jalview/test/jalview

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Tuesday 02 Nov 2021
12:10 pm

Jim Procter <j.procter@dundee.ac.uk>

JAL-3875 test case and patch to verify the query 3d beacons button is shown for proteins with uniprot ids but no canonical accessions

Options
    • -2
    • +23
    ./StructureChooserTest.java
  2. … 1 more file in changeset.
Monday 20 Sep 2021
2:56 pm

Jim Procter <j.procter@dundee.ac.uk>

JAL-3829 tests need to wait for dialog to be closed and background processes to finish before they can check functionality

Options
    • -0
    • +22
    ./StructureChooserTest.java
  2. … 1 more file in changeset.
Tuesday 14 Sep 2021
7:10 pm

Jim Procter <j.procter@dundee.ac.uk>

JAL-3829 parallel not welcome here

Options
    • -0
    • +1
    ./StructureChooserTest.java
6:59 pm

Jim Procter <j.procter@dundee.ac.uk>

JAL-3829 test flakiness and human flakiness

Options
    • -20
    • +10
    ./StructureChooserTest.java
6:55 pm

Jim Procter <j.procter@dundee.ac.uk>

JAL-3829 more info on test fail - seems to be flaky

Options
    • -2
    • +16
    ./StructureChooserTest.java
2:38 pm

Jim Procter <j.procter@dundee.ac.uk>

JAL-3829 move mock query and responses to files

Options
    • -2
    • +3
    ./StructureChooserTest.java
    • -2
    • +3
    ./structurechooser/StructureChooserQuerySourceTest.java
  3. … 6 more files in changeset.
12:34 pm

Jim Procter <j.procter@dundee.ac.uk>

JAL-3829 allow multiple URL mocks and include P01308 in 3d-beacons mocks

Options
    • -8
    • +23
    ./structurechooser/StructureChooserQuerySourceTest.java
  2. … 5 more files in changeset.
Monday 13 Sep 2021
5:04 pm

Jim Procter <j.procter@dundee.ac.uk>

JAL-3829 ensure unmock the FTS PDB and TDB clients after mocking for a test

Options
    • -0
    • +4
    ./StructureChooserTest.java
4:02 pm

Jim Procter <j.procter@dundee.ac.uk>

JAL-3829 minimal test of additional TDB filters - not at all robust

Options
    • -3
    • +13
    ./structurechooser/StructureChooserQuerySourceTest.java
Saturday 11 Sep 2021
12:10 pm

Jim Procter <j.procter@dundee.ac.uk>

JAL-3829 ensure tests use mocked service - proper exception for mocked 400 response

Options
    • -0
    • +6
    ./StructureChooserTest.java
  2. … 1 more file in changeset.
11:53 am

Jim Procter <j.procter@dundee.ac.uk>

JAL-3829 patch failing tests and todo for future

Options
    • -3
    • +1
    ./StructureChooserTest.java
    • -3
    • +9
    ./structurechooser/StructureChooserQuerySourceTest.java
  3. … 1 more file in changeset.
Friday 10 Sep 2021
1:45 pm

Jim Procter <j.procter@dundee.ac.uk>

JAL-3829 insert title for structures from PDBe

Options
    • -1
    • +3
    ./structurechooser/StructureChooserQuerySourceTest.java
  2. … 1 more file in changeset.
Wednesday 08 Sep 2021
1:33 pm

Jim Procter <j.procter@dundee.ac.uk>

JAL-3829 allow client-side selection of structures for a sequence by passing in discovered structures

Options
    • -0
    • +6
    ./structurechooser/StructureChooserQuerySourceTest.java
  2. … 4 more files in changeset.
Monday 06 Sep 2021
2:48 pm

Jim Procter <j.procter@dundee.ac.uk>

JAL-3829 work in progress - look up additional metadata from PDBe for structures discovered via TDBFTS

Options
    • -13
    • +30
    ./structurechooser/StructureChooserQuerySourceTest.java
  2. … 2 more files in changeset.
10:52 am

Jim Procter <j.procter@dundee.ac.uk>

JAL-3829 pull out structure chooser query source tests to new class

Options
    • -102
    • +18
    ./StructureChooserTest.java
    • -0
    • +280
    ./structurechooser/StructureChooserQuerySourceTest.java
Friday 03 Sep 2021
6:47 pm

Jim Procter <j.procter@dundee.ac.uk>

JAL-3829 JAL-3865 test structure chooser queries to mocked 3D Beacons FTS

Options
    • -1
    • +95
    ./StructureChooserTest.java
6:42 pm

Jim Procter <j.procter@dundee.ac.uk>

JAL-3829 use sequence dependent constructor for structure chooser query engine testing

Options
    • -1
    • +4
    ./StructureChooserTest.java
3:33 pm

Jim Procter <j.procter@dundee.ac.uk>

JAL-3829 refactored FilterOption provider to the StructureChooserQuerySource implementation - implementation now is completely independent of GUI code.

Options
    • -1
    • +1
    ./StructureChooserTest.java
  2. … 6 more files in changeset.
Monday 30 Aug 2021
2:44 pm

Jim Procter

Thursday 26 Aug 2021
2:56 pm

Jim Procter <j.procter@dundee.ac.uk>

JAL-3929 3d-beacons structure chooser logic (not yet finished)

Options
    • -4
    • +6
    ./StructureChooserTest.java
  2. … 9 more files in changeset.
2:56 pm

Jim Procter <j.procter@dundee.ac.uk>

JAL-3829 3d-beacons structure chooser logic (not yet finished)

Options
    • -4
    • +6
    ./StructureChooserTest.java
  2. … 9 more files in changeset.
Monday 23 Aug 2021
5:45 pm

Jim Procter <j.procter@dundee.ac.uk>

JAL-3829 pushed the PDBFTSClient specific code to new ‘StructureChooserQuerySource’ class in preparation for adapting it to query 3d-beacons

Options
    • -8
    • +9
    ./StructureChooserTest.java
  2. … 2 more files in changeset.
5:45 pm

Jim Procter <j.procter@dundee.ac.uk>

JAL-3929 pushed the PDBFTSClient specific code to new ‘StructureChooserQuerySource’ class in preparation for adapting it to query 3d-beacons

Options
    • -8
    • +9
    ./StructureChooserTest.java
  2. … 2 more files in changeset.
4:52 pm

Jim Procter

patch needed for 2.11.2 - JAL-3518 - catch case when no replies are available

patch needed for 2.11.2 - JAL-3518 - catch case when no replies are available

4:49 pm

Jim Procter

semantics for determining if a PDB file has a SIFTs mapping - could be absorbed into the PDB metadata object

semantics for determining if a PDB file has a SIFTs mapping - could be absorbed into the PDB metadata object

4:48 pm

Jim Procter

magic logic to recognise which structure database provider client to use - PDB or AlphaFold - ensures metadata and annotation rows are propagates

magic logic to recognise which structure database provider client to use - PDB or AlphaFold - ensures metadata and annotation rows are propagates

4:43 pm

Jim Procter

Reviewing the alphafold + contact matrix patch for 2.11.2
Reviewing the alphafold + contact matrix patch for 2.11.2
2:12 pm

Jim Procter

remove debugging printlns

remove debugging printlns

2:12 pm

Jim Procter

aim is normally to avoid creating query-specific data containers on the core query response class

aim is normally to avoid creating query-specific data containers on the core query response class

10:26 am

Jim Procter

? not sure this is correct

? not sure this is correct