16.04¶

Enhancements¶

Overhaul of Tools and Jobs Pull Request 1688
Implement an Embedded Pulsar Job Runner Pull Request 2057
Use the API to install repositories instead of loading the Tool Shed in an iframe. (Beta) Pull Request 1392

Phinch interactive environment (thanks to @shiltemann.) Pull Request 1647
Add iobio external display applications for BAM and VCF. Pull Request 1926
add chemical datatypes (thanks to @bgruening.) Pull Request 1941
Scratchbook tour Pull Request 1463
Work toward automating release management. Pull Request 1613
Basic tool error Sentry reporting. Pull Request 1900
disable ‘hg push’ to TS repositories Pull Request 2033
Generic GIE Launcher, GIE Image Chooser, multiple datasets (thanks to @erasche.) Pull Request 1403
The entire Python source code is now continuously checked with flake8 for PEP-8 style consistency and common errors. The last 3500 errors were fixed in this release (thanks to @nsoranzo.) Pull Request 1489, Pull Request 1713, Pull Request 1755

Implement new GIE proxy (thanks to @erasche.) Pull Request 1807
Workflow editor overview click navigation Pull Request 1843
API, history contents: allow filters, limit/offset, and ordering Pull Request 1602
datalibs: introduce folder management; fix various glitches; refactor Pull Request 1562
Add makefile target for release process (thanks to @erasche.) Pull Request 1433
libraries: provide select all/none options when importing Pull Request 1970
libraries: add ‘create history &import to it’ feature Pull Request 2017
Bcf.gz to bcf (and reverse) converters + bcf_bgzip data type (thanks to @markiskander.) Pull Request 1148
Update SnpEffDb and SnpSiftDbNSFP for SnpEff v4.1 (thanks to @jj-umn.) Pull Request 1280
Docker Testing - Newer versions of phantomjs and casperjs, in container wheels. Pull Request 1449
Add run_toolshed_tests.html to .gitignore . (thanks to @nsoranzo.) Pull Request 1456
Allow sorting of discover_datasets elements. Pull Request 1512
Cleanup common ui elements, add test cases Pull Request 1519
add minor styling to tour popover Pull Request 1539
Code design and legacy cleanup of datatypes and metadata. Pull Request 1556
show_params input walking Pull Request 1561
Add API endpoint for fetching all metadata for a repository. Pull Request 1565
Fix parameter validation Pull Request 1572
Remove recovery hack for REALLY old jobs. Pull Request 1574
Clarify area github tags. Pull Request 1579
update pinned-requirements.txt (thanks to @matthdsm.) Pull Request 1605
Improve dbkey handling for discovered datasets. Pull Request 1610
Various improvements to the heartbeat Pull Request 1614
Visualization plugins: add routes that more closely match potential static assets. Pull Request 1615
Disable individual file metadata changes in upload Pull Request 1625
added resolver dependency display to the tool view page (thanks to @zipho.) Pull Request 1632
Cherry-picked changes from pull request #1392. Pull Request 1821
Export toolshed repository information for workflow portability (thanks to @mvdbeek.) Pull Request 1636
Lint optional handling on conditional test parameters. Pull Request 1639
Updated hashes for bioblend v0.7.0 (thanks to @matthdsm.) Pull Request 1646
Add tox startup (run.sh) test and test on OS X and linux (thanks to @mvdbeek.) Pull Request 1649
Optionally pass dataset lists as a single file within tool wrappers (thanks to @einon.) Pull Request 1658
add a zip datatype which won’t be extracted (thanks to @lecorguille.) Pull Request 1665
Tour improvements and bugfixes Pull Request 1671
Add Marius van den Beek to Galaxy committer group. Pull Request 1699
Revise tool parameter handling, remove redundancies Pull Request 1711
Python 2/3 string handling (thanks to @mvdbeek.) Pull Request 1731
workaround for error message on tool lookup in case original toolshed had been disabled (thanks to @mvdbeek.) Pull Request 1738
Make api/tools return tool_shed_repository information. (thanks to @mvdbeek.) Pull Request 1752
Use visit inputs for check_and_update_param_values Pull Request 1764
Update makefile and add the script I used to apply security patches for 16.01 Pull Request 1793
Implement dataset empty input validator. Pull Request 1808
Makefile help target + formatting (thanks to @erasche.) Pull Request 1824
Add license and repository information to package.json. Pull Request 1829
Improved logging during tool executions. Pull Request 1832
Do not access the history when loading the workflow editor Pull Request 1861
Tones down the warning message about tool changes (thanks to @bwlang.) Pull Request 1893
Use shared value serialization for tool model Pull Request 1901
adding contrib init for reports and modifying status check to have output by process in case multiprocess (thanks to @miloaec.) Pull Request 1911
Retrieve authentification also for long urls (thanks to @mvdbeek.) Pull Request 1912
Modify run.sh to add –restart option, for a more consistent use of parameters. (thanks to @remimarenco.) Pull Request 1914
Rename tool_shed_get to url_get. Pull Request 1918
Allow testing element counts in tool output collections. Pull Request 1942
Use database query rather than dataset iteration to compute dataset counts in saved histories grid. Pull Request 1948
Add “new” state to list of dataset states in saved history list. Pull Request 1949
Add IUC as a new default bioconda channel (thanks to @bgruening.) Pull Request 1950
More job related timing logging. Pull Request 1956
Improvements to workflow scaling performance testing scripts. Pull Request 1958
Optimization for discovering datasets for dynamic output collection. Pull Request 1959
Improve tabular datatypes. (thanks to @brenninc and @nsoranzo.) Pull Request 1968, Pull Request 2317
Optimize adding datasets to large histories. Pull Request 1983
Much more friendly route mapping. Pull Request 2002
Revise content selection, add test cases Pull Request 2011
Don’t setup a default tool_data_table_config_path in the shed. Pull Request 2025
data_column to json config file (thanks to @bgruening.) Pull Request 2026
Revise input wrapper, add test cases Pull Request 2027
enable obfs datatype during upload (thanks to @bgruening.) Pull Request 2028
Better element_identifier handling in repeat sections (thanks to @mvdbeek.) Pull Request 2029
Pulsar-As-A-Dependency Pull Request 2052
Simplify Workflow sharing menu (thanks to @nturaga.) Pull Request 2060
Add Phinch as an external display application. Pull Request 2069
For non-shed tool data - read loc from sample if available. Pull Request 2070
tool lineage for versionless toolshed tool_ids (thanks to @mvdbeek.) Pull Request 2082
make new beta TS tools installation via API configurable Pull Request 2088
Patch in visual separation of section parameters (thanks to @erasche.) Pull Request 2091
Add sample supervisor config (thanks to @mvdbeek.) Pull Request 2096
Fix cli runner: use embed_metadata_in_job parameter (thanks to @ThomasWollmann.) Pull Request 2107
Switch Dockerized commands to use sh instead of bash. Pull Request 2282

Remove IPython IE, which was replaced by Jupyter IE. (thanks to @bgruening.) Pull Request 1402
Added py34-lint tox target but forgot to update .travis.yml. Pull Request 1457
fix old jobparam hack for importing files to library Pull Request 1488
An attempt to add limit/offset to history contents Pull Request 1490
Revise label handling in form Pull Request 1496
History UI: clean up. Pull Request 1522
Client-build, Webpack: add tasks to grunt for the common webpack tasks, update readme Pull Request 1523
Remove handlebars and rely solely on underscore templates Pull Request 1537
disable email notifications from travis Pull Request 1592
Remove unnecessary variable and assignment of job command (thanks to @einon.) Pull Request 1616
Implement the ratable mixin Pull Request 1618
Tour cleanup, remove a few globals. Pull Request 1621
Refactor workflow loading. Pull Request 1735
Swapping from svgfig to svgwrite Pull Request 1747
various libraries refactoring and bugfixes Pull Request 1751
Refactor the Html Datatype Class into text.py instead of images.py (thanks to @remimarenco.) Pull Request 1760
Drop python2.6 (deprecated, will not be supported in 16.04) from testing. Pull Request 1785
Rework history updating Pull Request 1788
Tests for some of the 16.01 security vulnerabilities Pull Request 1794
Reduce the use of mutable types in toolshed test framework’s method definitions. Pull Request 1813
Remove decryption/encryption of tool states Pull Request 1838
Do not import dumps and loads from galaxy.util.json . (thanks to @nsoranzo.) Pull Request 1840
Replace get_tool_shed_repository_by_tool_shed_name_owner_changeset_revision with get_repository_for_dependency_relationship. (thanks to @mvdbeek.) Pull Request 1868
Cosmetic comma fixes :) (thanks to @remimarenco.) Pull Request 1874
More debugging for transiently failing tool shed test. Pull Request 1939
Improve logging and retry for another TS test… Pull Request 1961
Add page layout test cases Pull Request 1991
Fix inconsistency in update state handling for tool modules Pull Request 1993
Functional Test Drivers Overhaul Pull Request 2016
Remove install and test code. Pull Request 2018
Remove twill functional tests we don’t actively run. Pull Request 2019
Fix transiently failing tool shed tests. Pull Request 2030
Libraries: faster, refactored, cleaned Pull Request 2031
Adjust testing directories so no python root is ever “tool_shed”. Pull Request 2067
Fix pbs runner file touch. Pull Request 2074
Move scripts out of lib/tool_shed. Pull Request 2093
Consolidate duplicated method in tool_shed/model. Pull Request 2099
Remove redundant ui divs, move masthead into #everything Pull Request 2182
Remove SLURM memory limit warning from stderr if the job was successful (thanks to @nsoranzo). Pull Request 2309

Fixes¶

upgrade mercurial wheel to latest (fixing CVE issues) Pull Request 2045
Add changeset_revision to tool attributes, avoid self.tool_shed_repository. (thanks to @mvdbeek.) Pull Request 1802
Do not convert spaces to tabs when importing datasets into a library (thanks to @nsoranzo). Pull Request 1985

Fix that typo in relation_builder. Pull Request 1453
URL generation tweaks for utils.js Pull Request 1478
Fix project linting for new pep8 Pull Request 1483
Fix Python 3 problem causing Travis failure of dev. Pull Request 1505
catch Exception and properly log errors Pull Request 1510
Change python print() format to be backward compatible with older versions. (thanks to @einon.) Pull Request 1520
Add js for mako based masthead Pull Request 1533
restrict blue popover to tours Pull Request 1577
small spelling error (thanks to @matthdsm.) Pull Request 1582
Fix installation of repository suites outside of tool panel section (thanks to @mvdbeek.) Pull Request 1601
Fixes <param argument=”–set” /> not working when help=”” is not set (thanks to @yhoogstrate.) Pull Request 1650
Fix validation for data source tools Pull Request 1654
Better fix for missing element identifier (thanks to @mvdbeek.) Pull Request 1693
Update david identifier types (thanks to @pavanvidem.) Pull Request 1696
Drop Ross from the committers group. Pull Request 1698
Wrap conditional test parameters Pull Request 1714
Remove len(stderr), breaks on recent docker versions (thanks to @mvdbeek.) Pull Request 1769
Strip URL of download_file and download_by_url install actions. (thanks to @nsoranzo.) Pull Request 1775
Fix tool form rendering of sections Pull Request 1783
Fix unused import. (thanks to @nsoranzo.) Pull Request 1796
Fix tool shed tests for commit e4a1d5727805168a9fd15aca1cdd21630ada2bbc (thanks to @nsoranzo). Pull Request 1798
Checks for api_key before checking for header from SSO. (thanks to @MatthewRalston.) Pull Request 1801
Ensure tool.changeset_revision is set… Pull Request 1806
Change many job mapped properties to lazy loads Pull Request 1809
Whitelist logging tweaks Pull Request 1819
Fix upload tool routing Pull Request 1827
Using node 5.7, ‘grunt style’ fails with the error: Pull Request 1841
Do not create text values for failed inputs Pull Request 1844
Prevent tours from kicking off within iframes Pull Request 1846
Fix repeat prefix Pull Request 1848
also update rrda when repairing or updating a repository (thanks to @mvdbeek.) Pull Request 1850
Fix regex validator Pull Request 1862
Tour routing overhaul Pull Request 1870
Add dedicated client endpoint to the root controller. Pull Request 1879
Update check_python.py now dropping Python 2.6 (thanks to @peterjc.) Pull Request 1883
Fix citation-model to fail silently/gracefully Pull Request 1884
Change to sentry middleware to work with modern raven clients. Pull Request 1895
svgfig->svgwrite in unpinned requirements Pull Request 1896
Fix icon sizes Pull Request 1934
Fix tool downloads in tool form Pull Request 1935
Fixing error in run.sh script (thanks to @kellrott.) Pull Request 1954
Fix typo: send–>sent Pull Request 1965
Fix farbtastic’s use of deprecated jquery fns by loading jq-migrate in galaxy.panels.mako . Pull Request 1972
Remove duplicate help target (thanks to @erasche.) Pull Request 1980
Fix booleans in workflow editor Pull Request 1990
libraries: change default size of fa in iconspans Pull Request 2000
libraries: move text out of icon spans for library dataset view Pull Request 2008
Fix unbound error that is possible if using tool bursting. Pull Request 2009
Fix multiple flag for workflow dataset inputs Pull Request 2021
fix duplication of select2 entries Pull Request 2022
Fix fluent query log serialization when datetime types are in use. Pull Request 2039
Workflow import fix when tools are missing. Pull Request 2048
Managers: remove UTC zone when parsing dates (thanks also to @nsoranzo). Pull Request 2042, Pull Request 2062, Pull Request 2065
Change user disk usage pgcalc function up a bit to make a slightly safer dry-run. Pull Request 2063
Allow tool confs with a tool_path to not be interpreted as shed confs. Pull Request 2066
Fix deps.command.download_command on Mac OS X. Pull Request 2075
Show sections in workflow run Pull Request 2087
Workflow section fix backport (thanks to @erasche.) Pull Request 2092
Run external local set_metadata jobs in the job’s working directory Pull Request 2094
make dependencies browsable again Pull Request 2101
Convert the DRMAA runner to use Pulsar’s DRMAA session wrapper Pull Request 2102
Updated to Dependency change in b167a741a444c3988447b0d63a1ba3dc5e4e62f5 (thanks to @Christian-B.) Pull Request 2104
Fix datatype list in workflow editor Pull Request 2105
Workaround for the toolshed’s hgweb. Pull Request 2106
Update debian init script (thanks to @mvdbeek.) Pull Request 2109
Rev Pulsar to 0.7.0.dev3. Pull Request 2122
change run_tool_shed.py to see the file in the correct lcoation (thanks to @nturaga.) Pull Request 2131
Fixes due to #2093 and #2018 (thanks to @nsoranzo.) Pull Request 2133
markupsafe.escape() in Python2 does not work on str containing non-ASCII characters (thanks to @nsoranzo.) Pull Request 2138
load options from config, not from options Pull Request 2139
fix/replace biomart data source Pull Request 2149
Add tool parameters back to parameters and expose for certain tools Pull Request 2156
Fix wrapper issue, overload __ne__ Pull Request 2161
Fix grouping tool and enhance performance when removing lines. Pull Request 2166
libraries: always fetch new permissions as we are reusing the view Pull Request 2176
Fix for redirecting a non-user when a tool has require_login=True. Pull Request 2180
Fix.published history long titles have to be truncated Pull Request 2189
fix a bug with missing history_id in libraries dataset import Pull Request 2190
Fix message in legacy panel mako Pull Request 2191
Prepass on remote user header based on maildomain and normalize config. Pull Request 2195
Extend to_json for dataset tool parameters Pull Request 2196
Pages parser fix Pull Request 2197
Translate data source tool parameters on parameter expansion Pull Request 2201
Sync job_script module with Pulsar to fix doctest. Pull Request 2203
Improve error message for data source tools, executed through the tool_runner controller Pull Request 2204
Add fixed validation check for data_source tools URL parameter Pull Request 2208
Fix tool action redirect url for non-default tools Pull Request 2211
Browse library date handling for non-ascii month abbreviations Pull Request 2214
Avoid reset of cursor position for input fields during manual entry Pull Request 2218
Add conditional statsd requirement Pull Request 2227
Fix js value validator Pull Request 2234
Encode collection reduce in serializable fashion Pull Request 2238
Update _condarc automatically (thanks to @bgruening.) Pull Request 2255
Truncate job name in DRMAA runner by default for PBSPro. Pull Request 2265
Cherrypick of encoding fix Pull Request 2266
If a Slurm post-mortem determines that a job is in a non-terminal state, return the job to the monitor queue Pull Request 2311
Unicodify pretty datetimes which can contain non-ASCII chars (thanks to @nsoranzo). Pull Request 2312
Relax default value acceptance condition Pull Request 2316
Fixes the proxy naming (thanks to @bgruening.) Pull Request 2333
Re-fix the bug with multiple preceding ‘/’ characters in the GIE proxy prefix Pull Request 2339
Do not pollute param_dict with a non JSONifiable dict (thanks to @nsoranzo.) Pull Request 2345