Mercurial > repos > bcclaywell > argo_navis

annotate venv/lib/python2.7/site-packages/planemo/galaxy_serve.py @ 0:d67268158946 draft

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planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
author bcclaywell
date Mon, 12 Oct 2015 17:43:33 -0400
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d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
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1 import contextlib
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2 import os
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3
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4 from planemo import galaxy_config
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5 from planemo import galaxy_run
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6 from planemo import io
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7
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8
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9 def serve(ctx, paths, **kwds):
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10 # TODO: Preceate a user.
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11 # TODO: Setup an admin user.
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12 # TODO: Pass through more parameters.
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13 # TODO: Populate test-data directory as FTP directory.
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14 daemon = kwds.get("daemon", False)
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15 if daemon:
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16 kwds["no_cleanup"] = True
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17
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18 with galaxy_config.galaxy_config(ctx, paths, **kwds) as config:
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19 # TODO: Allow running dockerized Galaxy here instead.
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20 run_script = os.path.join(config.galaxy_root, "run.sh")
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21 if daemon:
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22 run_script += " --daemon --wait"
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23 config.env["GALAXY_RUN_ALL"] = "1"
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24 else:
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25 run_script += " --server-name '%s' --reload" % config.server_name
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26 server_ini = os.path.join(config.config_directory, "galaxy.ini")
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27 config.env["GALAXY_CONFIG_FILE"] = server_ini
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28 cmds = [
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29 run_script,
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30 ]
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31 cmd = "; ".join(cmds)
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32 action = "Starting galaxy"
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33 galaxy_run.run_galaxy_command(
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34 ctx,
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35 cmd,
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36 config.env,
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37 action,
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38 )
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39 return config
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40
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41
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42 @contextlib.contextmanager
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43 def shed_serve(ctx, install_args_list, **kwds):
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44 config = serve(ctx, [], daemon=True, **kwds)
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45 install_deps = not kwds.get("skip_dependencies", False)
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46 try:
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47 io.info("Installing repositories - this may take some time...")
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48 for install_args in install_args_list:
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49 install_args["install_tool_dependencies"] = install_deps
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50 install_args["install_repository_dependencies"] = True
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51 install_args["new_tool_panel_section_label"] = "Shed Installs"
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52 config.install_repo(
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53 **install_args
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54 )
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55 config.wait_for_all_installed()
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56 yield config
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57 finally:
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58 config.kill()
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59 if not kwds.get("no_cleanup", False):
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60 config.cleanup()