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Author SHA1 Message Date
Dannon d76dbcec19 Merge pull request #10759 from mvdbeek/hide_hidden_workflows 
[20.09] Don't preload editor mako with hidden workflows
 2020-11-18 13:56:01 -05:00
mvdbeek 8968e0a256 Don't preload editor mako with hidden workflows 
Fixes https://github.com/galaxyproject/galaxy/issues/10746
 2020-11-18 17:33:43 +01:00
Björn Grüning 97e5c97359 Merge pull request #10747 from mvdbeek/make_extra_user_preferences_more_forgiving 
[20.09] Fix anonymous user uploads if file sources configured
 2020-11-18 15:59:26 +01:00
mvdbeek 6c76cf8178 Fix anonymous user uploads if file sources configured 
To get both file source uploads to work and anonymous uploads
you would need to use something like
```
${user.preferences.get('dropbox|access_token') if $user.preferences else ''}
```
This simplifies that back to the documented
```
${user.preferences['dropbox|access_token']
```

Overall I don't think we benefit from KeyErrors in the extra file
preferences, so I've made this `defaultdict(lambda: None)`, but we could
limit that to just the ProvidesUserFileSourcesUserContext.

Fixes https://github.com/galaxyproject/galaxy/issues/10595.
 2020-11-18 10:40:49 +01:00
John Chilton 4b331f1d38 Merge pull request #10744 from dannon/backportdocfix 
[20.09] typo in announce_user.rst
 2020-11-17 19:27:54 -05:00
Alex Ostrovsky e087762c15 Update 20.09_announce_user.rst 2020-11-17 17:52:41 -05:00
mvdbeek 00022427d5 Update version to 20.09 v20.09 2020-11-17 21:02:41 +01:00
Dannon c281eca1b5 Merge pull request #10739 from mvdbeek/20.09_release_notes 
[20.09] More release note updates
 2020-11-17 14:59:37 -05:00
mvdbeek a38dbc2db1 More updates 2020-11-17 20:54:41 +01:00
Dannon c5c6393eb0 Merge pull request #10730 from mvdbeek/backport_10508_plus_list_builder_fix 
[20.09] Backport list-of-pair copy fix, apply same fix to list builder
 2020-11-17 12:41:53 -05:00
Dannon 0878cc508c Merge pull request #10724 from OlegZharkov/pathbar-fix 
[20.09] Pathbar race bugfix
 2020-11-17 12:36:51 -05:00
mvdbeek e2032c1ca4 Merge branch 'release_20.05' into release_20.09 2020-11-17 16:50:05 +01:00
Marius van den Beek 587e5b0eb8 Merge pull request #10731 from mvdbeek/osx_startup_test_fix 
[20.05] Use newer setup-miniconda action
 2020-11-17 16:47:06 +01:00
mvdbeek 2696b7877e Use newer setup-miniconda action 2020-11-17 16:25:36 +01:00
Oleg Zharkov 75672b090d fix key 2020-11-17 16:16:47 +01:00
mvdbeek 69655b1b3a Only copy list elements if not hiding elements 
That syncs the behavior with the list pair builder.
 2020-11-17 16:00:50 +01:00
mvdbeek 60964cc64c Always hide HDAs when copying collections 2020-11-17 15:56:30 +01:00
Assunta DeSanto 4cfb166b03 fixing selenium test 2020-11-17 15:56:30 +01:00
Assunta DeSanto be3d16e7df modified list-of-pairs to copy datasets as hidden 2020-11-17 15:56:30 +01:00
Oleg Zharkov baadcdb4a7 merge pathbar with folderTopBar 2020-11-17 14:48:12 +01:00
Oleg Zharkov 30883a63ba vuefy pathbar 2020-11-17 14:00:04 +01:00
mvdbeek 6860ed0fd3 Merge branch 'release_20.05' into release_20.09 2020-11-16 21:08:13 +01:00
mvdbeek 3498fcf163 Merge branch 'release_20.01' into release_20.05 2020-11-16 21:05:27 +01:00
John Chilton 693191b132 Merge pull request #10723 from mvdbeek/backport_step_output_value_recovery 
[20.01] Backport invocation step output value recovery
 2020-11-16 14:49:15 -05:00
John Chilton ac74bfa720 Merge pull request #10704 from mvdbeek/cryptography_backport 
[20.01] Bump cryptography dependency to 3.2.1
 2020-11-16 14:49:00 -05:00
Oleg Zharkov 298dc9ae13 fix linting 2020-11-16 17:37:12 +01:00
Oleg Zharkov 7f3f0ce105 pathbar fix 2020-11-16 16:54:29 +01:00
mvdbeek f730e8b0a4 Silence DeprecationWarning for all job scripts 
Once we hit the job script we really don't want this to bleed through to
the stderr, since there's nothing a user can do to fix it.
It's a bit harsh, but I don't think this would hide dependency issues.
 2020-11-16 11:44:38 +01:00
mvdbeek 63a7cc1603 Add test for input parameter in nested workflow 2020-11-16 10:47:38 +01:00
mvdbeek 907b92845f Recover step output value 
in WorkflowProgress instance. Fixes running subworkflows with
parameter_input steps.
Fixes https://github.com/galaxyproject/galaxy/issues/8390 and
allows us to get rid of one FIXME I added when working around
https://github.com/galaxyproject/galaxy/issues/8248.
 2020-11-16 10:47:38 +01:00
John Chilton c11a3dc041 Merge pull request #10710 from mvdbeek/terminate_polling 
[20.09] Rework pollUntil* to avoid building up queries
 2020-11-12 20:53:46 -05:00
John Chilton 4e08413198 Merge pull request #10711 from mvdbeek/invocation_speedup 
[20.09] Speed up invocation serialization
 2020-11-12 20:53:02 -05:00
mvdbeek 22d67f003b Speed up invocation serialization 
Serializing a 2 step invocation with 2000 output datasets:
```
*** PROFILER RESULTS ***
show_invocation (/Users/mvandenb/src/galaxy/lib/galaxy/webapps/galaxy/api/workflows.py:905)
function called 1 times

         684631 function calls (643973 primitive calls) in 0.827 seconds

   Ordered by: cumulative time, internal time, call count
   List reduced from 942 to 40 due to restriction <40>

   ncalls  tottime  percall  cumtime  percall filename:lineno(function)
        1    0.000    0.000    0.812    0.812 workflows.py:905(show_invocation)
        1    0.000    0.000    0.752    0.752 workflows.py:161(get_invocation)
        1    0.000    0.000    0.746    0.746 query.py:935(get)
        1    0.000    0.000    0.746    0.746 query.py:1077(_get_impl)
        1    0.000    0.000    0.745    0.745 loading.py:211(load_on_pk_identity)
        1    0.000    0.000    0.745    0.745 query.py:3417(one)
        1    0.000    0.000    0.745    0.745 query.py:3381(one_or_none)
    24/21    0.000    0.000    0.745    0.035 loading.py:35(instances)
       11    0.000    0.000    0.742    0.067 loading.py:81(<listcomp>)
 16012/10    0.058    0.000    0.742    0.074 loading.py:509(_instance)
 14011/10    0.049    0.000    0.741    0.074 loading.py:710(_populate_full)
        1    0.000    0.000    0.741    0.741 strategies.py:1393(load_collection_from_subq)
        1    0.000    0.000    0.741    0.741 strategies.py:1332(get)
        1    0.000    0.000    0.741    0.741 strategies.py:1337(_load)
        1    0.003    0.003    0.614    0.614 loading.py:83(<listcomp>)
     2001    0.002    0.000    0.609    0.000 loading.py:84(<listcomp>)
     1999    0.002    0.000    0.596    0.000 strategies.py:2059(load_scalar_from_joined_existing_row)
     1999    0.003    0.000    0.586    0.000 strategies.py:2020(load_collection_from_joined_existing_row)
6002/2001    0.008    0.000    0.554    0.000 strategies.py:2054(load_scalar_from_joined_new_row)
     4036    0.006    0.000    0.290    0.000 attr.py:316(__call__)
     8012    0.023    0.000    0.284    0.000 custom_types.py:143(load)
7667/7291    0.005    0.000    0.187    0.000 langhelpers.py:880(__get__)
4001/3999    0.010    0.000    0.183    0.000 strategies.py:2010(load_collection_from_joined_new_row)
     6004    0.004    0.000    0.173    0.000 mutable.py:375(_parents)
     6004    0.169    0.000    0.169    0.000 weakref.py:343(__init__)
        2    0.000    0.000    0.097    0.048 query.py:3476(__iter__)
       12    0.000    0.000    0.095    0.008 query.py:3501(_execute_and_instances)
       12    0.000    0.000    0.094    0.008 base.py:952(execute)
       12    0.000    0.000    0.094    0.008 elements.py:296(_execute_on_connection)
       12    0.000    0.000    0.094    0.008 base.py:1088(_execute_clauseelement)
       12    0.000    0.000    0.078    0.007 base.py:1195(_execute_context)
       12    0.000    0.000    0.077    0.006 default.py:589(do_execute)
       12    0.076    0.006    0.077    0.006 {method 'execute' of 'psycopg2.extensions.cursor' objects}
     6012    0.004    0.000    0.062    0.000 type_api.py:1280(process)
        1    0.000    0.000    0.060    0.060 workflows.py:1355(__encode_invocation)
        1    0.000    0.000    0.060    0.060 workflows.py:275(serialize_workflow_invocation)
        1    0.009    0.009    0.060    0.060 __init__.py:5303(to_dict)
     6012    0.006    0.000    0.052    0.000 custom_types.py:98(process_result_value)
40190/40090    0.017    0.000    0.050    0.000 attributes.py:279(__get__)
     8012    0.025    0.000    0.047    0.000 state.py:677(unloaded)

```
without commit:
```
*** PROFILER RESULTS ***
show_invocation (/Users/mvandenb/src/galaxy/lib/galaxy/webapps/galaxy/api/workflows.py:905)
function called 1 times

         4006285 function calls (3865075 primitive calls) in 6.737 seconds

   Ordered by: cumulative time, internal time, call count
   List reduced from 730 to 40 due to restriction <40>

   ncalls  tottime  percall  cumtime  percall filename:lineno(function)
        1    0.000    0.000    6.723    6.723 workflows.py:905(show_invocation)
        1    0.000    0.000    6.720    6.720 workflows.py:1355(__encode_invocation)
        1    0.000    0.000    6.720    6.720 workflows.py:267(serialize_workflow_invocation)
        1    0.018    0.018    6.719    6.719 __init__.py:5303(to_dict)
40054/40052    0.024    0.000    6.688    0.000 attributes.py:279(__get__)
8034/4017    0.016    0.000    6.664    0.002 attributes.py:699(get)
     4017    0.022    0.000    6.600    0.002 strategies.py:665(_load_for_state)
     4013    0.007    0.000    6.494    0.002 <string>:1(<lambda>)
     4013    0.035    0.000    6.487    0.002 strategies.py:774(_emit_lazyload)
     4013    0.032    0.000    3.612    0.001 baked.py:421(__iter__)
        1    0.000    0.000    3.585    3.585 __init__.py:5476(jobs)
        1    0.000    0.000    3.584    3.584 __init__.py:1503(job_list)
        1    0.002    0.002    3.560    3.560 __init__.py:1505(<listcomp>)
     4014    0.014    0.000    3.411    0.001 query.py:3501(_execute_and_instances)
     2006    0.050    0.000    3.378    0.002 baked.py:557(_load_on_pk_identity)
     4014    0.006    0.000    3.167    0.001 base.py:952(execute)
     4014    0.005    0.000    3.159    0.001 elements.py:296(_execute_on_connection)
     4014    0.023    0.000    3.155    0.001 base.py:1088(_execute_clauseelement)
     4014    0.033    0.000    3.105    0.001 base.py:1195(_execute_context)
     4014    0.003    0.000    2.924    0.001 default.py:589(do_execute)
     4014    2.839    0.001    2.921    0.001 {method 'execute' of 'psycopg2.extensions.cursor' objects}
     2007    0.029    0.000    2.912    0.001 baked.py:539(all)
    10027    0.039    0.000    2.579    0.000 loading.py:35(instances)
     4014    0.005    0.000    1.283    0.000 loading.py:59(<listcomp>)
     4014    0.015    0.000    1.278    0.000 query.py:4345(row_processor)
10014/4014    0.304    0.000    1.261    0.000 loading.py:354(_instance_processor)
110078/56078    0.112    0.000    1.042    0.000 interfaces.py:559(create_row_processor)
6000/4000    0.030    0.000    0.871    0.000 strategies.py:1970(create_row_processor)
     4014    0.207    0.000    0.726    0.000 result.py:1268(fetchall)
     4014    0.005    0.000    0.501    0.000 loading.py:81(<listcomp>)
12013/6013    0.064    0.000    0.496    0.000 loading.py:509(_instance)
     4014    0.009    0.000    0.468    0.000 result.py:926(_soft_close)
     4014    0.010    0.000    0.451    0.000 base.py:899(close)
     4014    0.006    0.000    0.442    0.000 base.py:1031(close)
     4014    0.006    0.000    0.436    0.000 base.py:858(_checkin)
     4014    0.014    0.000    0.430    0.000 base.py:671(_finalize_fairy)
   110343    0.100    0.000    0.409    0.000 interfaces.py:518(_get_context_loader)
     4014    0.010    0.000    0.355    0.000 base.py:872(_reset)
     4014    0.012    0.000    0.343    0.000 default.py:539(do_rollback)
     4014    0.328    0.000    0.328    0.000 {method 'rollback' of 'psycopg2.extensions.connection' objects}
```
Of course we shouldn't serialize all of this if we don't need it,
but that's a quick and easy optimization.
 2020-11-12 23:47:16 +01:00
mvdbeek a366ba9dec Rework pollUntil* to avoid building up queries 
It won't fire off a new query before the previous hasn't been answered.
 2020-11-12 22:13:45 +01:00
Marius van den Beek b604d88ea9 Merge pull request #10709 from brinkmanlab/fix_safe_eval 
[20.09] Add 'Constant' to allowed node types.
 2020-11-12 22:05:48 +01:00
Marius van den Beek eb33b30b00 Merge pull request #10705 from bernt-matthias/topic/backport-fix-metadata 
[20.09] #8599 and #10691 backport dynamic options and metadata filter fix
 2020-11-12 20:04:53 +01:00
Nolan Woods ce8b463b15 Add 'Constant' to allowed node types. Resolves https://github.com/galaxyproject/galaxy/issues/10688 2020-11-12 11:00:58 -08:00
Matthias Bernt e044c307b4 revert previous and add element_is_set to MetadataWrapper 2020-11-12 16:03:30 +01:00
Matthias Bernt 8bc69affd5 allow access to metadata collection attributes 
follow up to https://github.com/galaxyproject/galaxy/pull/8599

in the planemo tests in the line https://github.com/bernt-matthias/galaxy/blob/1882aa641cdde1c51c077fd983f2241971308377/lib/galaxy/tools/parameters/dynamic_options.py#L205

r.metadata is sometimes a MetadataWrapper and sometimes a MetadataCollection

in the former case acccess to the `element_is_set` function defined in MetadataCollection is not possible.
 2020-11-12 16:03:30 +01:00
Matthias Bernt 0581e1b552 revert change to to_hda_representative 2020-11-12 16:02:35 +01:00
Matthias Bernt 0610084ec5 revert parsing of metadata files 2020-11-12 16:02:30 +01:00
M BerntandMarius van den Beek a5d44041eb Apply suggestions from code review 
Co-authored-by: Marius van den Beek <m.vandenbeek@gmail.com>
 2020-11-12 16:01:38 +01:00
mvdbeek 84f0ad4d4a Bump cryptography dependency to 3.2.1 2020-11-12 16:00:57 +01:00
M Bernt 4383bc6cce fix import order 2020-11-12 16:00:32 +01:00
M Bernt 99f9b1a636 import order 2020-11-12 15:57:24 +01:00
M Bernt a172943cad data_meta: linter fixes 2020-11-12 15:57:24 +01:00
M Bernt 7b503f36e0 data_meta: add separate test for paired collection 
otherwise the failing test can not be detected correctly
 2020-11-12 15:57:24 +01:00
M Bernt e5ac4f3143 dynamic options: from_dataset accept collections and multiple datasets 2020-11-12 15:57:24 +01:00
M Bernt 09c134c7d3 data_meta: simplify import and code 
code for getting ref_name from other_values and checking its type
has been simplified. to be reusable in the dynamic options it has been
moved to a function.
 2020-11-12 15:57:24 +01:00
M Bernt 76a96d371e data_meta: first test for metadata files 2020-11-12 15:57:24 +01:00