1+ package org .commonwl .view .workflow ;
2+
3+ import org .commonwl .view .cwl .CWLService ;
4+ import org .commonwl .view .github .GitHubService ;
5+ import org .commonwl .view .github .GithubDetails ;
6+ import org .commonwl .view .graphviz .GraphVizService ;
7+ import org .commonwl .view .researchobject .ROBundleFactory ;
8+ import org .eclipse .egit .github .core .RepositoryContents ;
9+ import org .junit .Rule ;
10+ import org .junit .Test ;
11+ import org .junit .rules .TemporaryFolder ;
12+ import org .mockito .Mockito ;
13+ import org .mockito .invocation .InvocationOnMock ;
14+ import org .mockito .stubbing .Answer ;
15+
16+ import java .io .File ;
17+ import java .util .ArrayList ;
18+ import java .util .Date ;
19+ import java .util .HashMap ;
20+ import java .util .List ;
21+
22+ import static org .junit .Assert .assertEquals ;
23+ import static org .junit .Assert .assertTrue ;
24+ import static org .mockito .Matchers .anyObject ;
25+ import static org .mockito .Matchers .anyString ;
26+ import static org .mockito .Mockito .when ;
27+
28+ public class WorkflowServiceTest {
29+
30+ /**
31+ * Folder for test research object bundles
32+ */
33+ @ Rule
34+ public TemporaryFolder roBundleFolder = new TemporaryFolder ();
35+
36+ /**
37+ * Getting a list of workflow overviews from a directory
38+ */
39+ @ Test
40+ public void getWorkflowsFromDirectory () throws Exception {
41+
42+ // Mock Github service redirecting content query to the filesystem
43+ GitHubService mockGithubService = Mockito .mock (GitHubService .class );
44+ Answer contentsAnswer = new Answer <List <RepositoryContents >>() {
45+ @ Override
46+ public List <RepositoryContents > answer (InvocationOnMock invocation ) throws Throwable {
47+ List <RepositoryContents > returnList = new ArrayList <>();
48+
49+ // Add all files from lobstr-v1 directory
50+ File [] fileList = new File ("src/test/resources/cwl/lobstr-v1/" ).listFiles ();
51+ for (File thisFile : fileList ) {
52+ RepositoryContents contentsEntry = new RepositoryContents ();
53+ if (thisFile .isFile ()) {
54+ contentsEntry .setType (GitHubService .TYPE_FILE );
55+ contentsEntry .setSize (100 );
56+ contentsEntry .setName (thisFile .getName ());
57+ contentsEntry .setPath ("workflows/lobSTR/" + thisFile .getName ());
58+ returnList .add (contentsEntry );
59+ }
60+ }
61+
62+ return returnList ;
63+ }
64+ };
65+ when (mockGithubService .getContents (anyObject ())).thenAnswer (contentsAnswer );
66+
67+ // Mock CWL service which returns simple overview once simulating 1 workflow found
68+ CWLService mockCWLService = Mockito .mock (CWLService .class );
69+ when (mockCWLService .getWorkflowOverview (anyObject ()))
70+ .thenReturn (new WorkflowOverview ("workflow.cwl" , "label" , "doc" ))
71+ .thenReturn (new WorkflowOverview ("workflow2.cwl" , "label2" , "doc2" ))
72+ .thenReturn (null );
73+
74+ // Create service under test
75+ WorkflowService testWorkflowService = new WorkflowService (
76+ mockGithubService , mockCWLService ,
77+ Mockito .mock (WorkflowRepository .class ), Mockito .mock (ROBundleFactory .class ),
78+ Mockito .mock (GraphVizService .class ), 1 );
79+
80+ // Get a list of workflows from the directory
81+ List <WorkflowOverview > list = testWorkflowService .getWorkflowsFromDirectory (
82+ Mockito .mock (GithubDetails .class ));
83+
84+ // 1 workflow should be found
85+ assertTrue (list .size () == 2 );
86+ assertEquals ("workflow.cwl" , list .get (0 ).getFileName ());
87+ assertEquals ("label" , list .get (0 ).getLabel ());
88+ assertEquals ("doc" , list .get (0 ).getDoc ());
89+
90+ assertEquals ("workflow2.cwl" , list .get (1 ).getFileName ());
91+ assertEquals ("label2" , list .get (1 ).getLabel ());
92+ assertEquals ("doc2" , list .get (1 ).getDoc ());
93+
94+ }
95+
96+ /**
97+ * Getting a workflow when cache has expired
98+ * And a new workflow needs to be created
99+ */
100+ @ Test
101+ public void getWorkflowCacheHasExpired () throws Exception {
102+
103+ Workflow oldWorkflow = new Workflow ("old" , "This is the expired workflow" ,
104+ new HashMap <>(), new HashMap <>(), new HashMap <>(), null );
105+ oldWorkflow .setId ("theworkflowid" );
106+ oldWorkflow .setRetrievedOn (new Date ());
107+ oldWorkflow .setRetrievedFrom (Mockito .mock (GithubDetails .class ));
108+ oldWorkflow .setLastCommit ("d46ce365f1a10c4c4d6b0caed51c6f64b84c2f63" );
109+ oldWorkflow .setRoBundle (roBundleFolder .newFile ("robundle.zip" ).getAbsolutePath ());
110+
111+ Workflow updatedWorkflow = new Workflow ("new" , "This is the updated workflow" ,
112+ new HashMap <>(), new HashMap <>(), new HashMap <>(), null );
113+ updatedWorkflow .setId ("newworkflowid" );
114+
115+ WorkflowRepository mockWorkflowRepo = Mockito .mock (WorkflowRepository .class );
116+ when (mockWorkflowRepo .findByRetrievedFrom (anyObject ())).thenReturn (oldWorkflow );
117+
118+ CWLService mockCWLService = Mockito .mock (CWLService .class );
119+ when (mockCWLService .parseWorkflow (anyObject (), anyString ())).thenReturn (updatedWorkflow );
120+
121+ // Create service under test with negative cache time (always create new workflow)
122+ WorkflowService testWorkflowService = new WorkflowService (
123+ Mockito .mock (GitHubService .class ), mockCWLService ,
124+ mockWorkflowRepo , Mockito .mock (ROBundleFactory .class ),
125+ Mockito .mock (GraphVizService .class ), -1 );
126+
127+ // Will use check cache algorithm, find expired,
128+ // check github and find commit IDs do not match,
129+ // and thus create a new workflow + matching RO bundle
130+ Workflow workflow = testWorkflowService .getWorkflow (Mockito .mock (GithubDetails .class ));
131+
132+ // Check the new workflow was returned
133+ assertEquals ("newworkflowid" , workflow .getID ());
134+ assertEquals ("new" , workflow .getLabel ());
135+ assertEquals ("This is the updated workflow" , workflow .getDoc ());
136+
137+ }
138+
139+ /**
140+ * Get the research object bundle associated with a workflow
141+ * TODO: Test retry for generation within this method
142+ */
143+ @ Test
144+ public void getROBundle () throws Exception {
145+
146+ Workflow workflow = new Workflow ("Label" , "Doc for the workflow" ,
147+ new HashMap <>(), new HashMap <>(), new HashMap <>(), null );
148+ String roBundlePath = roBundleFolder .newFile ("bundle.zip" ).getAbsolutePath ();
149+ workflow .setRoBundle (roBundlePath );
150+
151+ WorkflowRepository mockWorkflowRepo = Mockito .mock (WorkflowRepository .class );
152+ when (mockWorkflowRepo .findOne (anyString ())).thenReturn (workflow );
153+
154+ // Create service under test
155+ WorkflowService testWorkflowService = new WorkflowService (
156+ Mockito .mock (GitHubService .class ), Mockito .mock (CWLService .class ),
157+ mockWorkflowRepo , Mockito .mock (ROBundleFactory .class ),
158+ Mockito .mock (GraphVizService .class ), -1 );
159+
160+ File fetchedBundle = testWorkflowService .getROBundle ("workflowid" );
161+ assertEquals (roBundlePath , fetchedBundle .getAbsolutePath ());
162+
163+ }
164+
165+ }
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