galaxy

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Nicola Soranzo ff0d28c35c Fix unicode_stream framework tests on Docker

This fixes the following traceback:
```
( unicode_stream ) > Test-1 ... galaxy.tools DEBUG 2018-08-21 09:40:59,052 Validated and populated state for tool request (0.098 ms)
galaxy.tools.actions INFO 2018-08-21 09:40:59,076 Handled output named out_file1 for tool unicode_stream (1.337 ms)
galaxy.tools.actions INFO 2018-08-21 09:40:59,080 Added output datasets to history (4.399 ms)
galaxy.tools.actions INFO 2018-08-21 09:40:59,084 Verified access to datasets for Job[unflushed,tool_id=unicode_stream] (0.058 ms)
galaxy.tools.actions INFO 2018-08-21 09:40:59,086 Setup for job Job[unflushed,tool_id=unicode_stream] complete, ready to flush (5.220 ms)
galaxy.tools.actions INFO 2018-08-21 09:40:59,127 Flushed transaction for job Job[id=354,tool_id=unicode_stream] (40.627 ms)
galaxy.tools.execute DEBUG 2018-08-21 09:40:59,127 Tool [unicode_stream] created job [354] (56.506 ms)
galaxy.tools.execute DEBUG 2018-08-21 09:40:59,132 Executed 1 job(s) for tool unicode_stream request: (79.434 ms)
galaxy.jobs.mapper DEBUG 2018-08-21 09:40:59,556 (354) Mapped job to destination id: local
galaxy.jobs.handler DEBUG 2018-08-21 09:40:59,561 (354) Dispatching to local runner
galaxy.jobs DEBUG 2018-08-21 09:40:59,571 (354) Working directory for job is: /tmp/tmp3drfmr6x/tmp_ywd33ar/tmpbzo4a1d9/database/job_working_directory_azry9a1y/000/354
galaxy.jobs DEBUG 2018-08-21 09:40:59,574 (354) Persisting job destination (destination id: local)
galaxy.jobs.runners DEBUG 2018-08-21 09:40:59,589 Job [354] queued (27.361 ms)
galaxy.jobs.handler INFO 2018-08-21 09:40:59,604 (354) Job dispatched
galaxy.jobs.runners ERROR 2018-08-21 09:40:59,715 (354) Failure preparing job
Traceback (most recent call last):
  File "/galaxy/lib/galaxy/jobs/runners/__init__.py", line 187, in prepare_job
    job_wrapper.prepare()
  File "/galaxy/lib/galaxy/jobs/__init__.py", line 874, in prepare
    self.command_line, self.extra_filenames, self.environment_variables = tool_evaluator.build()
  File "/galaxy/lib/galaxy/tools/evaluation.py", line 435, in build
    raise e
  File "/galaxy/lib/galaxy/tools/evaluation.py", line 431, in build
    self.__build_config_files()
  File "/galaxy/lib/galaxy/tools/evaluation.py", line 504, in __build_config_files
    self.__write_workdir_file(config_filename, config_text, param_dict, is_template=is_template)
  File "/galaxy/lib/galaxy/tools/evaluation.py", line 578, in __write_workdir_file
    f.write(value)
UnicodeEncodeError: 'ascii' codec can't encode characters in position 0-5: ordinal not in range(128)
galaxy.tools.error_reports DEBUG 2018-08-21 09:40:59,869 Bug report plugin <galaxy.tools.error_reports.plugins.sentry.SentryPlugin object at 0x7f92efb81668> generated response None
FAIL
```

which is due to the fact that the default encoding in the Docker image
is `ANSI_X3.4-1968`.

Also update `unicode_stream` test tool to IUC best practices.

2018-08-21 16:04:27 +01:00

tool-data

Add test tool demontrating filtering selections based on dbkey.

2015-07-31 11:09:45 +01:00

tools

Fix unicode_stream framework tests on Docker

2018-08-21 16:04:27 +01:00

webhooks

simplify Webhooks' structure

2018-02-01 12:18:01 -05:00

__init__.py

New functional test harness. Update to recent nose. No longer rely on nose to manage the embedded web server (this is not done in functional_tests.py). Log page contents to a temporary file on check_page_for_string error.