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20523 Commits
Author SHA1 Message Date
Nicola Soranzo 4a87bb42e6 Merge branch 'release_19.01' into release_19.05 2019-06-03 18:13:05 +01:00
Nicola Soranzo fd02b745c3 Merge branch 'release_18.09' into release_19.01 2019-06-03 18:06:45 +01:00
mvdbeek 44256971eb Fix ColumnSetAction post job action 
If columns are specified as integers this would fail currently.
Reported by Peter Briggs on the [mailing list](https://lists.galaxyproject.org/archives/list/galaxy-dev@lists.galaxyproject.org/thread/PXLCVKIZ5LW3MLI6333PFMANYGOCDLD2/)
 2019-05-31 10:44:45 +02:00
John Chilton 9c960c2db8 Merge pull request #8056 from mvdbeek/possibly_fix_amqp_issue_on_mules 
[19.05] Release ampq connection after initial connect
 2019-05-30 14:15:21 -04:00
mvdbeek 514154e36b Release ampq connection after initial connect 
We need to call `connection.connect()` to avoid
`'kombu.transport.sqlalchemy.Message' is not mapped`` errrors.
This is fine for for sqlalchemy transports, but the connection
is still open if we don't release the connection.

This is a problem when acquiring the connection with rabbitmq
transports. So instead we release the connection and acquire
a blocking connection from the connection pool. This sets up
the mapping and avoids `'kombu.transport.sqlalchemy.Message' is not
mapped`.
Not sure if this will fix @natefoo's issue as I haven't exactly
been able to reproduce the same error, but acquiring a blocking
connection failed outright without releasing the connection, so this is
probably a step in the right direction.
 2019-05-30 15:54:56 +02:00
Nicola Soranzo e0a5e39435 Merge branch 'release_19.01' into release_19.05 2019-05-30 10:33:51 +01:00
Nate Coraor c0c39d5969 Default the maximum grab limit for handler database preassignment 
methods to unlimited as intended. Document the config param.
 2019-05-29 15:25:55 -04:00
Nicola Soranzo 25ea088647 Update Conda for new installs to v4.6.14 
and conda-build to v3.17.8 .
 2019-05-28 00:36:22 +01:00
John Chilton 0e33056989 Merge pull request #8039 from mvdbeek/non_legacy_object_store_fix 
[19.05] Backport 7939: Fix non-eager object store with nested object stores
 2019-05-27 12:09:34 -04:00
mvdbeek 5b05866545 Explicitly create extra_files_path when discovering outputs with extra files 2019-05-27 14:37:53 +02:00
mvdbeek 563ae4d7d3 Raise ObjectNotFound if file does not exist in object store 
And return an empty string if a path does not exist when calling
`get_filename` or` get_extra_files_path` on a Dataset.
 2019-05-27 14:37:53 +02:00
John Chilton 419bae1f09 Don't calculate real path in tool action code if unused. 2019-05-27 14:37:53 +02:00
Nicola Soranzo 5c2da643c6 [19.05] Use byte comparison for contains and files_re_match (#8010) 
[19.05] Use byte comparison for contains and files_re_match
 2019-05-27 12:27:17 +01:00
Nicola Soranzo d9b0f54906 Try to verify tool test output first as Unicode 2019-05-26 15:07:36 +01:00
mvdbeek e988fdee87 Skip recording workflow outputs for input parameters 
These can come in as a literal parameter value, or as a dictionary like
{'id': 'encoded_id', 'src': 'hda'}, none of which is quite right.
 2019-05-24 10:45:18 +02:00
mvdbeek 6ea862ff79 Use sqlalchemy.inspect to find detached repositories 
Thanks for the suggestion Nicola!
 2019-05-23 14:05:30 +02:00
mvdbeek a398127ede Work with bytestrings in files_contains, files_re_match_* 
But read utf-8 unicode in `lines_diff`. This will replace non-utf8
characters and seems like a reasonable tradeoff for text files
mixed with byte contents, like pdfs.
 2019-05-23 13:43:59 +02:00
mvdbeek f204b33bf3 Fix repo cache when no install database is present 
Fixes https://github.com/galaxyproject/galaxy/issues/8015
 2019-05-23 11:55:19 +02:00
mvdbeek 2d71b0bdfe Use io.open with errors="repalce" instead of comparing byte strings 2019-05-23 11:07:06 +02:00
mvdbeek 9f6bc89d69 Do non-shallow file comparison 2019-05-22 17:59:49 +02:00
mvdbeek 30bec0028d Use bytestring comparisons in verify module 2019-05-22 17:45:00 +02:00
mvdbeek 8fea7e9048 Use byte comparison for contains 
I don't think there's any drawback open this
in byte mode.

Fixes https://github.com/galaxyproject/galaxy/issues/7957#issuecomment-493954901
 2019-05-21 11:09:13 +02:00
John Chilton 47b27bea3b Merge pull request #7989 from mvdbeek/fix_force_datatype_changes 
[19.05] Update tool output datatype in workflow editor if datatype changes
 2019-05-20 08:17:41 -04:00
mvdbeek ecc453b646 Group with statements and clean up docstring 2019-05-19 09:30:26 +02:00
mvdbeek 9c06527bbb Simplify convert_newlines_sep2tabs 
Just call convert_newlines with a compiled regex
 2019-05-19 09:30:26 +02:00
mvdbeek b67ddbf036 Drop (seemingly?) unused sep2tabs function 2019-05-19 09:30:26 +02:00
mvdbeek 0638240c82 Operate on blocks directly 2019-05-19 09:30:26 +02:00
John Chilton 1543c0b711 Merge pull request #8000 from jmchilton/backport_newline_stuff 
[19.05] Backport #7995
 2019-05-17 18:23:47 -04:00
John Chilton a5c010413b Merge pull request #7967 from mvdbeek/use_node_watch_for_monitoring_db 
[19.05] Use node-watch instead of fs.watch to watch for db changes
 2019-05-17 15:47:21 -04:00
mvdbeek b6185fc7e4 Fix line counting 2019-05-17 15:41:14 -04:00
mvdbeek 06aa7d21a8 Use byte replacement strategy 2019-05-17 15:41:13 -04:00
John Chilton 6887398a49 Binary variant of convert_newlines. 2019-05-17 15:41:13 -04:00
John Chilton 0e707f2901 Improve sniffing test cases. 2019-05-17 15:41:13 -04:00
John Chilton 73b92af8d9 Binary upload fix for interaction with FilePrefix stuff. 2019-05-17 15:41:13 -04:00
John Chilton d3f2ce009e Attempt binary conversion of newlines if UTF conversion fails. 2019-05-17 15:41:13 -04:00
John Chilton 85f9ead2a2 Improved newline conversion handling. 
- Fix bug where sep2tabs didn't work with '\r\n'
- Fix bug where sep2tabs didn't work with '\r' - we were opening it with universal newlines.
- Fix memory bug where convert_newlines would read unbounded buffers - other methods still do though :(.
- Simplify convert_newlines to just let universal newline handling handle the conversion.
 2019-05-17 15:41:13 -04:00
John Chilton 6000f79b6d Fix extra newlines in peek code. 
Behavior changes:
 - Now includes a trailing new line if the input contained a trailing newline.
 - Now returns only as many lines as are present if the file contains fewer lines than LINE_COUNT.
 2019-05-17 15:41:13 -04:00
mvdbeek 322c68c7d5 Distinguish tool datatype and PJA (=forced_dataype) 
This makes it easier switching back to the default datatype
and unifies front- and backend changes.
This fixes https://github.com/galaxyproject/galaxy/issues/7965
and https://github.com/galaxyproject/galaxy/issues/4813
 2019-05-16 19:42:22 +02:00
John Chilton 96d3f85372 Merge pull request #7972 from mvdbeek/subworkflow_simple_inputs 
[19.05] Include type in subworkflow parameter input module
 2019-05-15 14:09:35 -04:00
mvdbeek 2e9deddfa2 Include type in subworkflow module 
Fixes https://github.com/galaxyproject/galaxy/issues/7964,
thanks for the report @innovate-invent
 2019-05-15 17:51:11 +02:00
M Bernt 9658bc6e0c output_checker: added missing state in output 2019-05-15 08:11:56 -04:00
M Bernt f05c20e85f output_checker: fixed linter issues 2019-05-15 08:11:55 -04:00
M Bernt 63959e1b5c output_checker: fixed wrong comparison 
- fixed comparison (which was always true before -- except if my
intuition on how Bunch works is wrong)
- always log state to info
 2019-05-15 08:11:54 -04:00
Marius van den Beek 0aba240bca Use node-watch instead of fs.watch to watch for db changes 
fs.watch doesn't trigger inside of docker.
 2019-05-15 13:11:20 +02:00
John Chilton b03f0136a2 Re-version 19.05 as 19.05. 2019-05-14 08:16:21 -04:00
John Chilton 703c968788 Merge pull request #7944 from mvdbeek/expression_tool_improvements 
[19.05] Allow mapping over of expression tool params
 2019-05-14 08:12:38 -04:00
Nicola Soranzo 9ec6e8e545 Merge pull request #7954 from mvdbeek/no_jwd_in_stdout 
[19.05] Fix job working directory in stdout
 2019-05-13 22:37:58 -04:00
mvdbeek 3fb32df829 Make sure collections are populated before replacing parameters 2019-05-14 00:14:34 +02:00
mvdbeek 284f7bc46b Rework delaying/cancelling workflow evalation with non-data inputs 
We try to fail early if any (expression.json) dataset in a dataset
collection is not OK. Probably cheaper then delaying execution
many times.
 2019-05-14 00:14:34 +02:00
mvdbeek 974f45b043 Allow mapping over of expression tool params 
This allows feeding a collection of parameters values to a parameter
value. This enables https://github.com/galaxyproject/tools-iuc/pull/2404#issuecomment-491740393
for instance, where we normalize a collection based on a computed
parameter.
 2019-05-14 00:14:34 +02:00