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60 lines
2.6 KiB
Python
60 lines
2.6 KiB
Python
import os
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import string
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import tempfile
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from base.driver_util import FRAMEWORK_UPLOAD_TOOL_CONF
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from base.populators import DEFAULT_TIMEOUT
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# Needs a longer timeout because of the conda_auto_install.
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CONDA_AUTO_INSTALL_JOB_TIMEOUT = DEFAULT_TIMEOUT * 3
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SCRIPT_DIRECTORY = os.path.abspath(os.path.dirname(__file__))
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TOOL_SHEDS_CONF = os.path.join(SCRIPT_DIRECTORY, "tool_sheds_conf.xml")
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SHED_TOOL_CONF = string.Template("""<?xml version="1.0"?>
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<toolbox tool_path="$shed_tools_path">
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</toolbox>""")
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SHED_DATA_MANAGER_CONF = """<?xml version="1.0"?>
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<data_managers>
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</data_managers>"""
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SHED_DATA_TABLES = """<?xml version="1.0"?>
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<tables>
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</tables>"""
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class UsesShed(object):
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@classmethod
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def configure_shed_and_conda(cls, config):
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cls.conda_tmp_prefix = tempfile.mkdtemp()
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cls.shed_tools_dir = tempfile.mkdtemp()
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cls.shed_tool_data_dir = tempfile.mkdtemp()
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cls._test_driver.temp_directories.extend([cls.conda_tmp_prefix, cls.shed_tool_data_dir, cls.shed_tools_dir])
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config["conda_auto_init"] = True
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config["conda_auto_install"] = True
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config["conda_prefix"] = os.environ.get('GALAXY_TEST_CONDA_PREFIX') or os.path.join(cls.conda_tmp_prefix, 'conda')
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config["tool_sheds_config_file"] = TOOL_SHEDS_CONF
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shed_tool_config = os.path.join(cls.shed_tools_dir, 'shed_tool_conf.xml')
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config["tool_config_file"] = "%s,%s" % (FRAMEWORK_UPLOAD_TOOL_CONF, shed_tool_config)
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config["shed_data_manager_config_file"] = os.path.join(cls.shed_tool_data_dir, 'shed_data_manager_config_file')
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config["shed_tool_data_table_config"] = os.path.join(cls.shed_tool_data_dir, 'shed_data_table_conf.xml')
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config["shed_tool_data_path"] = cls.shed_tool_data_dir
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with open(shed_tool_config, 'w') as tool_conf_file:
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tool_conf_file.write(SHED_TOOL_CONF.substitute(shed_tools_path=cls.shed_tools_dir))
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with open(config["shed_data_manager_config_file"], 'w') as shed_data_config:
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shed_data_config.write(SHED_DATA_MANAGER_CONF)
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with open(config["shed_tool_data_table_config"], 'w') as shed_data_table_config:
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shed_data_table_config.write(SHED_DATA_TABLES)
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def install_repository(self, owner, name, changeset, tool_shed_url='https://toolshed.g2.bx.psu.edu'):
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payload = {
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'tool_shed_url': tool_shed_url,
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'name': name,
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'owner': owner,
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'changeset_revision': changeset
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}
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create_response = self._post('/tool_shed_repositories/new/install_repository_revision', data=payload, admin=True)
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self._assert_status_code_is(create_response, 200)
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