search

ome / omero-parade

OMERO.web plugin for displaying Dataset thumbnails or Plates in webclient center panel
GNU Affero General Public License v3.0
1 stars 12 forks source link

try to use webgateway _bulk_file_annotations #57

Closed will-moore closed 5 years ago

will-moore commented 5 years ago

See https://github.com/openmicroscopy/openmicroscopy/pull/6054 Use the renamed _bulk_file_annotations() from webgateway (see PR above). NB: Use try/except so we don't rely on OMERO 5.5.1 since users may want to upgrade OMERO.parade without having latest OMERO.

will-moore commented 5 years ago

Travis failed with getting docker running?

travis_fold:end:app-deps
Error response from daemon: Container 5dfdd3c1549cdb97e0ace0285291e7eeaf54eb56b0c206413ad764aedfa8e2db is not running
Stopping omeroparade_db_1  ...
joshmoore commented 5 years ago

There have been a few issues with test-infra recently. I'll take a look.

joshmoore commented 5 years ago

Local run passed. I'm guessing resource starvation. Re-running with the hope that an early morning run has less contention. If OMERO is going to regular start failing in travis, we may have to rethink this strategy.

travis failure

``` 2019-06-23 21:02:33,190 [omego.artifa] INFO Unzipping OMERO.java-5.5.0-ice36-b121.zip app-deps Loaded plugins: fastestmirror, ovl Examining /var/tmp/yum-root-QsQmxV/nodesource-release-el7-1.noarch.rpm: nodesource-release-el7-1.noarch Marking /var/tmp/yum-root-QsQmxV/nodesource-release-el7-1.noarch.rpm to be installed Resolving Dependencies --> Running transaction check ---> Package nodesource-release.noarch 0:el7-1 will be installed --> Finished Dependency Resolution Dependencies Resolved ================================================================================ Package Arch Version Repository Size ================================================================================ Installing: nodesource-release noarch el7-1 /nodesource-release-el7-1.noarch 3.1 k Transaction Summary ================================================================================ Install 1 Package Total size: 3.1 k Installed size: 3.1 k Downloading packages: Running transaction check Running transaction test Transaction test succeeded Running transaction Installing : nodesource-release-el7-1.noarch 1/1 Verifying : nodesource-release-el7-1.noarch 1/1 Installed: nodesource-release.noarch 0:el7-1 Complete! Loaded plugins: fastestmirror, ovl Determining fastest mirrors * base: centos4.zswap.net * epel: mirror.team-cymru.com * extras: centos4.zswap.net * updates: repo1.dal.innoscale.net Resolving Dependencies --> Running transaction check ---> Package npm.x86_64 1:3.10.10-1.6.16.0.1.el7 will be installed --> Processing Dependency: nodejs = 1:6.16.0-1.el7 for package: 1:npm-3.10.10-1.6.16.0.1.el7.x86_64 --> Running transaction check ---> Package nodejs.x86_64 1:6.16.0-1.el7 will be installed --> Processing Dependency: libuv >= 1:1.9.1 for package: 1:nodejs-6.16.0-1.el7.x86_64 --> Processing Dependency: libicudata.so.50()(64bit) for package: 1:nodejs-6.16.0-1.el7.x86_64 --> Processing Dependency: libicui18n.so.50()(64bit) for package: 1:nodejs-6.16.0-1.el7.x86_64 --> Processing Dependency: libicuuc.so.50()(64bit) for package: 1:nodejs-6.16.0-1.el7.x86_64 --> Processing Dependency: libuv.so.1()(64bit) for package: 1:nodejs-6.16.0-1.el7.x86_64 --> Running transaction check ---> Package libicu.x86_64 0:50.1.2-17.el7 will be installed ---> Package libuv.x86_64 1:1.29.1-1.el7 will be installed --> Finished Dependency Resolution Dependencies Resolved ================================================================================ Package Arch Version Repository Size ================================================================================ Installing: npm x86_64 1:3.10.10-1.6.16.0.1.el7 epel 2.5 M Installing for dependencies: libicu x86_64 50.1.2-17.el7 base 6.9 M libuv x86_64 1:1.29.1-1.el7 epel 137 k nodejs x86_64 1:6.16.0-1.el7 epel 4.7 M Transaction Summary ================================================================================ Install 1 Package (+3 Dependent packages) Total download size: 14 M Installed size: 51 M Downloading packages: -------------------------------------------------------------------------------- Total 18 MB/s | 14 MB 00:00 Running transaction check Running transaction test Transaction test succeeded Running transaction Installing : 1:libuv-1.29.1-1.el7.x86_64 1/4 Installing : libicu-50.1.2-17.el7.x86_64 2/4 Installing : 1:npm-3.10.10-1.6.16.0.1.el7.x86_64 3/4 Installing : 1:nodejs-6.16.0-1.el7.x86_64 4/4 Verifying : libicu-50.1.2-17.el7.x86_64 1/4 Verifying : 1:libuv-1.29.1-1.el7.x86_64 2/4 Verifying : 1:npm-3.10.10-1.6.16.0.1.el7.x86_64 3/4 Verifying : 1:nodejs-6.16.0-1.el7.x86_64 4/4 Installed: npm.x86_64 1:3.10.10-1.6.16.0.1.el7 Dependency Installed: libicu.x86_64 0:50.1.2-17.el7 libuv.x86_64 1:1.29.1-1.el7 nodejs.x86_64 1:6.16.0-1.el7 Complete! Error response from daemon: Container 5dfdd3c1549cdb97e0ace0285291e7eeaf54eb56b0c206413ad764aedfa8e2db is not running Stopping omeroparade_db_1 ... Stopping omeroparade_web_1 ... oving omeroparade_db_1 ... Removing omeroparade_omero_1 ... Removing omeroparade_web_1 ... oving network omeroparade_default The command ".omero/docker app" exited with 1. ```

joshmoore commented 5 years ago

Interesting!

omero_1  | psql:omero-20190624-095938-201869.sql:9478: ERROR:  relation "i_logicalchannel_emissionwave" already exists

cc: @mtbc @jburel

joshmoore commented 5 years ago

Change looks fine. I don't assume a test is actually testing this, but travis is regardless green.