Difference between revisions of "Plugin test cases 0.89"

Latest revision as of 17:26, 25 June 2010

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

Load interaction between neighbours: 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.

Last tested: June 25, 2010

Plugin Version: 0.89

Data Version: 7.0 public (iRefDATA_06222010.irfz)

Result: PASS

Tester: Sabry

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

Load interaction between neighbours: 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. No results OK

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. No results. Ok.

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

Last tested: June 25, 2010

Plugin Version: 0.89

Data Version: 7.0 (iRefDATA_06222010.irfz)

Result: PASS

Tester: Sabry

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. No results : PASS

AHP2 ARATH returns no results. Ok.

ARATH no results : OK (Now UniProt_ID is exact match only)

AH2_ARATH returns no results. Ok.

AHP2_ARATH.2 returns no results. OK.

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. No result. Ok.

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

Last tested: June 25, 2010

Plugin Version: 0.83

Data Version: 7.0 public(iRefDATA_06152010.irfz)

Result: PASS

Tester: Sabry

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

Load interaction between neighbours: 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.

Last tested: June 25, 2010

Plugin Version: 0.89

Data Version: 7.0 public (iRefDATA_06222010.irfz)

Result: PASS

Tester: Sabry

Test case name: geneSymbol 1

Operation:

Query box:

CXCR4

Search type: geneSymbol

Taxon id: Any

Iterations: 0

Create new view: no

Use canonical expansion: no

Expected Observation:

Warning for user : "You have not limited your search to a specific organism. Proceed anyway? Yes No - Yes selected

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

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.

Link-outs to NCBI : removed, query Helper removed (Exact match search will not use query helper)

Search CXCR5 as a UniProt_ID : No results , UniProt_Id is now exact match only

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

Last tested: June 25, 2010

Plugin Version: 0.89

Data Version: 7.0 public (iRefDATA_06222010.irfz)

Result: PASS

Tester: Sabry

Test case name: rog search 1

Operation:

Query box:

5366033

Search type: rog

Taxon id: Any

Iterations: 1

Create new view: no

Use canonical expansion: no

Load interaction between neighbours: no

Expected Observation: 5366033 returns 7 interactions (5 self interactions + 2 interactions with 5366026)

Last tested: June 25, 2010

Plugin Version: 0.89

Data Version: 7.0 public (iRefDATA_06222010.irfz)

Result: PASS

Tester: Sabry

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 25, 2010

Plugin Version: 0.89

Data Version: 7.0 public(iRefDATA_06222010.irfz)

Result: PASS

Tester: Sabry

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

Load interaction between neighbours: 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 25, 2010

Plugin Version: 0.89

Data Version: 7.0 public(iRefDATA_06222010.irfz)

Result: PASS

Tester: Sabry

Notes:

Test case name: mass search #

Operation:

Query box:

72854<-->72866

Search type: mass

Taxon id: Any

Iterations: 0

Create new view: yes

Use canonical expansion: no

Load interaction between neighbours: no

Expected Observation:

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

Please select query from list (double click from yellow area)

Result: PASS

NCBI links removed.

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 . OK

Last tested: June 25, 2010

Plugin Version: 0.89

Data Version: 7.0 public (iRefDATA_06152010.irfz)

Result: PASS

Tester: Sabry

Notes: . The details in the sugested message ealier by Ian now included as a Tool-tip

Test case name: rog search 1

Operation:

Query box:

5366033

Search type: rog

Taxon id: Any

Iterations: 1

Create new view: no

Use canonical expansion: no

Load interaction between neighbours: no

Expected Observation: 5366033 returns 7 interactions (5 self interactions + 2 interactions with 5366026)

Last tested: June 25, 2010

Plugin Version: 0.89

Data Version: 7.0 public (iRefDATA_06222010.irfz)

Result: PASS

Tester: Sabry

Test case name: PMIDsearch 1

Operation:

Query box:

11401546

Search type: pmid

Taxon id: Any

Iterations: 1

Create new view: yes

Use canonical expansion: no

Load interaction between neighbours: no

Expected Observation:

4 nodes and 7 edges are returned. Three edges have PMID 11401546 and these involve the 4 nodes shown. All other edges (from different PMIDs) involve these proteins. Ok.

i.query for all four node set to 11401546 : Ok

11401546.1 returns 0 results. Ok.

1140154 returns 0 results Ok.

SPTAN1 returns 0 results. Ok.

11401546 SPTAN1 returns 0 results. Ok.

0 returns 0 results. Ok.

-1 returns 0 results. Ok.

10551855 [return character] 11401546 returns 6 nodes and 27 edges. Ok.

10551855|11401546 returns 6 nodes and 27 edges. Ok.

10551855| 11401546 returns 6 nodes and 27 edges. Ok.

10551855 | 11401546 returns 6 nodes and 27 edges. Ok.

10551855 [tab] 11401546 returns 6 nodes and 27 edges. Ok.

10551855, 11401546 returns 6 nodes and 27 edges. Ok.

10551855 11401546 returns 0 results. Ok. We dont say we support space delimited queries.

Last tested: June 25, 2010

Plugin Version: 0.89

Data Version: 7.0 public(iRefDATA_06222010.irfz)

Result: PASS

Tester: Sabry

Notes:

Test case name: digid search 1

Operation:

Query box: 4

Search type: digid

Taxon id: Any

Iterations: 0

Create new view: no

Use canonical expansion: no

Load interaction between neighbours: no

Expected Observation:

This query returns : 228 nodes and 389 edges

Two nodes with i.query=4 (Q96RQ3 and Q9HCC0)

Last tested: July 25th, 2010

Plugin Version: 0.89

Data Version: public 7.0 (iRefDATA_06222010.irfz)

Result: PASS

Tester: Sabry

Test case template

Test case name: what is being tested #

Operation:

Expected Observation:

Last tested:

Plugin Version:

Data Version:

Result: FAIL

Tester:

Notes:

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Difference between revisions of "Plugin test cases 0.89"

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Latest revision as of 17:26, 25 June 2010

Contents

Search cases

Test case name: UniProt_Ac 1

Test case name: RefSeq_Ac 1

Test case name: UniProt_ID 1

Test case name: geneID 1

Test case name: geneSymbol 1

Test case name: rog search 1

Test case name: Iterations 1

Test case name: ipi 1 #

Test case name: mass search #

Test case name: rog search 1

Test case name: PMIDsearch 1

Test case name: digid search 1

Test case template

Test case name: what is being tested #

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@@ Line 28: / Line 28: @@
 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 25, 2010'''
@@ Line 61: / Line 56: @@
 Use canonical expansion: no
+Load interaction between neighbours: no
 '''Expected Observation: '''
@@ Line 78: / Line 75: @@
 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 '''0'''.  No results. Ok.
 No results are returned if the query box is changed to '''abcde'''.
-'''Last tested: June 15, 2010'''
+'''Last tested: June 25, 2010'''
 '''Plugin Version: '''0.89
-'''Data Version: '''7.0 public(iRefDATA_06152010.irfz)
+'''Data Version: '''7.0 (iRefDATA_06222010.irfz)
 '''Result: ''' '''PASS'''
 '''Tester: '''Sabry
-<span style="color:red">'''Notes: ''':(SABRY)</span> : The index file name was included the control tag  _EXT_ (To perform only exact matches)
 ===Test case name: UniProt_ID 1 ===
@@ Line 131: / Line 126: @@
 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 '''0'''. No result. Ok.
 No results are returned if the query box is changed to '''abcde'''.
-'''Last tested: June 1, 2010'''
+'''Last tested: June 25, 2010'''
 '''Plugin Version: '''0.83
-'''Data Version: '''7.0 public
+'''Data Version: '''7.0 public(iRefDATA_06152010.irfz)
 '''Result: '''  '''PASS'''
-'''Tester: '''Ian
+'''Tester: '''Sabry
-<span style="color:red">'''Notes: ''':(SABRY)</span> : UniProt_ID is now EXACT match only. If the user failed to enter exactly matching query no results will be returned. Query helper will never be invoked.
 ===Test case name: geneID 1 ===
@@ Line 166: / Line 159: @@
 Use canonical expansion: no
+Load interaction between neighbours: no
 '''Expected Observation: '''
@@ Line 179: / Line 174: @@
 returned 34 nodes and 70 edges.  Ok.  1234 is CCR5.
-<span style="color:red">'''Expected results by Ian----------------------------- '''</span>
+'''Last tested: June 25, 2010'''
-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
-<span style="color:red">'''Expected results by Ian END.------------------ '''</span>
-<span style="color:red">'''Expected results by Sabry----------------------------- '''</span>
-# Steep 1
-Search for
-*Search type: geneID
-*Taxon id: Any
-*Iterations: 1
-*Create new view: no
-*Use canonical expansion: no
-Returns 33 nodes and 94 edges.
-# Steep 2
-collect all GeneIds from the above search and search for ZERO order interactions.
-*814707|814714|814714|817659|818662|818730|819356|819583|820940|821860|822593|823965|824871|827076|827297|828230|829038|829322
-|832208|833552|837587|838487|839621|842288|842783|842951|854659
-*Search type: geneID
-*Taxon id: Any
-*Iterations: 1
-*Create new view: yes
-*Use canonical expansion: no
-*Result: 29 nodes and 125 Edges returned. This is what was expected and works according to the implementation.
-*Reason for having different node count than Step one: 4 of the nodes in Step one did not have GeneIds.   Two nodes had the same GeneId (814714)
-*Reason for having different Edge count than step one: The two searches are different. The step 1 search for interactions of the products of the 2 genes. The second step searches for interactions in between the list of genes. So we will get more interactions in second step. This is because in the second step we will get interactions between nodes which were first order neighbors in the step 1.
-'''e.g. the interaction between 829322 and 814707 will not be shown in step one. because they are neighbors of the query proteins.'''
-Other observation by Ian using GeneID=7852 can not be reproduced as this Geneid never returned in my search for  821860 and 822593.
-<span style="color:red">'''Expected results by Sabry END.------------------ '''</span>
-'''Last tested: June 15, 2010'''
 '''Plugin Version: '''0.89
-'''Data Version: '''7.0 public
+'''Data Version: '''7.0 public (iRefDATA_06222010.irfz)
-'''Result: ''' '''FAIL''' (Zero order search algorithm need to be totally changed to achieve what has requested)
+'''Result: ''' '''PASS'''
 '''Tester: '''Sabry
-<span style="color:red">'''Notes: ''':(SABRY)</span> :
 ===Test case name: geneSymbol 1 ===
@@ Line 276: / Line 224: @@
 Search CXCR5 against other query types returned no results.  Ok.
-'''Last tested: June 15, 2010'''
+'''Last tested: June 25, 2010'''
 '''Plugin Version: '''0.89
-'''Data Version: '''7.0 public (iRefDATA_06152010.irfz)
+'''Data Version: '''7.0 public (iRefDATA_06222010.irfz)
 '''Result: '''  '''PASS'''
 '''Tester: '''Sabry
-<span style="color:red">'''Notes: ''':(SABRY)</span> :
-# hyperlink removed
-# The default batch file mode the user has to specify a taxonid, this was overridden as requested in an earlier release should this be reactivated as well?.
-===Test case name: geneSymbol 2 ===
-'''Operation: '''
-Query box:
-RPB1
-Search type: geneSymbol
-Taxon id: Any
-Iterations: 0
-Create new view: yes
-Use canonical expansion: no
-Warning for user : "You have not limited your search to a specific organism. Proceed anyway? Yes No - Yes selected
-'''Expected Observation: '''
-RPB1 for any taxon returns 1 node (RPB1_SCHPO).  Ok.
-RPB1 for taxon 4932 returns 0 nodes.  Ok.
-RPB1 for taxon 9606 returns 0 nodes.  Ok.
-'''Last tested: June 15, 2010'''
-'''Plugin Version: '''0.89
-'''Data Version: '''7.0 public (iRefDATA_06152010.irfz)
-'''Result: '''  '''PASS'''
-'''Tester: '''Sabry
-<span style="color:red">'  ''Notes: ''':(SABRY)</span> :Changed to  exact search. query helper will never pop-up.
 ===Test case name: rog search 1===
@@ Line 346: / Line 251: @@
 Use canonical expansion: no
+Load interaction between neighbours: no
 '''Expected Observation: '''
 5366033 returns 7 interactions (5 self interactions + 2 interactions with 5366026)
-(When canonical expansion turned on, 338 interactions and 96 nodes NP_057849,NP_705926,NP_705927,NP_705928,NP_789739,NP_789740,P04585)
-'''Last tested: June 14, 2010'''
+'''Last tested: June 25, 2010'''
 '''Plugin Version: '''0.89
-'''Data Version: '''7.0 public
+'''Data Version: '''7.0 public (iRefDATA_06222010.irfz)
 '''Result: '''  '''PASS'''
 '''Tester: '''Sabry
-<span style="color:red">'  ''Notes: ''':(SABRY)</span> The bug coursing freeze when performing ROG searches now fixed
 ===Test case name: Iterations 1===
@@ Line 372: / Line 278: @@
 Same number of edges (2 edges, 1 loop) in both cases.
-'''Last tested: June 1, 2010'''
+'''Last tested: June 25, 2010'''
-'''Plugin Version: '''0.83
+'''Plugin Version: '''0.89
-'''Data Version: '''7.0 public
+'''Data Version: '''7.0 public(iRefDATA_06222010.irfz)
 '''Result: '''PASS
-'''Tester: '''Ian
+'''Tester: '''Sabry
 '''Notes: '''
 ===Test case name: ipi 1 #===
@@ Line 403: / Line 308: @@
 Use canonical expansion: no
+Load interaction between neighbours: no
 '''Expected Observation: '''
@@ Line 420: / Line 327: @@
 Searching for IPI00543858 as any other search type returns no results.  Ok
-'''Last tested: June 1, 2010'''
+'''Last tested: June 25, 2010'''
-'''Plugin Version: '''0.83
+'''Plugin Version: '''0.89
-'''Data Version: '''7.0 public
+'''Data Version: '''7.0 public(iRefDATA_06222010.irfz)
 '''Result: '''PASS
-'''Tester: '''Ian
+'''Tester: '''Sabry
 '''Notes: '''
 ===Test case name: mass search #===
@@ Line 450: / Line 356: @@
 Use canonical expansion: no
+Load interaction between neighbours: no
 '''Expected Observation: '''
@@ Line 455: / Line 363: @@
 The user is presented with the query helper to refine the query.  A prompting message reads:
-The following message included, the message is very long and there is no new line in message pop-up
+Please select query from list (double click from yellow area)
-"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."
+Result: PASS
-Message too long : FAIL
@@ Line 474: / Line 380: @@
 kda returns no results . OK
-'''Last tested: June 15, 2010'''
+'''Last tested: June 25, 2010'''
 '''Plugin Version: '''0.89
@@ Line 480: / Line 386: @@
 '''Data Version: '''7.0 public (iRefDATA_06152010.irfz)
-'''Result: '''FAIL
+'''Result: '''PASS
-'''Tester: '''Sabry (Message can not be displayed in full)
+'''Tester: '''Sabry
-'''Notes: '''
+'''Notes: ''' . The details in the sugested message ealier by Ian now included as a Tool-tip
 ===Test case name: rog search 1===
+'''Operation: '''
+Query box:
+5366033
+Search type: rog
+Taxon id: Any
+Iterations: 1
+Create new view: no
+Use canonical expansion: no
+Load interaction between neighbours: no
+'''Expected Observation: '''
+5366033 returns 7 interactions (5 self interactions + 2 interactions with 5366026)
+'''Last tested: June 25, 2010'''
+'''Plugin Version: '''0.89
+'''Data Version: '''7.0 public (iRefDATA_06222010.irfz)
+'''Result: '''  '''PASS'''
+'''Tester: '''Sabry
 ===Test case name: PMIDsearch 1===
@@ Line 504: / Line 438: @@
 Taxon id: Any
-Iterations: 0
+Iterations: 1
 Create new view: yes
 Use canonical expansion: no
+Load interaction between neighbours: no
 '''Expected Observation: '''
@@ Line 514: / Line 450: @@
 nodes and 7 edges are returned.  Three edges have PMID 11401546 and these involve the 4 nodes shown.
 All other edges (from different PMIDs) involve these proteins.  Ok.
+i.query for all four node set to 11401546 : Ok
 11401546.1 returns 0 results.  Ok.
@@ Line 541: / Line 479: @@
 10551855 11401546 returns 0 results.  Ok. We dont say we support space delimited queries.
-'''Last tested: June 16, 2010'''
+'''Last tested: June 25, 2010'''
 '''Plugin Version: '''0.89
-'''Data Version: '''7.0 public
+'''Data Version: '''7.0 public(iRefDATA_06222010.irfz)
 '''Result: '''PASS
@@ Line 552: / Line 490: @@
 '''Notes: '''
-===Test case name: src_intxn_id search 1===
-===Test case name: omim search 1===
 ===Test case name: digid search 1===
@@ Line 573: / Line 507: @@
 Use canonical expansion: no
-'''Expected Observation: '''
+Load interaction between neighbours: no
-This query returns no results.  FAIL.
-Because queries for gene ids 56922 and 64087 return those nodes for those queries that have expected i.omim results (210210 and 210200) and both of these nodes have i.digid of 4.
-A similar search for digid 449 returns 24 nodes and 252 edges that seem reasonable - each protein node has a list of digids where at least one is 449. - Ok
-A similar search for digid 449 but with "use canonical expansion" returns 28 nodes.  The four additional nodes seem reasonable - they are FANCL, FANCD2 FANCI and BRCA2.  BRCA2 has a known role in FA.  Ok.
-'''Last tested: July 17th, 2010'''
-'''Plugin Version: 0.89'''
-'''Data Version: public 7.0'''
-'''Result: '''  '''FAIL'''
-'''Tester: Ian'''
-<span style="color:red">'''Notes: ''':(SABRY)</span> : Single digit matching was blocked in beta 0.89 and now I have enable it. Noe even if the user enters a 0 or a 1 as query the complete search operation will proceed.
-===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
-Query box: see below
-Search type: see below
-Taxon id: Any
-Iterations: 1
-Create new view: yes
-Use canonical expansion: yes
-'''Expected Observation: '''
-{|class="wikitable" style="text-align:left" border="1" cellpadding="5"
-!width="50" align="center" style="background:#f0f0f0;"|Search Type
-!width="50" align="center" style="background:#f0f0f0;"|Example
-!width="500" align="center" style="background:#f0f0f0;"|Results
-|-
-| UniProt_Ac||Q7KSF4||67 nodes, 146 edges. 1 blue node with i.order=0 directly from query. 3 with blue nodes i.order=10 by canonical expansion. All 4 blue nodes has the i.query attribute=Q7KSF4
-|-
-| RefSeq_Ac||NP_996224||67 nodes, 146 edges.  i.query updated to Q7KSF4|NP_996224
-|-
-| UniProt_ID||Q7KSF4_DROME||67 nodes, 146 edges. i.query updated to  Q7KSF4|NP_996224|Q7KSF4_DROME
-|-
-| geneID||42066||67 nodes, 146 edges. i.query updated to Q7KSF4|NP_996224|Q7KSF4_DROME|42066
-|-
-| geneSymbol||cher||67 nodes, 146 edges. i.query updated to Q7KSF4|NP_996224|Q7KSF4_DROME|42066|CHER
-|-
-| mass||72854<-->72866||44 nodes, 97 edges. Four molecular mass values are returned by the query helper.  Selecting all of these and doing the search returns 10 blue nodes and their interactors.  The 72855 mass node returns 1 node with that mass and three other members of the same canonical group.   Two of the nodes are returned with i.query=Q7KSF4|NP_996224|Q7KSF4_DROME|42066|CHER and Q7KSF4|Q7KSF4_DROME|42066|CHER and they are blue. This is because the connectivity of properties between views of cytoscape (we have visted this problem before and agreed to live with the outcome).
-|-
-| rog||10121899||FAIL.  This  return interactions of Q7KSF4
-|-
-| PMID||14605208||929 nodes and 1605 edges returned all with PMID of 14605208.  SAme results if iteration is set to 0. Ok.  Same results if canonical expansion is de-selected.  Ok.
-|-
-| src_intxn_id||47513|| 2 nodes and 1 edge returned.
-|-
-| src_intxn_id||EBI-212627|| 2 nodes and 4 edges returned (2 from intact, 1 from BIND and 1 from MINT).  Ok
-|-
-| src_intxn_id||147805||Returns 4 nodes and three interactions because BIND and BioGRID interaction id space overlap.
-|-
-| omim||227650||74 nodes and 224 edges returned.  Ok.
-|-
-| digid||449||498 nodes and 61033 edges returned.
-|-
-| dig_title||fanconi|| No index available for dig_title
-|-
-|}
-'''Last tested: June 16, 2010'''
-'''Plugin Version: '''0.89
-'''Data Version: '''7.0 public
-'''Result: '''FAIL (Results are not 100% compatible with what is requested, dig_title can not be distributed due to license)
-'''Tester: '''Sabry
-'''Notes: '''
-===Test case name: audit against external database - Intact===
-===Test case name: audit against external database - MINT===
-===Test case name: audit against external database - BioGRID===
-===Test case name: iterations 1===
-===Test case name: use canonical expansion 1===
-==Advanced options cases==
-==Preferences==
-===Test case name: what is being tested #===
-'''Operation: '''
-'''Expected Observation: '''
-'''Last tested: July 8, 2010'''
-'''Plugin Version: 0.83'''
-'''Data Version: 7.0'''
-'''Result: '''  '''FAIL'''
-'''Tester: Ian'''
-'''Notes: '''
-==iRefScape menu cases==
-===Show spoke-represented complexes===
-====Test case name: checking generated complexes belong to same pmid, db  and method====
-'''Operation: '''
-Query box:
- 17353931
-Search type: PMID
-Taxon id: 9606
-Iterations: 1
-Create new view: no
-Use canonical expansion: no
-Search & load
-Menu: iRefScape / View tools / Show spoke-represented complexes
-Filter1:
- Attribute: i.rog
- Condition: EQUAL
- Value: QEwKzfSB6ZCaXBi6jSNiTCIeAtg
- Selection: Show_as_selected
- Set i.alive: Do_not_change
-Press Set selected
-Filter2:
- Attribute: i.rog
- Condition: EQUAL
- Value: QEwKzfSB6ZCaXBi6jSNiTCIeAtg
- Selection: Append_neighbours
- Set i.alive: Do_not_change
-Press Set selected
-Menu iRefScape / Hide/Un-hide / Hide nodes not selected
-Menu Layout / Cytoscape Layouts / Degree Sorted Circle Layout
 '''Expected Observation: '''
-All interactions in the complex belong to same DB and same experimental method.
+This query returns : 228 nodes and 389 edges
-'''Last tested: '''
+Two nodes with i.query=4 (Q96RQ3 and Q9HCC0)
-June 18, 2010
-'''Plugin Version: '''
+'''Last tested: July 25th, 2010'''
-.89
-'''Data Version: '''
-iRefIndex 7.0
-'''Result: '''  '''PASS'''
-intact interactions and 1 grid interaction appeared, but grid's interaction is the same than one in intact.
-'''Tester: '''
-Antonio Mora
-====Test case name: comparing number of preys for a given bait, with the same method, pmid and sourcedb, between iRefScape and iRefIndex MITAB====
-'''Operation: '''
-Query box:
- 17353931
-Search type: PMID
-Taxon id: 9606
-Iterations: 1
-Create new view: no
-Use canonical expansion: no
-Search & load
-Menu: iRefScape / View tools / Show spoke-represented complexes
-Filter1:
- Attribute: i.rog
- Condition: EQUAL
- Value: 4761161
- Selection: Show_as_selected
- Set i.alive: Do_not_change
-Press Set selected
-Filter2:
- Attribute: i.rog
- Condition: EQUAL
- Value: 4761161
- Selection: Append_neighbours
- Set i.alive: Do_not_change
-Press Set selected
-Menu iRefScape / Hide/Un-hide / Hide nodes not selected
-Menu Layout / Cytoscape Layouts / Degree Sorted Circle Layout
-'''Expected Observation: '''
-There are 97 preys in iRefIndex for bait=4761161, pmid=17353931, sourcedb=INTACT and method="MI:0006"
-'''Last tested: '''
-June 18, 2010
-'''Plugin Version: '''
-.89
-'''Data Version: '''
-iRefIndex 7.0
-'''Result: '''  '''FAIL'''
-Only 10 interactions reported in iRefScape.
-Besides that, iRefScape generates two complexes, one of which is a subset of the other. In R, we are removing the small one.
-'''Tester: '''
-Antonio Mora
-====Test case name: ability to show complexes generated by R, using rogIDs====
-'''Operation: '''
-Query box:
-Search type: rog
-Taxon id: 9606
-Iterations: 2
-Create new view: no
-Use canonical expansion: no
-Search & load
-Menu: iRefScape / View tools / Show spoke-represented complexes
-Filter1:
- Attribute: i.rog
- Condition: EQUAL
- Value: 991650
- Selection: Show_as_selected
- Set i.alive: Do_not_change
-Press Set selected
-Filter2:
- Attribute: i.rog
- Condition: EQUAL
- Value: 991650
- Selection: Append_neighbours
- Set i.alive: Do_not_change
-Press Set selected
-Menu iRefScape / Hide/Un-hide / Hide nodes not selected
-Menu Layout / Cytoscape Layouts / Degree Sorted Circle Layout
-'''Expected Observation: '''
-complexes, all with a very high number of members (all >30, some >100).
-'''Last tested: '''
-June 18, 2010
-'''Plugin Version: '''
-.89
-'''Data Version: '''
-iRefIndex 5.1 in R, and iRefIndex 7.0 in the plugin
-'''Result: '''  '''FAIL'''
-complexes with small degree. 6 of them are heterodimers and not considered as complexes in R. The other one has only 3 components.
-'''Tester: '''
-Antonio Mora
-====Test case name: ability to show complexes generated by R, using PMIDs====
-'''Operation: '''
-Query box:
- 17353931
-Search type: PMID
-Taxon id: 9606
-Iterations: 1
-Create new view: no
-Use canonical expansion: no
-Search & load
-Menu: iRefScape / View tools / Show spoke-represented complexes
-Filter1:
- Attribute: i.order
- Condition: EQUAL
- Value: -4
- Selection: Show_as_selected
- Set i.alive: Do_not_change
-Press Set selected
-Filter2:
- Attribute: i.order
- Condition: EQUAL
- Value: -4
- Selection: Append_neighbours
- Set i.alive: Do_not_change
-Press Set selected
-'''Expected Observation: '''
-complexes expected.
-'''Last tested: '''
-June 18, 2010
-'''Plugin Version: '''
-.89
-'''Data Version: '''
-iRefIndex 5.1 in R, and iRefIndex 7.0 in the plugin
-'''Result: '''  '''FAIL'''
-complexes were generated.
-'''Tester: '''
-Antonio Mora
-===Select between nodes===
-====Test case name: Select between nodes 1====
-'''Operation: '''
-Query box: 449
-Search type: digid
-Taxon id: Any
-Iterations: 0
-Create new view: no
-Use canonical expansion: no
-'''Expected Observation: '''
-This query returns 24 nodes (10 are pseudonodes) and 252 edges - ok.
-Select all protein nodes and then select iRefScape menu/View tools/Select between nodes.
-All pseudonodes are now selected as expected. Ok.  Sorted these selected nodes based on i.alive_degree.
-Selected first node in list (i.alive_degree of 7) and then select first neighbours of this node 7 nodes are selected as expected - Ok. i.alive_degree was zero for three of the protein nodes (initially selected).  These had either no neighbours or pseudonode neighbours - so i.alive_degree was recalculated properly. Ok.
-Selected just one protein node and then Select between nodes.  Error message says "select at least two nodes first".  Good.
-Selected just two protein nodes (FANCI_HUMAN and BRCA2_HUMAN) then Select between nodes.  Only one node was correctly returned (FACD2_HUMAN) and view recentres on this.  Good.  This node has i.alive_degree of 2 as expected.  Ok.  All other nodes had either a i.alive_degree of 1 (they were adjacent to only one of the two nodes selected as expected) or zero as expected - so i.alive_degree was correctly recalculated. Ok.
-'''Last tested: June 17th, 2010'''
 '''Plugin Version: 0.89'''
-'''Data Version: public 7.0'''
+'''Data Version: public 7.0''' (iRefDATA_06222010.irfz)
 '''Result: '''  '''PASS'''
-'''Tester: Ian'''
+'''Tester: Sabry'''
-'''Notes: '''
-====Test case name: Select between nodes 2====
-'''Operation: '''
-Query box: 449
-Search type: digid
-Taxon id: Any
-Iterations: 1 (note difference to above test)
-Create new view: yes
-Use canonical expansion: no
-'''Expected Observation: '''
-This query returns 498 nodes and 1033 edges - ok.
-Select all nodes with i.query of 449 and then select iRefScape menu/View tools/Select between nodes.
-nodes are selected (11 are pseudonodes).
-Made a new integer feature i.isBetween and marked all 43 nodes as 1.  CAUTION. There is no other way to retrieve these nodes if the user deselects them (except by redoing the search); i.alive_degree => 2 cannot be used to retrieve them because some nodes from the original query list now have (correctly) a i.alive_degre of => 2.  Consider adding a feature for the user called i.isBetween for the user.
-Now I want to create a graph of 1) the original query nodes and 2) the between nodes.  This is difficult because I cant select the original query nodes using Cytoscape filters - this seems to be a bug in Cytoscape filters . I can filter on i.query =449 or i.isBetween = 1 BUT NOT ON BOTH!  Try doing this with iRefScape filters too -  I cant do this either. CAUTION.
-In the end, I sort all nodes on i.isBetween and then on i.query using the node attribute browser and then select those nodes I want from the table.  Then I create a new subgraph from the selected nodes and edges.  59 nodes and 443 edges.
-CAUTION.  This functionality needs to be made easier for the user.  Maybe keep original selection plus between nodes as selected.  Also mark between nodes with new feature called i.isBetween.  Could make the new network for the user.
-Consider more messaging to user.
-) Between nodes now have feature i.isBetween = 1.  Ok.
-) i.alive_degree has been recalculated for all nodes.  Ok.
-) Create new subgraph with between nodes and original selection.  Yes. No.
-'''Last tested: June 17th, 2010'''
-'''Plugin Version: 0.89'''
-'''Data Version: public 7.0'''
-'''Result: '''  '''PASS'''
-'''Tester: Ian'''
-<span style="color:red">'''Notes: ''':(SABRY)</span> : As we have removed the earlier feature calculate node degree related to selected nodes and replaced it between nodes the generalization is lost. I believe we could achieve what you wanted here very easily with iRefScape filters (may be I am wrong). discuss with Ian before making any changes.
-e.g use Cytoscape filter to select nodes interacting with at least two things in the query list for iteration =1 AND was not in the query list.
-# Filter-1 using following settings {i.order=0;condition=EQULA;Value=0; Selection=Show as selected; Set i.alive=True for this condition} *Use i.query instead of i.order if there were mutiple searches during same session.
-# Filter -2 using following settings {i.alive_degree=2;condition=GREATER_THAN_OR_EQULA;Value=2; Selection=Slect_not_in_current_selection; Set i.alive=do_not_change for this condition}
-==Right-click menu cases==
-==Node attribute cases==
-==Edge attribute cases==
-==Wizard cases==
-==Installations cases==
-==Help cases==
-==Windows and sessions cases==
-===Test case name: Load from file search 1 #===

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Difference between revisions of "Plugin test cases 0.89"

Latest revision as of 17:26, 25 June 2010

Contents

Search cases

Test case name: UniProt_Ac 1

Test case name: RefSeq_Ac 1

Test case name: UniProt_ID 1

Test case name: geneID 1

Test case name: geneSymbol 1

Test case name: rog search 1

Test case name: Iterations 1

Test case name: ipi 1 #

Test case name: mass search #

Test case name: rog search 1

Test case name: PMIDsearch 1

Test case name: digid search 1

Test case template

Test case name: what is being tested #

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