Build: #6 failed Manual run by James Procter
Code commits
Jalview Git
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James Procter <j.procter@dundee.ac.uk> 94efd5cf1c5065416f9a41b78bb1e3b93bdacd42
JAL-4243 Jalview 2.11.2.7’s biotool record as JSON complete with update instructions as a README
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James Procter <j.procter@dundee.ac.uk> 3dc34c42cf456deb5f97622de81e7dcfff1d9840
JAL-3855 tree title for PAE matrix tree is PAE Matrix (method) for (structure) (sequence)
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James Procter <j.procter@dundee.ac.uk> fa48c836ad6e85a9e8146177cc865f4a061dc1a4
JAL-3855 auto select clusters and fix up colouring/propagation on calculation & tree display
- src/jalview/analysis/AverageDistanceEngine.java (version fa48c836ad6e85a9e8146177cc865f4a061dc1a4) (diffs)
- src/jalview/datamodel/ContactMatrixI.java (version fa48c836ad6e85a9e8146177cc865f4a061dc1a4) (diffs)
- src/jalview/datamodel/GroupSet.java (version fa48c836ad6e85a9e8146177cc865f4a061dc1a4) (diffs)
- src/jalview/gui/AnnotationLabels.java (version fa48c836ad6e85a9e8146177cc865f4a061dc1a4) (diffs)
- src/jalview/gui/TreeCanvas.java (version fa48c836ad6e85a9e8146177cc865f4a061dc1a4) (diffs)
- src/jalview/gui/TreePanel.java (version fa48c836ad6e85a9e8146177cc865f4a061dc1a4) (diffs)
- src/jalview/util/ColorUtils.java (version fa48c836ad6e85a9e8146177cc865f4a061dc1a4) (diffs)
- test/jalview/analysis/AverageDistanceEngineTest.java (version fa48c836ad6e85a9e8146177cc865f4a061dc1a4) (diffs)
- test/jalview/datamodel/PAEContactMatrixTest.java (version fa48c836ad6e85a9e8146177cc865f4a061dc1a4) (diffs)
- test/jalview/project/Jalview2xmlTests.java (version fa48c836ad6e85a9e8146177cc865f4a061dc1a4) (diffs)
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James Procter <j.procter@dundee.ac.uk> 133c24e81c5edd0134239e1cf291b05a7389afb1
Merge branch 'patch/JAL-3855_fixup_pae' into develop
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James Procter <j.procter@dundee.ac.uk> d6fc0910df67f8eca4dd624ef16779937cfeeb20
Merge branch 'develop' into patch/JAL-3855_fixup_pae
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James Procter <j.procter@dundee.ac.uk> ad666cfa61c4d32ddc270d061bda207cdd96d570
JAL-4153 comments re patch incorrectly committed under JAL-4513
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Ben Soares <b.soares@dundee.ac.uk> d2fb2e89db496142f167273c671732461e378d64
JAL-4513 move comments
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Ben Soares <b.soares@dundee.ac.uk> 2de98d293f03069b1585e64b27666b2e3e801137
JAL-4513 now re-add the SwingUtilities.invokeAndWait() with minimal sleep
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James Procter <j.procter@dundee.ac.uk> cf3e8343ced61a995515cb96e2c638f26dc813b9
JAL-3855 PAE matrices are transposed on import from JSON so returned contact vectors correspond to errors predicted when superposing at a given column position
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James Procter <j.procter@dundee.ac.uk> ca47f64efa144d68e7f6e01ad2c147a7832e97a7
JAL-3855 JAL-4124 test checks asymmetric matrices are stored and restored correctly
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James Procter <j.procter@dundee.ac.uk> 011df19c7cd01c6355a885fb0c2fff33a236d6ff
JAL-3858 fix off-by-one in matrix visualisation and interactive tooltip
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James Procter <j.procter@dundee.ac.uk> a50364b26e0ab302562f6c99dcf29ccbe54aa67d
JAL-3858 flip diagonal so matrix visualisation is top left to bottom right
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James Procter <j.procter@dundee.ac.uk> 8f5766ed1f40e637824924ae810b5c033d185d60
JAL-3858 annotation .height is bigger than graphHeight so adjacent PAE matrices are clearly separated
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Ben Soares <b.soares@dundee.ac.uk> 4b0cc64ad6d62223f1cc63089ce3f3b551e726e5
JAL-4513 reduce wait to invoke fail
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Ben Soares <b.soares@dundee.ac.uk> 7ade43ed57bd37b8a7d9655bc36c71e615793a1a
JAL-4513 add a SwingUtilities.invokeAndWait() to see what happens
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Ben Soares <b.soares@dundee.ac.uk> 06eaa901379256f8db2114acb4e1bc75002b2527
JAL-3599 Updated default eclipse to 'latest' and made jalviewjsLaunchTest timeouts a bit more flexible
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James Procter <j.procter@dundee.ac.uk> 11bbccaab947ba4465c27c5d0619ef202fc4e75e
JAL-4119 TRACE level console message reporting download URL for sifts. Also more informative message when ‘Sifts Mapping Failed’ is reported as an exception - since this message can be reported when some chains in the PDB file do not match sequences being associated (but others do!!).
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James Procter <j.procter@dundee.ac.uk> ce2818d5561e02b79b10eea326e8d448df9f2143
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James Procter <j.procter@dundee.ac.uk> 1ffff7be869b7a4e52d146dcf6611144c87cc5da
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James Procter <j.procter@dundee.ac.uk> 5771e6a607dac958b1174178b807bf6c5e17a47f
JAL-4223 add testdata for test
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James Procter <j.procter@dundee.ac.uk> 982963f55ceecf1c0591656b79dba5ad3aba0b06
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James Procter <j.procter@dundee.ac.uk> bf2b9bfde805dbd7ea0dc38e70532204b68071ed
JAL-4217 move Commands.structureImageTest to testTask1
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James Procter <j.procter@dundee.ac.uk> 320583fd2ac3ea714e6afdac050961978bd34c81
JAL-4223 - test and patch to ensure numbering matches sequence data from RNAML file
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James Procter <j.procter@dundee.ac.uk> 1c82b91f2e6a692a2e43238a779c14633c1bd0f0
Merge branch 'patch/JAL-4195_cli_eps_export_npe' into develop
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James Procter <j.procter@dundee.ac.uk> 80720b941dbf0fc9c1f036f6a4efa5b3b40a0bdc
JAL-4217 JAL-629 built in 25s time out waiting for structure viewer to load data before attempting to grab an image.
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James Procter <j.procter@dundee.ac.uk> 7c40be8c2aed396b01242811c74d90c6cf3f5ccd
JAL-4090 update 2.11.3.0 release notes (with in-progress bits too) and what's new
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James Procter <j.procter@dundee.ac.uk> a350dc895531b6249b12267525f99be74448378e
Merge branch 'patch/JAL-4119_sifts_ftp_split' into develop
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James Procter <j.procter@dundee.ac.uk> 4b031bc957ad1c5512798c6206adac7ed0364331
Merge branch 'develop' into patch/JAL-4195_cli_eps_export_npe
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James Procter <j.procter@dundee.ac.uk> 6723fff70de0a8576fab9196e99ece7ae67f3dbf
JAL-4195 add exception handling for all other CommandsTest tests and remove errant class-level @Test tag
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James Procter <j.procter@dundee.ac.uk> cd886ae669962ea7fff5fb46627b3f84e77d295d
JAL-4221 update description when transferring annotation and no description already set
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James Procter <j.procter@dundee.ac.uk> 59e9fd112bcb8cb4c5cfd344562e7edfc3ea8359
JAL-629 even more console debug for --structureviewer opening arguments
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James Procter <j.procter@dundee.ac.uk> fb1fb73bd1e6b08de09932c98d39b847dda1cf9a
JAL-629 liberal defensive coding, comments about refactoring and DEBUG output for --structureimage
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James Procter <j.procter@dundee.ac.uk> b101d3b57771a1c8bf2314e1a29748e23b23d3c0
JAL-629 make —structure image work again after threading it off
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James Procter <j.procter@dundee.ac.uk> b8719513e0b9b89a731d462cc6d1930e2dc5bb48
JAL-4217 catch case when the structure viewer doesn't get added to the desktop window (possible knock on for flatlaf JAL-3416)
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James Procter <j.procter@dundee.ac.uk> 1ce72d485ca335eff45f1d7904b8f547548c0558
JAL-4217 interruptedExceptions should also break any wait loops
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James Procter <j.procter@dundee.ac.uk> 261d2ca1b0eef309cd9d178e023c6bfecbd62017
JAL-2292 verify mixed case alignment actually aligns
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James Procter <j.procter@dundee.ac.uk> af1bb2283d7b4efb3d1f487d2831178b39f075fd
JAL-4217 wrap imageExport CLI method's call to imageExport in a separate thread and hang around until it completes…
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James Procter <j.procter@dundee.ac.uk> 4e0bf08fc16e9388bb76cdd3eac84d767d102690
JAL-4217 wrap imageExport CLI method's call to imageExport in an invokeAndWait
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James Procter <j.procter@dundee.ac.uk> a531ac7b834790181ea13394160b04b81c8772fd
Merge branch 'patch/JAL-2292_caseSensitivePAE' into develop
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James Procter <j.procter@dundee.ac.uk> 790b54c090f675f4ba4f698d8d0d0d1fb2bb7fd4
Merge branch 'patch/JAL-4213_addref_with_selection' into develop
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James Procter <j.procter@dundee.ac.uk> dc39f665e7095040ecc56b0833c0a1960f4020e3
Merge branch 'merge/from_2_11_2_7_to_2_11_3_0' into develop
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James Procter <j.procter@dundee.ac.uk> bb8a28402c05e04f04c8eddb1dd005e89d382808
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James Procter <j.procter@dundee.ac.uk> f09d2b239f0bad6d5cae25fd8fbe94b3596f0a79
JAL-4117 Fri June 30th release of 2.11.2.7 with Jalview Plausible analytics
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James Procter <j.procter@dundee.ac.uk> 74c36ac68e07e85da17fc5897ddb3bda4075084a
JAL-4217 try really hard to shut down and dispose of Desktop resources and any lurking threads
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James Procter <j.procter@dundee.ac.uk> 2ca18cf90f7525cb3f4129744a26397376956fc8
JAL-4216 release notes
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James Procter <j.procter@dundee.ac.uk> f3c0a009ab04c4e92d00cb72abbea5cbac3baeb1
JAL-4216 compute size of annotation using start/end of sequence and given length. This might not work...
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James Procter <j.procter@dundee.ac.uk> 03cb597dc859686fec4425334dd90237392c6a31
Merge branch 'task/JAL-4001_Plausible_API' into develop
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Ben Soares <b.soares@dundee.ac.uk> 3a39fb5cc1a7483fbf64d0fca8e57f8fc4bc57c2
JAL-4001 Added a random id to User-Agent to ensure separate visits recorded in Plausible. Changed default URL to self-hosted site
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James Procter <j.procter@dundee.ac.uk> 939ec650efeb1e26a64f4ea8238a5f73ad7a1150
Merge branch 'task/JAL-4001_Plausible_API' into develop
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James Procter <j.procter@dundee.ac.uk> f65da43ae027f971382e08b42f9ae7cd09d794b8
JAL-4117 JAL-4001 plausible analytics release notes and privacy docs
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James Procter <j.procter@dundee.ac.uk> 3181dbc7acba94a40f06ee43c07064664ecb2a0e
JAL-4090 update from 2.11.2.7 JAL-4117 - version bump and release notes for JAL-4116
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James Procter <j.procter@dundee.ac.uk> 4df160b74ec147b59ed73b5d91c2def54391b4c4
JAL-4001 analytics url provided by https://www.jalview.org/services/config/analytics/url
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Ben Soares <b.soares@dundee.ac.uk> 1f9ca4896d57bfb16a25c87cfc0b8cd19fcdf148
JAL-4001 change Plausible discovery URL
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Ben Soares <b.soares@dundee.ac.uk> 4fb4e63368e9a74e207c226739bde148acacd9cb
JAL-4001 remove headless code from analytics
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Ben Soares <b.soares@dundee.ac.uk> c545cf4453c712dbb3d708b5af4368aeeddb5199
JAL-4001 Remove analytics for --headless mode
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Ben Soares <b.soares@dundee.ac.uk> 675982336ef7772ca635baca391c48fb868501b7
JAL-4001 Added useful props information
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Ben Soares <b.soares@dundee.ac.uk> 612715a5a4150366df57eb7690d68d163b7080cb
Merge branch 'develop' into task/JAL-4001_Plausible_API
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Ben Soares <b.soares@dundee.ac.uk> 052bf616f3923a74abeef9afd8720f61e8ce0ab4
JAL-4001 Fix default API url
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James Procter <j.procter@dundee.ac.uk> a55e4576868379847eebc4f5741ae24a48ef2476
JAL-4213 don’t pass active selection when actioning the addReferenceAnnotation
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James Procter <j.procter@dundee.ac.uk> eb64fc14cebadcfbb286bd4865d9df66e428a5d8
JAL-4213 - document the addReferenceAnnotations method’s behaviour when given a selection
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Ben Soares <b.soares@dundee.ac.uk> 18615246e3b259faacbc97d97a34a72ef600195b
JAL-4001 Added 'installation' property.
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James Procter <j.procter@dundee.ac.uk> c9e6efcdf33bcd88bd19a48b2934c28e48892fab
JAL-2292 - ensure mapping is built for equal symbols with mismatched case
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Ben Soares <b.soares@dundee.ac.uk> 48536fa26d81ec9faff30d2d3b45ba446160816e
JAL-4001 Added lookup to https://www.jalview.org/config/analytics/url to check API base url. Changed terminology to match Plausible API
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Ben Soares <b.soares@dundee.ac.uk> 3acfdb3ddd5e3b785fd0880bcebc9e267a717bbe
JAL-4019 corrected to '>' to '>=' for percentage comparisons
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James Procter <j.procter@dundee.ac.uk> 4a6e033ecbe830a86d77f8910beb90b09522aceb
Merge branch 'patch/JAL-4196_structure_viewer_synchronising' into develop
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Ben Soares <b.soares@dundee.ac.uk> 2acaf6533dd61f649b4394082e0e600b7bc0f62d
JAL-4001 Rationalise user-agent string into HttpUtils
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Ben Soares <b.soares@dundee.ac.uk> a55c72d54f73d625bf6dc1f01f148f94fa84a0c7
JAL-4001 Change wording from google to plausible or generic analytics
- resources/lang/Messages.properties (version a55c72d54f73d625bf6dc1f01f148f94fa84a0c7) (diffs)
- resources/lang/Messages_es.properties (version a55c72d54f73d625bf6dc1f01f148f94fa84a0c7) (diffs)
- src/jalview/bin/Cache.java (version a55c72d54f73d625bf6dc1f01f148f94fa84a0c7) (diffs)
- src/jalview/bin/Jalview.java (version a55c72d54f73d625bf6dc1f01f148f94fa84a0c7) (diffs)
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Ben Soares <b.soares@dundee.ac.uk> 52f14b6e936c51474df2486a8a7db182cae15ba2
JAL-4001 rename the init method
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Ben Soares <b.soares@dundee.ac.uk> 16f9a5d9288821419534eecbdba9eda073196f3b
JAL-4001 Working Plausible analytics
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Ben Soares <b.soares@dundee.ac.uk> b8fad524f57f852bcdfcfdbcf68d4360b550feb0
JAL-4001 Plausible class
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Ben Soares <b.soares@dundee.ac.uk> a971d440b2079bd1c351a563d9a17e866710ae5a
JAL-4001 Added a genuine client_id (from gtag). Added /debug/mp/collect with response content
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Ben Soares <b.soares@dundee.ac.uk> a6f0678764ea06034460236c7a811bbfcad682aa
JAL-4001 Check --nousagestats before doing analytics in headless mode
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Ben Soares <b.soares@dundee.ac.uk> 093211ab0209394015e87ba8a467d6ee792b055a
JAL-4001 Add a _geo=1 to query string and JSON. Add a headless flag to path and JSON, and send analytics in headless mode if USAGESTATS=true.
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Ben Soares <b.soares@dundee.ac.uk> 77e37b9460441033c19756d8e75b681c087cb615
JAL-4001 Remove jgoogleanalytics code and jar
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Ben Soares <b.soares@dundee.ac.uk> 0f72eae506d32d20f11908522330d49889818f10
JAL-4001 make page_location the same encoding as the old jgoogleanalytics
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Ben Soares <b.soares@dundee.ac.uk> d27e73b6519abfe5922ae716efe9a8dcc58c7751
JAL-4001 Changed for Java 8 compatibility
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Ben Soares <b.soares@dundee.ac.uk> 6d7f8d4aa0233a07520fe7c21645df8ae27e63ba
JAL-4001 Trying to see extra information in GA dashboard
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Ben Soares <b.soares@dundee.ac.uk> 851faa2a632ed84bd2c58244414c2336f1697741
Merge branch 'develop' into task/JAL-4001_migrate_googleanalytics_to_GA4
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Ben Soares <b.soares@dundee.ac.uk> ee6877a44862ab0dcdd1b7096bfa113d6196fb5a
JAL-3599 Tidyup for all OS to use ScheduledExecutor
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Ben Soares <b.soares@dundee.ac.uk> 16cd80621c3dc4ba72686d198d80b0a4eb3f1ed5
JAL-3599 replaced a build dependency for jalviewjsLaunchTest
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Ben Soares <b.soares@dundee.ac.uk> 20d8cc2bb3e2fab2b7f637a3d523c90ceb58903d
JAL-3599 Cater for macOS. ScheduledExecutor timeout implemented
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Ben Soares <b.soares@dundee.ac.uk> 582ab44aced084d311b002781f3b7f6c1be3cb6d
JAL-3599 Cater for macOS. --timeout not working yet
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Ben Soares <b.soares@dundee.ac.uk> dda0407943edf42c3ad816d9ec9a30ba1ba2b921
JAL-3599 Make jalviewjs dependOn jalviewjsLaunchTest. Change jalviewjsLaunchTest to only stop the task (not trigger a failure) if chrome not found. Remove deliberate NPE.
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Ben Soares <b.soares@dundee.ac.uk> 3fac1f93347ade5faa14c3f1c3fb2fd3d9b9e5bb
JAL-3599 Deliberate NPE to see if build plan fails
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Ben Soares <b.soares@dundee.ac.uk> f3c41d0e8b0a342c12eec87903c89c38762f2b6d
JAL-3599 fixed placement of 'First Run' file for chromium profile
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Ben Soares <b.soares@dundee.ac.uk> 76d097b3838f90f842b90f3520d18fee0d86ac62
JAL-3599 --no-sandbox --disable-gpu and Thorium flatpak on build server
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Ben Soares <b.soares@dundee.ac.uk> 674d18698adf462cf905af5407ef44b468471982
JAL-3599 STDOUT and STDERR saved and sent to System.out/err
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Ben Soares <b.soares@dundee.ac.uk> 9ca56c016427b44f565994198707b403b23e21b9
JAL-3599 Not redirecting STDOUT or STDERR just for build server debuggin
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Ben Soares <b.soares@dundee.ac.uk> be8d1428f129ec7d39e353717bf8756805d1e803
JAL-3599 More stderr/stdout output to logs when anything
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Ben Soares <b.soares@dundee.ac.uk> 904f57a60f53040ade71b0ac26df83ed20afb911
JAL-3599 More stderr/stdout output to logs when failed
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Ben Soares <b.soares@dundee.ac.uk> 3d2f8c71a2f26449a678fe97de69b369b8158fbe
JAL-3599 increase real and virtual time chrome runs for to 60s (in real-time this is still about 3s)
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Ben Soares <b.soares@dundee.ac.uk> 3ba8b399b3f6e8163b748e208465dbb7bf4efbd5
JAL-3599 gradle tasks to test JalviewJS launches in a chrome or chromium browser
- build.gradle (version 3ba8b399b3f6e8163b748e208465dbb7bf4efbd5) (diffs)
- gradle.properties (version 3ba8b399b3f6e8163b748e208465dbb7bf4efbd5) (diffs)
- src/jalview/gui/Desktop.java (version 3ba8b399b3f6e8163b748e208465dbb7bf4efbd5) (diffs)
- utils/jalviewjs/chromium_test/jalview_bin_Jalview-stderr.html (version 3ba8b399b3f6e8163b748e208465dbb7bf4efbd5) (diffs)
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Ben Soares <b.soares@dundee.ac.uk> dc15acb6fdd00e6e7463cda8be6abba7490c098d
JAL-4001 Only send defaultParams for application_launch event
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Ben Soares <b.soares@dundee.ac.uk> a767af2c8864dd3a713943d7719d6cf9ff987429
Merge branch 'develop' into task/JAL-4001_migrate_googleanalytics_to_GA4
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James Procter <j.procter@dundee.ac.uk> b15a4dfe51ded457b2850f14c19b5245aadb918e
Merge branch 'develop' into patch/JAL-4196_structure_viewer_synchronising
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James Procter <j.procter@dundee.ac.uk> 3d15945cbf4a0f70bde108bcceb42bb9553c1967
JAL-4196 make very sure we avoid CME by defensively copying the Map.values() to another list and synchronising on it
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James Procter <j.procter@dundee.ac.uk> dae873d07c9cba8be54c6c48b3da5e6116552a15
JAL-4196 report an error if structure view doesn’t get created (for whatever reason) during CLI arg processing, and wait around until the viewer has finished importing before doing anything
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James Procter <j.procter@dundee.ac.uk> 91b3af9bfa70fc853ec6e74096454e17882a7543
JAL-4196 structure view cli tests wait using new jalview.Desktop.instance.operationsAreInProgress() returns true if any desktop windows have a progress indicator still active
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Ben Soares <b.soares@dundee.ac.uk> a27b3832ad1bbe70548bcc53301446c75d02672a
JAL-3416 FlatLaf SystemInfo failing in JalviewJS. Look and Feel not relevant to JalviewJS so setLookAndFeel commented out for j2s with @j2sIgnore
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Ben Soares <b.soares@dundee.ac.uk> bf478b2e1087fb03bf6b9fb07f14a9e4f096892c
Merge branch 'develop' into task/JAL-4001_migrate_googleanalytics_to_GA4