Module Expr Str Import alias Import alias Import alias ImportFrom alias ImportFrom alias alias alias alias ImportFrom alias alias alias alias ImportFrom alias ImportFrom alias ImportFrom alias ImportFrom alias ClassDef bases AttributeLoad NameLoad attr body Expr Str Assign NameStore Call NameLoad Str Assign NameStore Call NameLoad Str Assign NameStore Call NameLoad Str Assign NameStore Call NameLoad Str FunctionDef arguments args NameParam NameParam defaults Str body Expr Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad NameLoad decorator_list FunctionDef arguments args NameParam NameParam defaults body Assign NameStore AttributeLoad NameLoad attr If CompareEq AttributeLoad NameLoad attr Num body Assign AttributeStore NameLoad attr AttributeLoad NameLoad attr orelse If CompareEq AttributeLoad NameLoad attr Num body Assign AttributeStore NameLoad attr AttributeLoad NameLoad attr orelse If CompareEq AttributeLoad NameLoad attr Num body Assign AttributeStore NameLoad attr AttributeLoad NameLoad attr orelse If CompareEq AttributeLoad NameLoad attr Num body Assign AttributeStore NameLoad attr AttributeLoad NameLoad attr Assign NameStore Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad NameLoad Assign AttributeStore NameLoad attr NameLoad Return NameLoad decorator_list decorator_list FunctionDef arguments args NameParam defaults body Assign AttributeStore NameLoad attr Call AttributeLoad NameLoad attr Str Expr Call AttributeLoad AttributeLoad NameLoad attr attr AttributeLoad NameLoad attr Assign NameStore Call AttributeLoad NameLoad attr Expr Call AttributeLoad NameLoad attr AttributeLoad NameLoad attr Expr Call AttributeLoad NameLoad attr Call NameLoad Expr Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad decorator_list FunctionDef arguments args NameParam NameParam NameParam defaults body Expr Str If UnaryOpNot NameLoad body Assign NameStore Call AttributeLoad NameLoad attr Str NameLoad If UnaryOpNot NameLoad body Assign NameStore Str orelse Assign NameStore AttributeLoad NameLoad attr If UnaryOpNot NameLoad body Assign NameStore Call AttributeLoad NameLoad attr Str NameLoad If UnaryOpNot NameLoad body Assign NameStore Str orelse Assign NameStore AttributeLoad NameLoad attr Assign NameStore Str Assign NameStore BinOpAdd BinOpAdd BinOpAdd Str NameLoad Str NameLoad Expr Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad If AttributeLoad NameLoad attr body Expr Call AttributeLoad NameLoad attr BinOpAdd BinOpAdd BinOpAdd Str NameLoad Str NameLoad decorator_list FunctionDef arguments args NameParam NameParam NameParam NameParam defaults NameLoad NameLoad NameLoad body If UnaryOpNot NameLoad body Assign NameStore NameLoad Expr Call NameLoad NameLoad NameLoad Expr Call NameLoad NameLoad Expr Call NameLoad keyword NameLoad Expr Call NameLoad NameLoad decorator_list FunctionDef arguments args NameParam NameParam defaults body Expr Str Assign AttributeStore NameLoad attr Call NameLoad NameLoad Assign AttributeStore NameLoad attr NameLoad If NameLoad body If BoolOpOr Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad body Assign NameStore NameLoad orelse Assign NameStore Call AttributeLoad AttributeLoad NameLoad attr attr Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad Str Str Str NameLoad Assert Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad Call AttributeLoad Str attr NameLoad NameLoad Assign AttributeStore NameLoad attr NameLoad Assign NameStore SubscriptLoad Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad Index Num Import alias TryExcept body Assign AttributeStore NameLoad attr Call Call NameLoad AttributeLoad NameLoad attr Call AttributeLoad NameLoad attr NameLoad handlers ExceptHandler type NameLoad body Pass Assign AttributeStore AttributeLoad NameLoad attr attr NameLoad For NameStore ListLoad Str Str body Assign NameStore BinOpAdd SubscriptLoad Call AttributeLoad AttributeLoad NameLoad attr attr Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad Index Num NameLoad Assign NameStore Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad Call AttributeLoad Str attr NameLoad If Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad body Expr Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad Assign NameStore Call NameLoad NameLoad keyword ListLoad NameLoad Expr Call AttributeLoad AttributeLoad NameLoad attr attr AttributeLoad NameLoad attr Expr Call AttributeLoad AttributeLoad NameLoad attr attr BinOpMod Str AttributeLoad AttributeLoad NameLoad attr attr decorator_list FunctionDef arguments args NameParam defaults body Expr Str Assign AttributeStore NameLoad attr Call AttributeLoad AttributeLoad NameLoad attr attr Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad Str Str Assign AttributeStore NameLoad attr Call AttributeLoad AttributeLoad NameLoad attr attr AttributeLoad NameLoad attr Str Str Str If BoolOpAnd UnaryOpNot Call AttributeLoad NameLoad attr Str UnaryOpNot Call AttributeLoad NameLoad attr Str body Expr Call AttributeLoad AttributeLoad NameLoad attr attr Str Expr Call AttributeLoad NameLoad attr Call NameLoad AttributeLoad Call NameLoad NameLoad Str attr If CompareNotIn Str NameLoad body Assign AttributeStore NameLoad attr Str If CompareNotIn Str NameLoad body Assign AttributeStore NameLoad attr Str decorator_list FunctionDef arguments args NameParam defaults body Expr Str With Call NameLoad Call NameLoad Str Str Str Str keyword NameLoad body Expr Call AttributeLoad AttributeLoad NameLoad attr attr Str Assign NameStore Call AttributeLoad NameLoad attr Str If CompareNotEq NameLoad NameLoad body Expr Call AttributeLoad AttributeLoad NameLoad attr attr Str orelse Raise Call NameLoad Str Expr Call AttributeLoad AttributeLoad NameLoad attr attr Str If CompareIn Str NameLoad body If UnaryOpNot Call AttributeLoad NameLoad attr AttributeLoad NameLoad attr body Expr Call AttributeLoad NameLoad attr BinOpMod Str AttributeLoad NameLoad attr Assign NameStore Call AttributeLoad NameLoad attr Str Expr Call AttributeLoad NameLoad attr BinOpMod Str TupleLoad NameLoad AttributeLoad NameLoad attr With Call NameLoad AttributeLoad NameLoad attr body Assign NameStore Call AttributeLoad NameLoad attr Str Assign AttributeStore NameLoad attr NameLoad decorator_list
N/A N/A Utilities for logging and progress tracking.
 N/A logging N/A os N/A sys fabric.main load_settings fabric.colors yellow red green magenta fabric.api settings hide cd run fabric.contrib.files exists cloudbio.distribution _setup_distribution_environment cloudbio.flavor Flavor cloudbio.flavor.config get_config_file ColorFormatter N/A N/A logging Formatter N/A N/A  Format log message based on the message level
        http://stackoverflow.com/questions/1343227/can-pythons-logging-format-be-modified-depending-on-the-message-log-level
     N/A err_fmt N/A red ERR [%(filename)s(%(lineno)d)] %(msg)s N/A warn_fmt N/A magenta WARN [%(filename)s(%(lineno)d)]: %(msg)s N/A dbg_fmt N/A yellow DBG [%(filename)s]: %(msg)s N/A info_fmt N/A green INFO: %(msg)s __init__ N/A N/A self fmt N/A %(name)s %(levelname)s: %(msg)s N/A N/A N/A N/A N/A logging Formatter __init__ self fmt N/A format N/A N/A self record N/A N/A N/A format_orig N/A self _fmt N/A N/A N/A record levelno 10 N/A N/A N/A self _fmt N/A ColorFormatter dbg_fmt N/A N/A N/A N/A record levelno 20 N/A N/A N/A self _fmt N/A ColorFormatter info_fmt N/A N/A N/A N/A record levelno 30 N/A N/A N/A self _fmt N/A ColorFormatter warn_fmt N/A N/A N/A N/A record levelno 40 N/A N/A N/A self _fmt N/A ColorFormatter err_fmt N/A result N/A N/A N/A logging Formatter format self record N/A N/A self _fmt format_orig N/A result N/A N/A _setup_logging N/A N/A env N/A N/A N/A N/A env logger N/A N/A logging getLogger cloudbiolinux N/A N/A N/A N/A env logger setLevel N/A logging DEBUG N/A ch N/A N/A logging StreamHandler N/A N/A N/A ch setLevel N/A logging DEBUG N/A N/A N/A ch setFormatter N/A ColorFormatter N/A N/A N/A N/A env logger addHandler ch N/A _update_biolinux_log N/A N/A env target flavor N/A N/A N/A Updates the VM so it contains information on the latest BioLinux
       update in /var/log/biolinux.log.

       The latest information is appended to the file and can be used to see if
       an installation/update has completed (see also ./test/test_vagrant).
     N/A N/A target N/A N/A target N/A N/A env get target None N/A N/A target N/A N/A target unknown N/A N/A target N/A target name N/A N/A flavor N/A N/A flavor N/A N/A env get flavor None N/A N/A flavor N/A N/A flavor unknown N/A N/A flavor N/A flavor name N/A logfn /var/log/biolinux.log N/A info N/A N/A N/A Target= target ; Flavor= flavor N/A N/A N/A N/A env logger info info N/A N/A env use_sudo N/A N/A N/A N/A env safe_sudo N/A N/A N/A date +"%D %T - Updated  info " >>  logfn N/A _configure_fabric_environment N/A N/A env flavor fabricrc_loader ignore_distcheck N/A None None False N/A N/A N/A fabricrc_loader N/A N/A fabricrc_loader _parse_fabricrc N/A N/A _setup_flavor env flavor N/A N/A fabricrc_loader env N/A N/A _setup_distribution_environment ignore_distcheck ignore_distcheck N/A N/A _create_local_paths env N/A _setup_flavor N/A N/A env flavor N/A N/A N/A Setup a flavor, providing customization hooks to modify CloudBioLinux installs.

    Specify flavor as a name, in which case we look it up in the standard
    flavor directory (contrib/flavor/your_flavor), or as an absolute path to a
    flavor directory outside of cloudbiolinux.
     N/A N/A env flavor N/A Flavor env N/A N/A env flavor_dir None N/A flavor N/A N/A N/A N/A N/A N/A os path isabs flavor N/A N/A N/A os path exists flavor N/A N/A flavor_dir flavor N/A N/A flavor_dir N/A N/A N/A os path join N/A N/A N/A os path dirname __file__ .. contrib flavor flavor N/A N/A N/A N/A os path exists flavor_dir N/A N/A Did not find directory {0} for flavor {1} format flavor_dir flavor N/A N/A env flavor_dir flavor_dir N/A flavor_name N/A N/A N/A N/A os path split flavor_dir N/A -1 N/A cloudbio.flavor N/A N/A N/A N/A env flavor N/A N/A getattr N/A cloudbio flavor N/A N/A flavor_name capitalize env N/A N/A N/A AttributeError N/A N/A N/A N/A N/A env flavor name flavor_name N/A ext N/A flavor N/A N/A py_flavor N/A N/A N/A N/A N/A os path split N/A N/A N/A os path realpath flavor_dir N/A 1 ext N/A flavor_custom_py N/A N/A N/A os path join flavor_dir N/A N/A {0}.py format py_flavor N/A N/A N/A N/A os path exists flavor_custom_py N/A N/A N/A N/A N/A sys path append flavor_dir N/A mod N/A __import__ py_flavor fromlist N/A py_flavor N/A N/A N/A N/A env logger info N/A env flavor N/A N/A N/A N/A env logger info N/A This is a %s flavor N/A N/A env flavor name N/A _parse_fabricrc N/A N/A env N/A N/A N/A Defaults from fabricrc.txt file; loaded if not specified at commandline.
     N/A N/A env config_dir N/A N/A N/A os path join N/A N/A N/A os path dirname __file__ .. config N/A N/A env tool_data_table_conf_file N/A N/A N/A os path join N/A env config_dir .. installed_files tool_data_table_conf.xml N/A N/A N/A N/A N/A env has_key distribution N/A N/A N/A env has_key system_install N/A N/A N/A N/A N/A env logger info Reading default fabricrc.txt N/A N/A N/A env update N/A load_settings N/A N/A get_config_file env fabricrc.txt base N/A N/A shell_config env N/A N/A N/A env shell_config ~/.bashrc N/A N/A shell env N/A N/A N/A env shell /bin/bash -i -c N/A _create_local_paths N/A N/A env N/A N/A N/A Expand any paths defined in terms of shell shortcuts (like ~).
     N/A N/A settings N/A hide warnings running stdout stderr warn_only True N/A N/A N/A N/A N/A env logger info Now, testing connection to host... N/A test N/A N/A env safe_run pwd N/A N/A test None N/A N/A N/A N/A N/A env logger info Connection to host appears to work! N/A N/A N/A NotImplementedError Connection to host failed N/A N/A N/A N/A env logger debug Expand paths N/A N/A local_install env N/A N/A N/A N/A N/A env safe_exists N/A env local_install N/A N/A N/A N/A env safe_sudo N/A mkdir -p %s N/A env local_install N/A user N/A N/A env safe_run_output echo $USER N/A N/A N/A env safe_sudo N/A chown -R %s %s N/A user N/A env local_install N/A N/A cd N/A env local_install N/A N/A result N/A N/A env safe_run_output pwd N/A N/A env local_install result N/A