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Commit Graph
2599 Commits
Author SHA1 Message Date
Enis Afgan 2f2153292b Merge pull request #6583 from VJalili/cloud_download_tool 
Send data to cloud
 2018-11-06 16:36:19 -05:00
Enis Afgan 566ffaf9d5 Update send tool help text 2018-11-05 15:53:47 -05:00
John Chilton f035d642ce Merge pull request #6844 from jmchilton/compressed_types_and_extra_files 
Infrastructure/API Support for Composite Uploads/Downloads
 2018-11-01 10:57:09 -04:00
vahid 6c07a0370d Update description on send tool wrapper. 2018-10-31 10:33:03 -07:00
vahid 341f7d6372 Update output label & tool name to compose a more intuitive log label. 2018-10-31 10:31:48 -07:00
vahid 43e5a1828d In Cloud send tool: surround error raising blocks of code in try-catch. 2018-10-29 11:05:46 -07:00
vahid 7433e2640b Extend the help section and refactor Authz to Cloud Authorization. 2018-10-28 12:09:23 -07:00
vahid 39bdb67273 Make duplicate object timestamp shorter and use _ instead of -. 2018-10-28 11:39:47 -07:00
vahid 6f56ff10b9 Remove @ & msec from send tool timestamp. 2018-10-28 11:11:51 -07:00
vahid ef70f20a58 Swap authz_id and bucket; bucket is the first parameter now. 2018-10-28 10:07:50 -07:00
vahid e30460049f Remove _ and capitalize each work in "overwrite_existing". 2018-10-28 10:04:34 -07:00
vahid a236c64ea7 Repalce "sys.exc_info" with "Exception as e" in cloud Send tool wrapper. 2018-10-25 20:48:06 -07:00
vahid b72e08e8b8 Merge and resolve conflicts. 2018-10-25 19:07:33 -07:00
vahid d4d659a851 Replace the hardcoded msg with the exception msg in the cloud send tool. 2018-10-25 13:23:18 -07:00
vahid 8c95f174ba Fix lint issues. 2018-10-24 21:45:46 -07:00
vahid 8543231b40 Surround getting cloudauthz cred. in Send tool in a try-catch block. 2018-10-24 21:21:45 -07:00
Nicola Soranzo f4203ca051 Fix errors reported by flake8 3.6.0 
Ignore W504.
 2018-10-24 23:22:19 +01:00
John Chilton dd6b185ab8 Implement composite uploads on arbitrary datatypes. 
Prior to this, composite uploads were only allowed for select data types. As far as I can tell, the framework itself allows arbitrary datatypes to have extra files. This allows the upload API to take in extra files for datatypes that aren't explicitly annotated has having extra files.

These may be specified one at a time or in directory structures via tar files.
 2018-10-24 09:55:25 -04:00
Nicola Soranzo 949dcfdbc3 Do not log exceptions twice 
`logging.exception()` already adds the the exception information after
the supplied message.

Also: the `message` attribute of `Exception` class has been dropped in
Python 3, always use `str(e)`.

xref. https://github.com/galaxyproject/galaxy/issues/1715
 2018-10-24 12:57:05 +01:00
vahid 47b41d1bb0 Add timestamp, and transfer ET & rate to the Send to cloud tool's log. 2018-10-23 16:27:13 -07:00
Pierrick ROGER efc7864cab Merge branch 'dev' into feature/isa_data_type 2018-10-18 10:36:49 +02:00
vahid 8f11f78aa2 download > send refactoring in the tool. 2018-10-16 12:30:00 -07:00
vahid b62e0476be cloud Download > Send refactoring in tool wrapper, & related places. 2018-10-16 12:28:42 -07:00
vahid 01a124314d Rename cloud/download.* to cloud/send.* 2018-10-16 12:25:12 -07:00
vahid e943ec2bb4 Rename cloud download tool log dataset. 2018-10-15 10:43:13 -07:00
vahid 3ce2a35647 Update print func syntax in cloud download tool to adhere with py3 req. 2018-10-15 10:40:55 -07:00
vahid 847f66340d Remove a comment from download tool wrapper. 2018-10-11 13:42:51 -07:00
vahid 4305e2c56c Add some logging steps in the cloud download tool. 2018-10-11 13:18:12 -07:00
vahid 6504fe6ef1 Always pass user_id as int to authnz/managers so to avoid check & cast. 2018-10-11 09:55:35 -07:00
vahid 9eabf5c6c6 Only download tool wrapper creates tmp credentials tmp file. 2018-10-10 23:42:33 -07:00
vahid 1efa294198 Encode and decode authnz id in download tool wrapper & manager. 2018-10-10 23:35:31 -07:00
vahid 8cd1b0e118 Remove hidden credentials_file arg from download tool wrapper. 2018-10-10 23:24:39 -07:00
vahid d9baf394d5 Cloud download tool: don't create cred. files if manager has provided. 2018-10-10 23:03:22 -07:00
vahid b3a12919ca Update download tool wrapper to leverage tmp credentials in tmp file. 2018-10-10 20:51:11 -07:00
vahid 81eabec6e6 Update cloud download to adhere with cloudbridge v1 interface changes. 2018-10-10 20:47:51 -07:00
vahid cf919d7bef Do not assert provider name in cloud download tool. 2018-10-10 20:46:23 -07:00
vahid 9cf7cf6b1e In the cloud download tool, accept credentials via a tmp file only. 2018-10-10 20:45:33 -07:00
vahid 8413f77829 Merge remote-tracking branch 'upstream/dev' into cloud_download_tool 
# Conflicts:
#	lib/galaxy/managers/cloud.py
#	lib/galaxy/webapps/galaxy/api/cloud.py
 2018-09-25 09:50:06 -07:00
Nicola Soranzo 0c931235af Change all remaining old-style classes to new style 2018-09-17 12:26:07 +01:00
Nicola Soranzo ba22818ff4 Merge pull request #6668 from gvlproject/genomespaceclient_upgrade 
Upgraded genomespaceclient to newer version
 2018-09-07 17:56:38 +01:00
mvdbeek c939e7bb61 Bump version of Summary Statistics for rpy2 version update 2018-09-05 18:24:05 +02:00
mvdbeek 7f220276cc py3: Fix comp1 tool 2018-09-05 17:43:53 +02:00
mvdbeek 72f95ba9c4 Test bed_to_bigbed using compare="sim_size" 2018-09-05 14:22:01 +02:00
mvdbeek 906951f28e Single-quote paths in solid_qual_stats and fix test 
by using sim_size -- we have different float precision between py2 and
py3.
 2018-09-05 14:22:01 +02:00
mvdbeek 36196bd2be Specify maf ftype in maf_to_interval.xml 2018-09-05 14:22:01 +02:00
mvdbeek aee261daf7 Fix random header order in MAF to FASTA 2018-09-05 14:22:01 +02:00
mvdbeek e8d0ce39cf Fix random order of fasta headers in maf_to_bed 2018-09-05 14:22:01 +02:00
mvdbeek f22f0ebb2f Sort maf_split_by_species test output 2018-09-05 14:22:01 +02:00
mvdbeek 4acfd9a770 Fix sffextractor tests by requiring python 2.7 2018-09-05 14:22:01 +02:00
mvdbeek 05f18d029b Fix linkToGProfile test 2018-09-05 14:22:01 +02:00