Package schrodinger :: Package pipeline :: Module pipeline

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Module pipeline

Classes

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StageJob
A "Job" that is used by Pipeline to run a Stage.

Pipeline
A controller responsible for running the stages in the correct order.

Functions

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log(text)
Prints specified text to the log pipe; adds a return at the end

logn(text)
Print the specified text to the log pipe with no newline.

add_host_lists(list1, list2)
Append hosts in list2 to list1.

subtract_host_lists(list1, dict2)
Return available (not used) hosts.

_host_is_queue(hostname)
Return True if hostname is a queue.

_get_job(jobid)
Return the job object for job with jobid.

importName(modulename, name)
Import a named object from a module in the context of this function.

Restart(restart_file, restartbeg=False)
Recover a saved Pipeline instance.

Variables

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__doc__ = ...

DEBUG = log.get_environ_log_level() <= log.DEBUG

WAITING = 'WAITING'

RUNNING = 'RUNNING'

COMPLETED = 'COMPLETED'

FAILED = 'FAILED'

RESTARTING = 'RESTARTING'

updated_from_dump = {}

old_stage_classes = {"merge.MergeStage": "glide.MergeStage", "...

global_logfh = sys.stdout

_job_objects = {}

Function Details

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logn(text)

Print the specified text to the log pipe with no newline. This is especially useful when printing progress periods.

add_host_lists(list1, list2)

Append hosts in list2 to list1.

Example:

 list1 = a:5,b:10
 list2 = a:2,c:12
 output = a:7,b:10,c:12

The order of hosts is retained (first list is given priority).

subtract_host_lists(list1, dict2)

Return available (not used) hosts. This function subtracts the host dict dict2 from the host dict list1.

Parameters:

list1 (dict) - All available hosts (specified by user), with hostname as key and cpu count as value.
dict2 (dict) - All used hosts (used by stages)

importName(modulename, name)

Import a named object from a module in the context of this function.

For example, if you would like to create an instance of the Foo class from the bar.py module:

   foo_class = importName("bar", "Foo")
   foo_instance = foo_class()

Raises:

ImportError - Raised when the object can not be imported.

Restart(restart_file, restartbeg=False)

Recover a saved Pipeline instance.

Specify new options only if the settings need to change.

Returns a Pipeline instance recovered from the restart_file. You need to call pipeline.run() in order to get the pipeline running.

Parameters:

restartbeg - Whether to start failed stages from beginning.

Raises:

RuntimeError - Raised if a Pipeline can't be loaded from the specified file.

Variables Details

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doc

Value:

"""
Classes for running pipelines.

The main class is called Pipeline. This class parses the input file, c
reates
appropriate stages, and runs them in their own subdirectories.

The StageJob class represents a pipeline job linked to a specific stag
...

old_stage_classes

Value:

{"merge.MergeStage": "glide.MergeStage", "ligfilter.LigFilterStage": "
filtering.LigFilterStage", "phase.DBManage": "phase.DBManageStage", "p
hase.DBConfSites": "phase.DBConfSitesStage", "chargefilter.ChargeFilte
rStage": "filtering.ChargeFilterStage", "mmgbsa.MMGBSAStage": "prime.M
MGBSAStage", "mopac.MopacStage": "semiemp.SemiEmpStage", "gencodes.Gen
CodesStage": "gencodes.Recombine",}