| Previous changeset 30:2191bd0798a9 (2017-10-13) Next changeset 32:7b955a58d8f2 (2017-10-20) |
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Commit message:
planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty |
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modified:
TrackHub.py apollo/ApolloInstance.py jbrowseArchiveCreator.py tool_dependencies.xml util/Reader.py util/subtools.py |
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added:
templates/apollo-arrow.yml |
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| diff -r 2191bd0798a9 -r 127037c49bc8 TrackHub.py --- a/TrackHub.py Fri Oct 13 16:19:03 2017 -0400 +++ b/TrackHub.py Mon Oct 16 18:03:58 2017 -0400 |
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| @@ -16,7 +16,7 @@ class TrackHub: - def __init__(self, inputFastaFile, apollo_user, outputFile, extra_files_path, tool_directory, trackType, apollo_host): + def __init__(self, inputFastaFile, apollo_user, outputFile, extra_files_path, tool_directory, trackType, apollo_host, user_email): self.rootAssemblyHub = None @@ -37,7 +37,7 @@ self.chromSizesFile = None # Set up apollo - self.apollo = ApolloInstance(apollo_host) + self.apollo = ApolloInstance(apollo_host, tool_directory, user_email) self.apollo_user = apollo_user # Set all the missing variables of this class, and create physically the folders/files |
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| diff -r 2191bd0798a9 -r 127037c49bc8 apollo/ApolloInstance.py --- a/apollo/ApolloInstance.py Fri Oct 13 16:19:03 2017 -0400 +++ b/apollo/ApolloInstance.py Mon Oct 16 18:03:58 2017 -0400 |
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| @@ -1,23 +1,52 @@ #!/usr/bin/env python +import os import json +import shutil +import tempfile import logging from util import subtools +from mako.lookup import TemplateLookup + class ApolloInstance(object): - def __init__(self, apollo_host): + def __init__(self, apollo_host, tool_directory, user_email): self.apollo_host = apollo_host + self.tool_directory = tool_directory + self.default_user = user_email self.logger = logging.getLogger(__name__) + self.apolloTemplate = self._getApolloTemplate() + self._arrow_init() + + def _arrow_init(self): + arrow_config = tempfile.NamedTemporaryFile(bufsize=0) + with open(arrow_config.name, 'w') as conf: + htmlMakoRendered = self.apolloTemplate.render( + apollo_host = self.apollo_host, + admin_user = self.default_user, + admin_pw = '1234' + ) + conf.write(htmlMakoRendered) + + home_dir = os.path.expanduser('~') + arrow_config_dir = os.path.join(home_dir, '.apollo-arrow.yml') + shutil.copyfile(arrow_config.name, arrow_config_dir) + self.logger.debug("Initated arrow: apollo-arrow.yml= %s", arrow_config_dir) + + + def _getApolloTemplate(self): + mylookup = TemplateLookup(directories=[os.path.join(self.tool_directory, 'templates')], + output_encoding='utf-8', encoding_errors='replace') + apolloTemplate = mylookup.get_template("apollo-arrow.yml") + return apolloTemplate def getHost(self): return self.apollo_host def createApolloUser(self, apollo_user, admin=None): p = subtools.arrow_create_user(apollo_user.user_email, apollo_user.firstname, apollo_user.lastname, apollo_user.password, admin) - print p - if p: - user_info = json.loads(p) - user_id = user_info.get('userId') - if not p or not user_id: + user_info = json.loads(p) + user_id = user_info.get('userId') + if not user_id: self.logger.debug("Cannot create new user: %s; The user may already exist", apollo_user.user_email) user_id = subtools.arrow_get_users(apollo_user.user_email) self.logger.debug("Got user_id for new or existing user: user_id = %s", str(user_id)) |
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| diff -r 2191bd0798a9 -r 127037c49bc8 jbrowseArchiveCreator.py --- a/jbrowseArchiveCreator.py Fri Oct 13 16:19:03 2017 -0400 +++ b/jbrowseArchiveCreator.py Mon Oct 16 18:03:58 2017 -0400 |
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| @@ -40,6 +40,7 @@ debug_mode = reader.getDebugMode() track_type = reader.getTrackType() #jbrowse_path = reader.getJBrowsePath() + apollo_path = reader.getApolloPath() apollo_host = reader.getApolloHost() apollo_user = reader.getApolloUser() @@ -54,7 +55,7 @@ # Create the Track Hub folder logging.info('#### JBrowseArchiveCreator: Creating the Track Hub folder ####\n') - trackHub = TrackHub(reference_genome, apollo_user, outputFile, extra_files_path, toolDirectory, track_type, apollo_host) + trackHub = TrackHub(reference_genome, apollo_user, outputFile, extra_files_path, toolDirectory, track_type, apollo_host, user_email) # Create Ordered Dictionary to add the tracks in the tool form order logging.info('#### JBrowseArchiveCreator: Preparing track data ####\n') |
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| diff -r 2191bd0798a9 -r 127037c49bc8 templates/apollo-arrow.yml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/templates/apollo-arrow.yml Mon Oct 16 18:03:58 2017 -0400 |
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| @@ -0,0 +1,10 @@ +## Apollo's Arrow: Global Configuration File. +# Each stanza should contian a single galaxy server to control. +# +# You can set the key __default to the name of a default instance +__default: local + +local: + url: ${apollo_host} + username: ${admin_user} + password: ${admin_pw} |
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| diff -r 2191bd0798a9 -r 127037c49bc8 tool_dependencies.xml --- a/tool_dependencies.xml Fri Oct 13 16:19:03 2017 -0400 +++ b/tool_dependencies.xml Mon Oct 16 18:03:58 2017 -0400 |
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| @@ -58,9 +58,6 @@ <actions architecture="x86_64" os="linux"> <action type="download_by_url">http://jbrowse.org/wordpress/wp-content/plugins/download-monitor/download.php?id=105</action> <action type="make_directory">$INSTALL_DIR/jbrowse</action> - <action type="set_environment"> - <environment_variable action="set_to" name="HOME">$INSTALL_DIR/jbrowse</environment_variable> - </action> <action type="shell_command"> export HOME=$INSTALL_DIR/jbrowse && ./setup.sh </action> @@ -89,6 +86,8 @@ export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/apollo && python setup.py install --install-lib $INSTALL_DIR/apollo </action> + <action type="make_directory">$INSTALL_DIR/apollo/config</action> + <action type="set_environment"> <environment_variable action="append_to" name="PYTHONPATH">$INSTALL_DIR/apollo</environment_variable> <environment_variable action="append_to" name="PATH">$INSTALL_DIR/apollo</environment_variable> |
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| diff -r 2191bd0798a9 -r 127037c49bc8 util/Reader.py --- a/util/Reader.py Fri Oct 13 16:19:03 2017 -0400 +++ b/util/Reader.py Mon Oct 16 18:03:58 2017 -0400 |
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| @@ -74,6 +74,10 @@ track_type = self.args.get("track_type") return track_type + def getApolloPath(self): + apollo_path = self.args.get("apollo_path") + return apollo_path + def getApolloHost(self): apollo_host = self.args.get("apollo_host") return apollo_host |
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| diff -r 2191bd0798a9 -r 127037c49bc8 util/subtools.py --- a/util/subtools.py Fri Oct 13 16:19:03 2017 -0400 +++ b/util/subtools.py Mon Oct 16 18:03:58 2017 -0400 |
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| @@ -342,7 +342,10 @@ array_call = ['arrow', 'users', 'create_user', user_email, firstname, lastname, password] if admin: array_call += ['--role', 'admin'] + logging.debug("%s", array_call) + print array_call p = subprocess.check_output(array_call) + print ("p = %s", p) return p def arrow_update_organism_permissions(user_id, organism, **user_permissions): @@ -364,9 +367,12 @@ def arrow_get_users(user_email): array_call = ['arrow', 'users', 'get_users'] + logging.debug("%s", array_call) + print array_call p = subprocess.check_output(array_call) all_users = json.loads(p) for d in all_users: if d['username'] == user_email: return d['userId'] logging.error("Cannot find user %s", user_email) + |