Class jalview.gui.StructureChooserTest

4

tests

0

failures

0

ignored

0.781s

duration

100%

successful

Tests

Test Duration Result
displayTDBQueryTest 0.291s passed
fetchStructuresInfoMockedTest 0.318s passed
populateFilterComboBoxTest 0.171s passed
sanitizeSeqNameTest 0.001s passed

Standard output

registry.getSupportedServices: [MSAprobsWS, DisemblWS, TcoffeeWS, RNAalifoldWS, MafftWS, IUPredWS, GlobPlotWS, ProbconsWS, AAConWS, JronnWS, ClustalWS, MuscleWS, ClustalOWS, GLprobsWS]
Attempting to connect with MafftWS...
https://www.ebi.ac.uk/pdbe/search/pdb/select?wt=json&fl=pdb_id,title,experimental_method,resolution&rows=500&start=0&q=(uniprot_accession:P38398+OR+uniprot_id:P38398)+AND+molecule_sequence:%5B''+TO+*%5D+AND+status:REL&sort=overall_quality+desc
query >>>>>>> jalview.fts.core.FTSRestRequest@31560a27
>>> JOption Message : 400 response (Mocked)

Discovered service: http://www.compbio.dundee.ac.uk/jabaws jalview.ws.jws2.jabaws2.Jws2Instance@39160d24
https://www.ebi.ac.uk/pdbe/pdbe-kb/3dbeacons/api/uniprot/summary/P38398.json
https://www.ebi.ac.uk/pdbe/search/pdb/select?wt=json&fl=pdb_id,title,experimental_method,resolution&rows=500&start=0&q=(4igk+OR+7lyb+OR+3k0h+OR+3k0k+OR+1t15+OR+3pxc+OR+3pxd+OR+3pxe+OR+1jm7+OR+7jzv+OR+3pxa+OR+3pxb+OR+1y98+OR+1n5o+OR+4ifi+OR+4y2g+OR+3k15+OR+3k16+OR+4jlu+OR+2ing+OR+4ofb+OR+6g2i+OR+3coj+OR+1jnx+OR+4y18+OR+4u4a+OR+1oqa+OR+1t29+OR+1t2u+OR+1t2v)+AND+molecule_sequence:%5B''+TO+*%5D+AND+status:REL&sort=
query >>>>>>> jalview.fts.core.FTSRestRequest@20e31d20
Attempting to connect with MuscleWS...
https://www.ebi.ac.uk/pdbe/pdbe-kb/3dbeacons/api/uniprot/summary/P38398.json
https://www.ebi.ac.uk/pdbe/search/pdb/select?wt=json&fl=pdb_id,title,experimental_method,resolution&rows=500&start=0&q=(4igk+OR+7lyb+OR+3k0h+OR+3k0k+OR+1t15+OR+3pxc+OR+3pxd+OR+3pxe+OR+1jm7+OR+7jzv+OR+3pxa+OR+3pxb+OR+1y98+OR+1n5o+OR+4ifi+OR+4y2g+OR+3k15+OR+3k16+OR+4jlu+OR+2ing+OR+4ofb+OR+6g2i+OR+3coj+OR+1jnx+OR+4y18+OR+4u4a+OR+1oqa+OR+1t29+OR+1t2u+OR+1t2v)+AND+molecule_sequence:%5B''+TO+*%5D+AND+status:REL&sort=
query >>>>>>> jalview.fts.core.FTSRestRequest@5d95c7c2
Discovered service: http://www.compbio.dundee.ac.uk/jabaws jalview.ws.jws2.jabaws2.Jws2Instance@59d41672
https://www.ebi.ac.uk/pdbe/search/pdb/select?wt=json&fl=pdb_id,title,experimental_method,resolution&rows=500&start=0&q=(pdb_id:1tim)+AND+molecule_sequence:%5B''+TO+*%5D+AND+status:REL&sort=overall_quality+desc
query >>>>>>> jalview.fts.core.FTSRestRequest@23f6732a
>>> JOption Message : 400 response (Mocked)

Attempting to connect with ClustalWS...
Items (no data, no cache): 

Standard error

Rebuild WS Menu for service change
Rebuild WS Menu for service change
Rebuild WS Menu for service change
Rebuild WS Menu for service change
Rebuild WS Menu for service change
Rebuild WS Menu for service change
Rebuild WS Menu for service change
Rebuild WS Menu for service change
DEBUG - Displaying news.
Jul 02, 2023 10:12:01 AM compbio.ws.client.Jws2Client connectToRegistry
INFO: Connected to RegistryWS successfully!
DEBUG - Scanning news items: newsnew=false and lastDate is Fri Jun 30 20:04:22 CEST 2023
DEBUG - Saved last read date as 30 Jun 2023, 20:04:22
java.lang.Exception: 400 response (Mocked)
	at jalview.fts.service.pdb.PDBFTSRestClient.executeRequest(PDBFTSRestClient.java:232)
	at jalview.gui.structurechooser.PDBStructureChooserQuerySource.fetchStructuresMetaData(PDBStructureChooserQuerySource.java:254)
	at jalview.gui.StructureChooser.fetchStructuresMetaData(StructureChooser.java:479)
	at jalview.gui.StructureChooser.initialStructureDiscovery(StructureChooser.java:242)
	at jalview.gui.StructureChooser$2.run(StructureChooser.java:209)
	at java.base/java.lang.Thread.run(Thread.java:829)
DEBUG - Scanning news items: newsnew=false and lastDate is Fri Jun 30 20:04:22 CEST 2023
DEBUG - Saved last read date as 30 Jun 2023, 20:04:22
DEBUG - Scanning news items: newsnew=false and lastDate is Fri Jun 30 20:04:22 CEST 2023
DEBUG - Saved last read date as 30 Jun 2023, 20:04:22
Jul 02, 2023 10:12:01 AM compbio.ws.client.Jws2Client connect
INFO: Connected successfully!
DEBUG - Not enabling Google Tracking.
DEBUG - Scanning news items: newsnew=false and lastDate is Fri Jun 30 20:04:22 CEST 2023
DEBUG - Saved last read date as 30 Jun 2023, 20:04:22
DEBUG - Scanning news items: newsnew=false and lastDate is Fri Jun 30 20:04:22 CEST 2023
DEBUG - Saved last read date as 30 Jun 2023, 20:04:22
DEBUG - Scanning news items: newsnew=false and lastDate is Fri Jun 30 20:04:22 CEST 2023
DEBUG - Saved last read date as 30 Jun 2023, 20:04:22
Jul 02, 2023 10:12:01 AM compbio.ws.client.Jws2Client connect
INFO: Connected successfully!
java.lang.Exception: 400 response (Mocked)
	at jalview.fts.service.pdb.PDBFTSRestClient.executeRequest(PDBFTSRestClient.java:232)
	at jalview.gui.structurechooser.PDBStructureChooserQuerySource.fetchStructuresMetaData(PDBStructureChooserQuerySource.java:254)
	at jalview.gui.StructureChooser.fetchStructuresMetaData(StructureChooser.java:479)
	at jalview.gui.StructureChooser.initialStructureDiscovery(StructureChooser.java:242)
	at jalview.gui.StructureChooser$2.run(StructureChooser.java:209)
	at java.base/java.lang.Thread.run(Thread.java:829)