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GMOD / Apollo

Genome annotation editor with a Java Server backend and a Javascript client that runs in a web browser as a JBrowse plugin.
http://genomearchitect.readthedocs.io/
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Tracks not loading after latest build #296

Closed littlebunch closed 9 years ago

littlebunch commented 9 years ago

After I pulled and deployed yesterday (4/17) and today (4/18), tracks won't load, i.e. RequestError: Unable to load http://gmod-dev.nal.usda.gov:8080/apollo/jbrowse/data/tracks.conf status: 500. The log indicates some sort of database issue. The species were added while running the 4/16 build and seemed to be OK.

`2015-04-18 11:56:57,411 [http-bio-8080-exec-4] ERROR errors.GrailsExceptionResolver - PSQLException occurred when processing request: [GET] /apollo/jbrowse/data/trackList.json ERROR: null value in column "name" violates not-null constraint Detail: Failing row contains (308641, 0, null, null, org.bbop.apollo.UserOrganismPreference,3,Scaffold1069, 6, t).. Stacktrace follows:org.postgresql.util.PSQLException: ERROR: null value in column "name" violates n ot-null constraint Detail: Failing row contains (308641, 0, null, null, org.bbop.apollo.UserOrgan ismPreference, 3, Scaffold1069, 6, t). at org.postgresql.core.v3.QueryExecutorImpl.receiveErrorResponse(QueryEx ecutorImpl.java:2161) at org.postgresql.core.v3.QueryExecutorImpl.processResults(QueryExecutorImpl.java:1890) at org.postgresql.core.v3.QueryExecutorImpl.execute(QueryExecutorImpl.java:255) at org.postgresql.jdbc2.AbstractJdbc2Statement.execute(AbstractJdbc2Statement.java:559) at org.postgresql.jdbc2.AbstractJdbc2Statement.executeWithFlags(AbstractJdbc2Statement.java:417)

nathandunn commented 9 years ago

I changed one of the domain objects columns from null to not-null as part of the dev process. It should be switched back now. If not do:

“delete from preference” on the SQL table.

Conversely:

"alter table preference alter name column drop not null ; "

Once we do a formal release I’ll use the DB_migration plugin (or something similar) to manage any of these small changes between stable version.

Nathan

On Apr 18, 2015, at 9:03 AM, Gary Moore notifications@github.com wrote:

After I pulled and deployed yesterday (4/17) and today (4/18), tracks won't load, i.e. RequestError: Unable to load http://gmod-dev.nal.usda.gov:8080/apollo/jbrowse/data/tracks.conf http://gmod-dev.nal.usda.gov:8080/apollo/jbrowse/data/tracks.conf status: 500. The log indicates some sort of database issue:

2015-04-18 11:56:57,411 [http-bio-8080-exec-4] ERROR errors.GrailsExceptionResolver - PSQLException occurred when processing request: [GET] /apollo/jbrowse/data/trackList.json ERROR: null value in column "name" violates not-null constraint Detail: Failing row contains (308641, 0, null, null, org.bbop.apollo.UserOrganismPreference,3,Scaffold1069, 6, t).. Stacktrace follows:org.postgresql.util.PSQLException: ERROR: null value in column "name" violates n ot-null constraint Detail: Failing row contains (308641, 0, null, null, org.bbop.apollo.UserOrgan ismPreference, 3, Scaffold1069, 6, t). at org.postgresql.core.v3.QueryExecutorImpl.receiveErrorResponse(QueryEx ecutorImpl.java:2161) at org.postgresql.core.v3.QueryExecutorImpl.processResults(QueryExecutorImpl.java:1890) at org.postgresql.core.v3.QueryExecutorImpl.execute(QueryExecutorImpl.java:255) at org.postgresql.jdbc2.AbstractJdbc2Statement.execute(AbstractJdbc2Statement.java:559) at org.postgresql.jdbc2.AbstractJdbc2Statement.executeWithFlags(AbstractJdbc2Statement.java:417)

— Reply to this email directly or view it on GitHub https://github.com/GMOD/Apollo/issues/296.

littlebunch commented 9 years ago

Thanks. That worked.

monicacecilia commented 9 years ago

@nathandunn can you please do the same on icebox? Tracks are not loading there either.

nathandunn commented 9 years ago

I think this is unrelated to Gary's problem, but something is seriously wrong, nonetheless. It is loading the JBrowse mainline inexplicably instead of the release.

Anyway, I patched it on icebox. You may need to quit your browse entirely. I'll look for a more permanent solution.

nathandunn commented 9 years ago

Closing this in favor of #297.

monicacecilia commented 9 years ago

@nathandunn gracias.