ensembl-hive-python3
2.3
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This is the counterpart of GuestProcess. More...
Public Member Functions | |
def | __init__ (self, read_fileno, write_fileno) |
def | warning (self, message, is_error=False) |
Store a message in the log_message table with is_error indicating whether the warning is actually an error or not. More... | |
def | dataflow (self, output_ids, branch_name_or_code=1) |
Dataflows the output_id(s) on a given branch (default 1). More... | |
def | worker_temp_directory (self) |
Returns the full path of the temporary directory created by the worker. More... | |
def | param_defaults (self) |
Returns the defaults parameters for this runnable. More... | |
def | param_required (self, param_name) |
Returns the value of the parameter "param_name" or raises an exception if anything wrong happens. More... | |
def | param (self, param_name, args) |
When called as a setter: sets the value of the parameter "param_name". More... | |
def | param_exists (self, param_name) |
Returns True or False, whether the parameter exists (it doesn't mean it can be successfully substituted) More... | |
def | param_is_defined (self, param_name) |
Returns True or False, whether the parameter exists, can be successfully substituted, and is not None. More... | |
Public Attributes | |
debug | |
input_job | |
autoflow | |
Private Member Functions | |
def | __print_debug (self, args) |
def | __send_message (self, event, content) |
seralizes the message in JSON and send it to the parent process More... | |
def | __send_response (self, response) |
Sends a response message to the parent process. More... | |
def | __read_message (self) |
Read a message from the parent and parse it. More... | |
def | __send_message_and_wait_for_OK (self, event, content) |
Send a message and expects a response to be 'OK'. More... | |
def | __process_life_cycle (self) |
Simple loop: wait for job parameters, do the job's life-cycle. More... | |
def | __job_life_cycle (self, config) |
Job's life-cycle. More... | |
def | __run_method_if_exists (self, method) |
method is one of "pre_cleanup", "fetch_input", "run", "write_output", "post_cleanup". More... | |
def | __traceback (self, skipped_traces) |
Remove "skipped_traces" lines from the stack trace (the eHive part) More... | |
Private Attributes | |
__read_pipe | |
__write_pipe | |
__pid | |
__created_worker_temp_directory | |
__params | |
This is the counterpart of GuestProcess.
Note that most of the methods are private to be hidden in the derived classes.
This class can be used as a base-class for people to redefine fetch_input(), run() and/or write_output() (and/or pre_cleanup(), post_cleanup()). Jobs are supposed to raise CompleteEarlyException in case they complete before reaching. They can also raise JobFailedException to indicate a general failure
Definition at line 50 of file Process.py.
def eHive.Process.BaseRunnable.__init__ | ( | self, | |
read_fileno, | |||
write_fileno | |||
) |
Definition at line 55 of file Process.py.
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Job's life-cycle.
See GuestProcess for a description of the protocol to communicate with the parent
Definition at line 131 of file Process.py.
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private |
Simple loop: wait for job parameters, do the job's life-cycle.
Definition at line 117 of file Process.py.
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Read a message from the parent and parse it.
Definition at line 95 of file Process.py.
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private |
method is one of "pre_cleanup", "fetch_input", "run", "write_output", "post_cleanup".
We only the call the method if it exists to save a trip to the database.
Definition at line 188 of file Process.py.
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seralizes the message in JSON and send it to the parent process
Definition at line 71 of file Process.py.
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private |
Send a message and expects a response to be 'OK'.
Definition at line 109 of file Process.py.
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Sends a response message to the parent process.
Definition at line 85 of file Process.py.
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Remove "skipped_traces" lines from the stack trace (the eHive part)
Definition at line 195 of file Process.py.
def eHive.Process.BaseRunnable.dataflow | ( | self, | |
output_ids, | |||
branch_name_or_code = 1 |
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) |
Dataflows the output_id(s) on a given branch (default 1).
Returns whatever the Perl side returns
Definition at line 213 of file Process.py.
def eHive.Process.BaseRunnable.param | ( | self, | |
param_name, | |||
args | |||
) |
When called as a setter: sets the value of the parameter "param_name".
When called as a getter: returns the value of the parameter "param_name". It does not raise an exception if the parameter (or another one in the substitution stack) is undefined
Definition at line 254 of file Process.py.
def eHive.Process.BaseRunnable.param_defaults | ( | self | ) |
Returns the defaults parameters for this runnable.
Definition at line 236 of file Process.py.
def eHive.Process.BaseRunnable.param_exists | ( | self, | |
param_name | |||
) |
Returns True or False, whether the parameter exists (it doesn't mean it can be successfully substituted)
Definition at line 268 of file Process.py.
def eHive.Process.BaseRunnable.param_is_defined | ( | self, | |
param_name | |||
) |
Returns True or False, whether the parameter exists, can be successfully substituted, and is not None.
Definition at line 273 of file Process.py.
def eHive.Process.BaseRunnable.param_required | ( | self, | |
param_name | |||
) |
Returns the value of the parameter "param_name" or raises an exception if anything wrong happens.
The exception is marked as non-transient.
Definition at line 242 of file Process.py.
def eHive.Process.BaseRunnable.warning | ( | self, | |
message, | |||
is_error = False |
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) |
Store a message in the log_message table with is_error indicating whether the warning is actually an error or not.
Definition at line 208 of file Process.py.
def eHive.Process.BaseRunnable.worker_temp_directory | ( | self | ) |
Returns the full path of the temporary directory created by the worker.
Runnables can implement "worker_temp_directory_name()" to return the name they would like to use
Definition at line 224 of file Process.py.
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private |
Definition at line 120 of file Process.py.
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private |
Definition at line 135 of file Process.py.
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private |
Definition at line 59 of file Process.py.
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private |
Definition at line 57 of file Process.py.
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private |
Definition at line 58 of file Process.py.
eHive.Process.BaseRunnable.autoflow |
Definition at line 215 of file Process.py.
eHive.Process.BaseRunnable.debug |
Definition at line 60 of file Process.py.
eHive.Process.BaseRunnable.input_job |
Definition at line 138 of file Process.py.