Plugin test cases 0.8

Search cases

Test case name: UniProt_Ac 1

Operation:

Query box: Q39009 Q9ZNV8

Search type: UniProt_Ac

Taxon id: Any

Iterations: 1

Create new view: no

Use canonical expansion: no

Expected Observation:

33 nodes, 94 edges. 2 queried nodes are blue (DMC_ARATH and AHP2_ARATH). Checked node AHP2_ARATH linkout from i.RefSeq_Ac_TOP attribute to Entrez/protein was correct. IRefIndex has correct i.taxid and i.geneID.

Checked node AHP2_ARATH linkout from i.UniProt_Ac_TOP attribute to UniProt/KB beta was correct. IRefIndex has correct i.taxid and i.geneID. UniProt record agreed with iRefIndex on iRefSeq_Ac_TOP, i.taxid, i.geneID.

Selected two edges between query nodes : EBI-1555390, EBI-1555417. Checked linkouts for both edges (i.src_intxn_id) to Interaction databases/Intact. Confirmed that i.PMID and i.method_name were correct. Viewed EBI-1555390 in MI-XML 2.5 format and confirmed that i.RefSeq_Ac_TOP, i.UniProt_Ac_TOP, i.type_cv, i.type_name were correct. Note that NP_188928.2 was listed by IntAct while i.RefSeq_Ac_TOP listed NP_188928.

Checked linkout to http://wodaklab.org/iRefWeb/interaction/show/102203 from both interactions above.

Last tested: June 1, 2010

Plugin Version: 0.83

Data Version: 7.0 public

Result: PASS

Tester: Ian

Notes:

Test case name: RefSeq_Ac 1

Operation:

Query box: NP_188928.2

Search type: RefSeq_Ac

Taxon id: Any

Iterations: 1

Create new view: yes

Use canonical expansion: no

Expected Observation:

11 nodes, 29 edges. i.RefSeq_Ac = NP_188928 was returned. Edges returned include two edges described in test UniProt_Ac 1.

The same results are returned if the query box is changed to NP_188928.

The same results are returned if the query box is changed to NP_188928.567.

The same results are returned if the query box is changed to 188928. This should return 0 results. FAIL. What if the user meant to search for geneIds and had mistakenly selected this search type. This is an exact match search except for characters trailing the .

No results are returned if the query box is changed to NP 188928. Ok.

Change the search type to UniProt_Ac. The interface says no results and when user presses ok, shows a blank panel. Ok.

The search type can also be changed to UniProt_ID, geneID, geneSymbol, ipi,, mass or rog with no results returned.

No results are returned if the query box is changed to 0. Error message says : Error resolving query. Ok.

No results are returned if the query box is changed to abcde.

Last tested: June 1, 2010

Plugin Version: 0.83

Data Version: 7.0 public

Result: FAIL

Tester: Ian

Notes:

Test case name: UniProt_ID 1

Operation:

Query box: AHP2_ARATH

Search type: UniProt_ID

Taxon id: Any

Iterations: 1

Create new view: yes

Use canonical expansion: no

Expected Observation:

26 nodes, 67 edges.

The same results are returned if the query box is changed to AHP2. FAIL. This should not be allowed. The user might have entered gene names, selected UniProt_ID by mistake and would not be aware of their mistake because their search returned results. Also, first few characters of UniProt_ID's may be shared by multiple proteins from different organisms. If you want to allow for inexact matches, use the query helper.

AHP2 ARATH returns no results. Ok.

ARATH returns "1001 matches and only first 1000 are shown". Ok. Inexact matches trigger the query helper.

AH2_ARATH returns CAH2_ARATH. It should return 0 results. FAIL. Imagine if the user accidently had such a query term imbedded in a long list. They would never detect this search error! This should be is an exact match search by default (or use the query helper to allow the user to decide.

AHP2_ARATH.2 returns results. It should return 0 results. FAIL.

23 returns query helper dialog for disambiguation. Ok. But not very useful in this artificial test case.

Searching for AHP2_ARATH but with search type UniProt_Ac, geneID, geneSymbol, ipi or mass all return 0 results. The interface says no results and when user presses ok, shows a blank panel. Ok.

No results are returned if the query box is changed to 0. Error message says : Error resolving query. Ok.

No results are returned if the query box is changed to abcde.

Last tested: June 1, 2010

Plugin Version: 0.83

Data Version: 7.0 public

Result: FAIL

Tester: Ian

Notes:

Test case name: geneID 1

Operation:

Query box:

821860 822593

Search type: geneID

Taxon id: Any

Iterations: 1

Create new view: yes

Use canonical expansion: no

Expected Observation:

Should return the same result as a UniProt_Ac query for Q39009 and Q9ZNV8 (33 nodes and 94 edges). Ok.

0 returned "error resolving query. Ok.

00001 returned 0 results. Ok.

abcdes returned 0 results. Ok.

1234 returned 34 nodes and 70 edges. Ok. 1234 is CCR5.

Retrieved all geneIds from above query and queried (iterations = 0). Should return same number of nodes as above (33 protein nodes). But 30 protein nodes are returned and there are differences. NOTE. Keep this example for further reference. Explanation. Two of the nodes from the first graph did not have a gene id. Two nodes had the same gene id 7852. If you search for 7852, a graph of 12 nodes, 21 edges is returned. But only one of the nodes has a gene id of 7852. This seems like the search does not continue past the first match found?! FAIL until this is resolved. Also check that all other searches that are exact match searches are "continue after first match found" and write in test cases to ensure that this happens.

The gene in question is CXCR4 and has two isoforms (P61073-2 and P61073).

A geneSymbol search for CXCR4 (iteration=0) returns two nodes as expected.

A UniProt_Ac search for P61073-2 or P61073 each return only one node when use canonical expansion is turned off. Each search returns two nodes when canonical expansion is turned on. By default, canonical expansion should be turned on. A hidden advanced option should be made available to turn this off.

This can be used as a test case for the Export function "on Target network Node ID type"= i.Canonical_ROGID_TOP

Searched 821860 but by each other search type. No results returned in any case. Ok

Last tested: June 1, 2010

Plugin Version: 0.83

Data Version: 7.0 public

Result: FAIL

Tester: Ian

Notes:

Test case name: geneSymbol 1

Operation:

Query box:

CXCR4

Search type: geneSymbol

Taxon id: Any

Iterations: 0

Create new view: yes

Use canonical expansion: no

Expected Observation:

Returns two nodes with i.UniProt_Ac_TOP of P61073 and P61073-2.

Change search to PTK2. The user should be warned that they have not selected a taxon. "You have not limited your search to a specific organism. Proceed anyway? Yes No

FAIL. No warning is given. With no taxon specifier present, the search (iteration=0) returns 6 nodes and 5 taxons. This will create havoc if the user has searched using a list of identifiers.

0 returns no results. Ok.

0000 returns no results. Ok.

12345 returns no results. Ok.

abcde returns no results. Ok.

cxcR4 returns identical results to CXCR4. Ok.

CXCR prompts the user to select from a set of possibilities. Linkouts to NCBI are impossible to use. FAIL. Take this hyperlink feature out until a later release. This should be an exact match search unless the user specifically asks for related terms.

A search for "CXC CXCR CXCR4" returns results identical for CXCR4. Ok. The provides a helper window and a chance to refine the query. User can select one or more specific terms for each ambiguous term (using shift or cntrl keys and pressing return to add the selected items to a new search). The user should be informed of their options. FAIL. Message should read:

"One or more of your query terms did not have an exact match. For each term on the left, you may select one or more of the refined terms on the right (shift-click and cntrl-click are supported). Press return to add the selected terms to a new query. Clear the "Create new view" tick-box if you want to add the results to the current view."

Search CXCR5 as a UniProt_ID, presented user with option for refining the query. Ok

Search CXCR5 against other query types returned no results. Ok.

Last tested: June 1, 2010

Plugin Version: 0.83

Data Version: 7.0 public

Result: FAIL

Tester: Ian

Notes:

Test case name: rog search 1

Searching for something as a rog that has no results hangs the system.

Test case name: Iterations 1

Operation:

Perform search described in test UniProt_Ac 1 with Iterations=1. Then again with Iterations = 0 and confirm that the number of edges between the query nodes is identical.

Expected Observation:

Same number of edges (2 edges, 1 loop) in both cases.

Last tested: June 1, 2010

Plugin Version: 0.83

Data Version: 7.0 public

Result: PASS

Tester: Ian

Notes:

Test case name: ipi 1 #

Operation:

Query box:

IPI00543858 IPI00517160

Search type: ipi

Taxon id: Any

Iterations: 1

Create new view: no

Use canonical expansion: no

Expected Observation:

Returns results identical to test case UniProt_Ac 1. Ok

Changing the query to "IPI00543858.1 IPI00517160.1" produces identical results. Ok.

Changing the query to "00543858 00517160" produces identical results. Ok.

Changing the query to "00543858 0051716" produces identical results for first query term and initiates query helper to resolve second term. Ok.

Changing the query to "abcd" produces no results. Ok.

Changing the query to "IPI" initiates query helper. Ok.

Searching for IPI00543858 as any other search type returns no results. Ok

Last tested: June 1, 2010

Plugin Version: 0.83

Data Version: 7.0 public

Result: PASS

Tester: Ian

Notes:

Test case name: mass search #

Operation:

Query box:

72854<-->72866

Search type: ipi

Taxon id: Any

Iterations: 0

Create new view: yes

Use canonical expansion: no

Expected Observation:

The user is presented with the query helper to refine the query. A prompting message reads:

"One or more of your mass query terms corresponds to a range. You may select one or more of the masses on the right (shift-click and cntrl-click are supported). Press return to add the selected terms to a new query. Clear the "Create new view" tick-box if you want to add the results to the current view."

FAIL. The message given should be replaced with the above text. Also, there are inappropriate and unusable links to NCBI given in the query helper. Also, interface changes my selected iterations from 0 to 1 without asking. Annoying.

The query returns 4 nodes with mass in the expected range. Ok.

0 returns no results. Ok.

-1 returns no results. Ok.

MW returns no results. Ok.

72854 kda returns no results but hangs the interface. FAIL.

Last tested: June 1, 2010

Plugin Version: 0.83

Data Version: 7.0 public

Result: FAIL

Tester: Ian

Notes:

Test case name: example search 1

Operation:

Test the example searches listed at http://irefindex.uio.no/wiki/README_Cytoscape_plugin_0.8x#Using_the_Search_Panel

Test case template

Test case name: what is being tested #

Operation:

Expected Observation:

Last tested:

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Result: FAIL

Tester:

Notes: