent {
7557

7658
const pipelineLink = this.pipelineLinksByAnalysisProtocolKey[analysisProtocolKey];
7759

78-
return this.portalURL + pipelineLink;
60+
return `${this.portalURL}${pipelineLink}`;
7961
};
8062

8163
/**
@@ -86,9 +68,36 @@ export class AnalysisProtocolPipelineLinkerComponent {
8668
*/
8769
public isAnalysisProtocolLinked(analysisProtocol: string): boolean {
8870

89-
return Object.keys(this.pipelineLinksByAnalysisProtocolKey).some(key => {
71+
return !!this.findAnalysisProtocolKey(this.pipelineLinksByAnalysisProtocolKey, analysisProtocol);
72+
}
73+
74+
/**
75+
* Returns concatenated string array of workflow values.
76+
*
77+
* @returns {string[]}
78+
*/
79+
public listAnalysisProtocols(): string[] {
80+
81+
if ( !this.workflow ) {
82+
83+
return [];
84+
}
85+
86+
return this.workflow.split(", ");
87+
}
88+
89+
/**
90+
* Returns the analysis protocol key for the specified analysis protocol.
91+
*
92+
* @param {Object} pipelineLinksByAnalysisProtocol
93+
* @param {string} analysisProtocol
94+
* @returns {string}
95+
*/
96+
private findAnalysisProtocolKey(pipelineLinksByAnalysisProtocol: Object, analysisProtocol: string): string {
97+
98+
return Object.keys(pipelineLinksByAnalysisProtocol).find(key => {
9099

91100
return analysisProtocol.includes(key);
92-
})
101+
});
93102
}
94103
}

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