component.py 14.6 KB
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#
# Copyright (C) 2012 INRA
# 
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
# 
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
# GNU General Public License for more details.
# 
# You should have received a copy of the GNU General Public License
# along with this program.  If not, see <http://www.gnu.org/licenses/>.
#

import os
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import sys
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import inspect
import tempfile
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import types
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from jflow.workflows_manager import WorkflowsManager
from jflow.config_reader import JFlowConfigReader
from jflow.dataset import ArrayList
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from jflow.utils import which
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from jflow.parameter import *
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from weaver.util import parse_string_list


class Component(object):
    """
    """
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    def __init__(self):
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        self.prefix = "default"
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        self.params_order = []
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        self.output_directory = None
        self.config_reader = JFlowConfigReader()
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        self.version = self.get_version()
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        self.batch_options = self.config_reader.get_component_batch_options(self.__class__.__name__)
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    def is_dynamic(self):
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        return len(self.get_dynamic_outputs()) != 0

    def get_dynamic_outputs(self):
        """
         @return : the list of outputs updated at the end of component execution.
        """
        dynamic_outputs = list()
        for attribute_value in self.__dict__.values():
            if issubclass( attribute_value.__class__, DynamicOutput ):
                dynamic_outputs.append( attribute_value )
        return dynamic_outputs
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    def get_output_files(self):
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        outputs = {}
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        for attribute_value in self.__dict__.values():
            if ( issubclass( attribute_value.__class__, DynamicOutput ) or
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                 issubclass( attribute_value.__class__, OutputFileList) ):
                for f in attribute_value:
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                    outputs[os.path.basename(f)] = f
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            elif issubclass( attribute_value.__class__, OutputFile):
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                outputs[os.path.basename(attribute_value)] = attribute_value
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        return outputs
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    def add_input_file(self, name, help, file_format="any", default=None, type="inputfile", 
                       required=False, flag=None, group="default", display_name=None, add_to=None):
        new_param = InputFile(name, help, flag=flag, file_format=file_format, default=default, 
                              type=type, required=required, group=group, display_name=display_name)
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        new_param.component_nameid = self.get_nameid()
        if issubclass( default.__class__, AbstractOutputFile ):
            new_param.parent_component_nameid = default.component_nameid
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        # if this input should be added to a particular parameter
        if add_to:
            try:
                self.__getattribute__(add_to).add_sub_parameter(new_param)
            except: pass
        # otherwise, add it to the class itself
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        else:
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            self.params_order.append(name)
            self.__setattr__(name, new_param)
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    def reset(self):
        for file in os.listdir(self.output_directory):
            os.remove(os.path.join(self.output_directory, file))
    
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    def add_input_file_list(self, name, help, file_format="any", default=None, type="inputfile", 
                            required=False, flag=None, group="default", display_name=None, add_to=None):
        if default == None: default = []
        new_param = InputFileList(name, help, flag=flag, file_format=file_format, default=default, 
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                                  type=type, required=required, group=group, display_name=display_name)
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        new_param.component_nameid = self.get_nameid()
        if issubclass( default.__class__, AbstractOutputFile ):
            new_param.parent_component_nameid = default.component_nameid        
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        # if this input should be added to a particular parameter
        if add_to:
            try:
                self.__getattribute__(add_to).add_sub_parameter(new_param)
            except: pass
        # otherwise, add it to the class itself
        else:
            self.params_order.append(name)
            self.__setattr__(name, new_param)
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    def add_parameter(self, name, help, default=None, type=types.StringType, choices=None, 
                      required=False, flag=None, group="default", display_name=None, add_to=None):
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        new_param = ParameterFactory.factory(name, help, flag=flag, default=default, type=type, choices=choices, 
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                              required=required, group=group, display_name=display_name)
        # if this input should be added to a particular parameter
        if add_to:
            try:
                self.__getattribute__(add_to).add_sub_parameter(new_param)
            except: pass
        # otherwise, add it to the class itself
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        else:
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            self.params_order.append(name)
            self.__setattr__(name, new_param)

    def add_parameter_list(self, name, help, default=None, type=types.StringType, choices=None, 
                           required=False, flag=None, group="default", display_name=None, add_to=None):
        if default == None: default = []
        new_param = ParameterList(name, help, flag=flag, default=default, type=type, choices=choices, 
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                                  required=required, group=group, display_name=display_name)
        # if this input should be added to a particular parameter
        if add_to:
            try:
                self.__getattribute__(add_to).add_sub_parameter(new_param)
            except: pass
        # otherwise, add it to the class itself
        else:
            self.params_order.append(name)
            self.__setattr__(name, new_param)
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    def add_output_file(self, name, help, file_format="any", filename=None, group="default", display_name=None, add_to=None):
        filename = os.path.basename(filename)
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        new_param = OutputFile(name, help, default=os.path.join(self.output_directory, filename),
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                               file_format=file_format, group=group, display_name=display_name)
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        new_param.component_nameid = self.get_nameid()
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        # if this input should be added to a particular parameter
        if add_to:
            try:
                self.__getattribute__(add_to).add_sub_parameter(new_param)
            except: pass
        # otherwise, add it to the class itself
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        else:
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            self.params_order.append(name)
            self.__setattr__(name, new_param)
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    def add_output_file_list(self, name, help, file_format="any", pattern='{basename_woext}.out', 
                             items=None, group="default", display_name=None, add_to=None):
        new_param = OutputFileList(name, help, default=self.get_outputs(pattern, items), 
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                                   file_format=file_format, group=group, display_name=display_name)
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        new_param.component_nameid = self.get_nameid()
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        # if this input should be added to a particular parameter
        if add_to:
            try:
                self.__getattribute__(add_to).add_sub_parameter(new_param)
            except: pass
        # otherwise, add it to the class itself
        else:
            self.params_order.append(name)
            self.__setattr__(name, new_param)
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    def add_output_file_endswith(self, name, help, file_format="any", pattern='.stderr', behaviour="exclude",
                               group="default", display_name=None, add_to=None):
        new_param = OutputFilesEndsWith(name, help, self.output_directory, pattern, include=(behaviour != "exclude"), 
                                       file_format="any", group="default", display_name=None)
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        new_param.component_nameid = self.get_nameid()
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        # if this input should be added to a particular parameter
        if add_to:
            try:
                self.__getattribute__(add_to).add_sub_parameter(new_param)
            except: pass
        # otherwise, add it to the class itself
        else:
            self.params_order.append(name)
            self.__setattr__(name, new_param)

    def add_output_file_pattern(self, name, help, file_format="any", pattern='.stderr$', behaviour="exclude",
                               group="default", display_name=None, add_to=None):
        new_param = OutputFilesPattern(name, help, self.output_directory, pattern, include=(behaviour != "exclude"), 
                                       file_format="any", group="default", display_name=None)
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        new_param.component_nameid = self.get_nameid()
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        # if this input should be added to a particular parameter
        if add_to:
            try:
                self.__getattribute__(add_to).add_sub_parameter(new_param)
            except: pass
        # otherwise, add it to the class itself
        else:
            self.params_order.append(name)
            self.__setattr__(name, new_param)

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    def _longestCommonSubstr(self, data, clean_end=True):
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        substr = ''
        if len(data) > 1 and len(data[0]) > 0:
            for i in range(len(data[0])):
                for j in range(len(data[0])-i+1):
                    if j > len(substr) and all(data[0][i:i+j] in x for x in data):
                        substr = data[0][i:i+j]
        else:
            substr = data[0]
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        if clean_end:
            while substr.endswith("_") or substr.endswith("-") or substr.endswith("."):
                substr = substr[:-1]
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        return substr
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    def get_outputs(self, output_list=None, input_list=None):
        """
        If `output_list` is a string template, then it may have the following
        fields:
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        - `{fullpath}`, `{FULL}`         -- Full input file path.
        - `{basename}`, `{BASE}`         -- Base input file name.
        - `{fullpath_woext}`, `{FULLWE}` -- Full input file path without extension
        - `{basename_woext}`, `{BASEWE}` -- Base input file name without extension
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        """
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        if output_list is None:
            return []
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        if isinstance(output_list, str):
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            ilist = []
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            if not input_list or not '{' in str(output_list):
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                if input_list is not None and len(input_list) == 0:
                    return []
                else:
                    return [output_list]
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            # if multiple list of inputs is used
            elif isinstance(input_list[0], list):
                for i, val in enumerate(input_list[0]):
                    iter_values = []
                    for j, ingroup in enumerate(input_list):
                        iter_values.append(os.path.basename(input_list[j][i]))
                    ilist.append(self._longestCommonSubstr(iter_values))
            else:
                ilist = parse_string_list(input_list)
                            
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            return [os.path.join(self.output_directory, str(output_list).format(
                        fullpath       = input,
                        FULL           = input,
                        i              = '{0:05X}'.format(i),
                        NUMBER         = '{0:05X}'.format(i),
                        fullpath_woext = os.path.splitext(input)[0],
                        FULL_WOEXT     = os.path.splitext(input)[0],
                        basename       = os.path.basename(input),
                        BASE           = os.path.basename(input),
                        basename_woext = os.path.splitext(os.path.basename(input))[0] if os.path.splitext(os.path.basename(input))[1] != ".gz" else os.path.splitext(os.path.splitext(os.path.basename(input))[0])[0],
                        BASE_WOEXT     = os.path.splitext(os.path.basename(input))[0] if os.path.splitext(os.path.basename(input))[1] != ".gz" else os.path.splitext(os.path.splitext(os.path.basename(input))[0])[0]))
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                    for i, input in enumerate(ilist)]
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    def execute(self):
        # first create the output directory
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        if not os.path.isdir(self.output_directory):
            os.makedirs(self.output_directory, 0751)
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        # then run the component
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        self.process()
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    def process(self):
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        """ 
        Run the component, has to be implemented by subclasses
        """
        raise NotImplementedError
    
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    def get_version(self):
        """ 
        Return the tool version, has to be implemented by subclasses
        """
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        return None
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    def get_temporary_file(self, suffix=".txt"):
        # first check if tmp directory exists
        if not os.path.isdir(self.config_reader.get_tmp_directory()):
            os.makedirs(self.config_reader.get_tmp_directory(), 0751)
        tempfile_name = os.path.basename(tempfile.NamedTemporaryFile(suffix=suffix).name)
        return os.path.join(self.config_reader.get_tmp_directory(), tempfile_name)
    
    def define_parameters(self, *args):
        """ 
        Define the component parameters, has to be implemented by subclasses
        """
        raise NotImplementedError
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    def get_resource(self, resource):
        return self.config_reader.get_resource(resource)
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    def get_exec_path(self, software):
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        exec_path = self.config_reader.get_exec(software)
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        if exec_path is None and os.path.isfile(os.path.join(os.path.dirname(inspect.getfile(self.__class__)), "../../bin", software)):
            exec_path = os.path.join(os.path.dirname(inspect.getfile(self.__class__)), "../../bin", software)
        elif exec_path is None and os.path.isfile(os.path.join(os.path.dirname(inspect.getfile(self.__class__)), "../bin", software)):
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            exec_path = os.path.join(os.path.dirname(inspect.getfile(self.__class__)), "../bin", software)
        elif exec_path is None and os.path.isfile(os.path.join(os.path.dirname(inspect.getfile(self.__class__)), "bin", software)):
            exec_path = os.path.join(os.path.dirname(inspect.getfile(self.__class__)), "bin", software)
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        elif exec_path is None and which(software) == None:
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            sys.stderr.write("Error: '" + software + "' path connot be retrieved either in the PATH and in the application.properties file!\n")
            sys.exit(1)
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        elif exec_path is None and which(software) != None: 
            exec_path = software
        elif exec_path != None and not os.path.isfile(exec_path):
            sys.stderr.write("Error: '" + exec_path + "' set for '" + software + "' does not exists, please provide a valid path!\n")
            sys.exit(1)
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        return exec_path
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    def get_nameid(self):
        return self.__class__.__name__ + "." + self.prefix
    
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    def __eq__(self, other):
        return self.__class__ == other.__class__ and self.prefix == other.prefix