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30042 Commits
Author SHA1 Message Date
Marius van den Beek 99e36b0035 Merge pull request #13224 from natefoo/use-gravity 
Use Gravity to run Galaxy
 2022-01-28 19:25:38 +01:00
Marius van den Beek 4fe4737e3a Merge pull request #13186 from bernt-matthias/topic/lint-context2 
Provide even more context to the lint context
 2022-01-28 19:21:00 +01:00
M BerntandMarius van den Beek 1bc2b4f2c6 Fix typo 
Co-authored-by: Marius van den Beek <m.vandenbeek@gmail.com>
 2022-01-28 19:18:54 +01:00
Matthias Bernt 8f94fbeb61 more linting refactoring 
Special LintMessage for XML:

- one adding line and file name and
- one adding XPath

added error and report level class

also added doc string
 2022-01-28 17:14:58 +01:00
Nate Coraor b7dce6e06b Gravity 0.9.0 is released 2022-01-27 15:11:05 -05:00
Matthias Bernt 665d83e5ef eliminate node_props 2022-01-27 17:14:46 +01:00
Matthias Bernt f3ba64e977 refactoring of LintMessage 
subclassed XMLLintMessage
 2022-01-27 15:35:01 +01:00
Matthias Bernt 33807be8c7 add type annotations 2022-01-27 12:14:18 +01:00
Matthias Bernt 9d6bfad255 adapt tool loader test 
when loading macros from imported files
the base property of the node is
overwritten.

this adds a xml:base property to the node
which is printed in the test
 2022-01-26 20:51:39 +01:00
Nate Coraor 11441c8c68 Use git URL in requirements for testing, thanks @mvdbeek 2022-01-26 14:51:27 -05:00
Matthias Bernt 1d1bae8453 add function to return lint context 
this adds functionality to the linter functions to return the lint
context. without breaking previous behavior.

Planemo seems to use

- lint_tool_source (which returned the fail state) and
- lint_tool_source_with (which returned nothing)

For the later a parameter has been added to make the linter silent
and the lint context is now returned.

For the former a variant has been added which returns the lint context.
 2022-01-26 20:16:02 +01:00
mvdbeek 28072009d2 Rewrite parameterized pytests to regular test 
The .. and  ... and ... and within a lambda gives you
no chance to debug the test without a print statement or
a debugger.

Co-authored-by: Marius van den Beek <m.vandenbeek@gmail.com>
 2022-01-26 18:27:44 +01:00
Marius van den Beek 4df0914d3d Merge pull request #13139 from bernt-matthias/fix/metadata-validation 
fix MetadataValidator
 2022-01-26 17:24:32 +01:00
Marius van den Beek fce520f335 Merge pull request #13188 from guerler/route_import_for_anon 
Fix redirect to login page when login is required to perform operations
 2022-01-26 12:47:27 +01:00
Marius van den Beek c6bf4cfb3b Merge pull request #13223 from gallardoalba/Add_compression_tools 
Add compression converter
 2022-01-26 12:45:01 +01:00
mvdbeek 32a1bfddc2 Bind tool_xml to node_props, so we don't have to pass it around 2022-01-26 12:40:03 +01:00
M BerntandMarius van den Beek aba0e58aac Fix yaml tool type 
Co-authored-by: Marius van den Beek <m.vandenbeek@gmail.com>
 2022-01-26 09:51:39 +01:00
Matthias Bernt 6706ddb69e fix deprecation warning 
if general_node is not None that this syntax is deprecated
(would return True if the node has no children)
 2022-01-26 09:51:39 +01:00
Matthias Bernt 19e9ea37fb revert str function for lint messages 
such that the original bahavior is unchanged
and add pretty print for use in external apps like planemo
 2022-01-26 09:51:39 +01:00
Matthias Bernt 29f3f40296 add file name to linter message 
- add fname to LintMessage
- LintContext make lint messages persistent over multiple linter calls
  before the messages were reset before the call of the next linter
  which is "impractical" if we want to use the lintmessages eg in
  planemo
- add test for linting a tool + (internal and external) macros
  to ensure that the fname and line number is correct
- add a simple linter test for yaml and json tools
 2022-01-26 09:51:38 +01:00
Matthias Bernt 977f0fa881 xsd: make name attribute required 2022-01-26 09:50:59 +01:00
Matthias Bernt b7ef626fdf fix node.base to macro file 
while parsing macros
 2022-01-26 09:50:59 +01:00
Matthias Bernt 5ea6253e65 two minor improvements to cwl and yaml tools 
in preparation to get linter tests running for such tools

cwl:

- remove a print from SchemaLoader

yaml:

- define YamlToolSource.parse_tool_type otherwise yaml tools are parsed
  like xml tools
- parse_version: return a string, otherwise 1.0 is treated as float
  which makes the linter (and probably more) fail
 2022-01-26 09:50:59 +01:00
Matthias Bernt 4e237d84e2 lint for invalid regex in stdio regex 2022-01-26 09:50:58 +01:00
mvdbeek 0b2ca51c17 Remove CONVERTER_interval_to_bed_0 from suitable converter 
There's no point in converting from bed to bed.
 2022-01-26 09:40:24 +01:00
mvdbeek 7e2e9bbe9f Fix test section 2022-01-26 09:40:24 +01:00
mvdbeek e4407b4c88 Don't offer converting to the same datatype 2022-01-25 21:30:54 +01:00
mvdbeek 0a0e835659 Make tests more robust 2022-01-25 21:07:33 +01:00
mvdbeek c57b90e9b4 Fix input and output names 2022-01-25 20:56:10 +01:00
guerler 15edf02de4 Fix redirect to login page when login is required to perform operations 2022-01-25 14:31:50 -05:00
Marius van den Beek ecf714475c Merge pull request #13175 from annefou/grib 
Add new datatype GRIB
 2022-01-25 16:04:53 +01:00
Dannon 2547da5586 Merge pull request #12528 from bernt-matthias/topic/n-col-assert 
Various extensions and improvements for asserts
 2022-01-25 08:42:05 -05:00
mvdbeek 302ff009c8 Open grib file in binary mode 2022-01-25 14:24:23 +01:00
Cristóbal Gallardo 92b2f6f99a Include modifications suggested by Marius 2022-01-25 13:57:11 +01:00
mvdbeek feb99b3a20 Seek to right position, then read 2022-01-25 13:02:38 +01:00
mvdbeek d879f94ead Fix grib sniffer 
The initial code had two read(4) calls, so the offsets weren't correct.
 2022-01-25 12:58:27 +01:00
Marius van den Beek a68b716743 Merge pull request #13178 from bernt-matthias/topic/stdio/exit-code-parsing 
Fix stdio parsing
 2022-01-25 12:40:02 +01:00
Cristóbal GallardoandMarius van den Beek bb5672cbfe Apply suggestions from code review 
Co-authored-by: Marius van den Beek <m.vandenbeek@gmail.com>
 2022-01-25 12:12:32 +01:00
Cristóbal GallardoandMarius van den Beek 60db87fa51 Update lib/galaxy/datatypes/converters/uncompressed_to_gz.xml 
Co-authored-by: Marius van den Beek <m.vandenbeek@gmail.com>
 2022-01-25 12:09:31 +01:00
Simon Bray a8e85bf0e8 change display_in_upload to true for PHAR datatype 2022-01-25 09:21:47 +01:00
Dannon 6df67a9038 Merge pull request #13228 from itisAliRH/Remove-jquery.complexify-from-everywhere 
Remove `jquery.complexify` from everywhere
 2022-01-24 23:06:36 -05:00
Alireza Heidari f23f5d9cc7 Remove toolshed password strength from register and change password 2022-01-25 02:49:03 +03:30
Marius van den Beek 98734112e7 Merge pull request #12900 from galaxyproject/dependabot/pip/lib/galaxy/dependencies/tensorflow-2.5.2 
Bump tensorflow from 2.5.1 to 2.5.2 in /lib/galaxy/dependencies
 2022-01-24 20:34:41 +01:00
Alireza Heidari 98d2a34acc Update change_password.mako 2022-01-24 23:04:25 +03:30
Alireza Heidari c41b890a19 Replace check password strength in toolshed register 2022-01-24 23:04:25 +03:30
Alireza Heidari 04ed8f123c Replace check password strength in toolshed change_password 2022-01-24 23:04:25 +03:30
Dannon b69e656b12 Merge pull request #13219 from wm75/patch-1 
Enable display of BAM data without sequence info
 2022-01-24 14:21:02 -05:00
Dannon 976cbebe6c Merge pull request #13159 from davelopez/fix_libraries_non_admin_permissions 
Assorted Data Libraries fixes
 2022-01-24 13:50:07 -05:00
Marius van den Beek 1bb557c74a Merge pull request #13003 from galaxyproject/dependabot/pip/lib/galaxy/dependencies/python-ldap-3.4.0 
Bump python-ldap from 3.2.0 to 3.4.0 in /lib/galaxy/dependencies
 2022-01-24 18:49:44 +01:00
Marius van den Beek 5df80bd0b7 Merge pull request #13171 from ic4f/dev_sa20warning 
Enable setting SQLALCHEMY_WARN_20
 2022-01-24 18:47:35 +01:00