Commit cf1652f8 authored by Penom Nom's avatar Penom Nom
Browse files

update to jflow1.0

parent de61d13b
#
# Copyright (C) 2012 INRA
# Copyright (C) 2015 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
......
#
# Copyright (C) 2012 INRA
# Copyright (C) 2015 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
......
#
# Copyright (C) 2012 INRA
# Copyright (C) 2015 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
......
#
# Copyright (C) 2009 INRA
# Copyright (C) 2015 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
......
#
# Copyright (C) 2012 INRA
# Copyright (C) 2015 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
......
#
# Copyright (C) 2012 INRA
# Copyright (C) 2015 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
......@@ -270,7 +270,7 @@ class Component(object):
inputs = sorted(inputs, key=attrgetter('argpos'))
outputs = sorted(outputs, key=attrgetter('argpos'))
filteredparams = []
commandline = self.get_command()
commandline = self.get_exec_path(self.get_command())
for p in parameters :
if isinstance(p, BoolParameter) :
......
#
# Copyright (C) 2012 INRA
# Copyright (C) 2015 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
......
#
# Copyright (C) 2012 INRA
# Copyright (C) 2015 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
......
#
# Copyright (C) 2012 INRA
# Copyright (C) 2015 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
......
#
# Copyright (C) 2012 INRA
# Copyright (C) 2015 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
......@@ -21,4 +21,5 @@ from featureiolib.gff3 import GFF3Record, GFF3IO
from featureiolib.mpileup import MpileupReader
from featureiolib.obo import OboReader
from featureiolib.vcf import VCFReader
from featureiolib.wego import WEGOReader
\ No newline at end of file
from featureiolib.wego import WEGOReader
from featureiolib.separatedvalue import SeparatedValueIO
\ No newline at end of file
#
# Copyright (C) 2012 INRA
# Copyright (C) 2015 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
......
#
# Copyright (C) 2014 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/>.
#
class SeparatedValueIO(object):
"""
@summary : Specific handler for separated value file (examples : TSV, CSV).
"""
def __init__(self, file_path, separator="\t", mode="r"):
"""
@param file_path : [str] The filepath.
@param separator : [str] The value separator.
@param mode : [str] Mode to open the file ('r', 'w', 'a').
"""
self._path = file_path
self._handle = open( file_path, mode )
self._line = 1
self._separator = separator
def __del__(self):
self.close()
def close(self):
if hasattr(self, '_handle') and self._handle is not None:
self._handle.close()
self._handle = None
self._line = None
def __iter__(self):
for line in self._handle:
line = line.rstrip('\n')
self._line += 1
try:
record = line.split(self._separator)
except:
raise IOError( "The line " + str(self._line) + " in '" + self._path + "' cannot be parsed by " + self.__class__.__name__ +
" with separator '" + self._separator + "'.\n" + "Line content : " + line )
else:
yield record
def next(self):
"""
@summary : Returns the next line record.
@return : [list] The line record.
"""
line = self._handle.readline()
self._line += 1
try:
record = line.split(self._separator)
except:
raise IOError( "The line " + str(self._line) + " in '" + self._path + "' cannot be parsed by " + self.__class__.__name__ +
" with separator '" + self._separator + "'.\n" + "Line content : " + line )
def write(self, record):
"""
@summary : Write one line on SparatedValue file.
@param record : [list] the list to write.
"""
self._handle.write( record.join(self._separator) + "\n" )
self._line += 1
\ No newline at end of file
#
# Copyright (C) 2012 INRA
# Copyright (C) 2015 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
......
#
# Copyright (C) 2012 INRA
# Copyright (C) 2015 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
......@@ -914,7 +914,7 @@ class ParameterList(list, AbstractParameter):
action="append", sub_parameters=sub_parameters, group=group, display_name=display_name,
cmd_format=cmd_format, argpos=argpos)
liste = []
if default.__class__.__name__ == "list":
if isinstance( default, list ):
for val in default :
liste.append(ParameterFactory.factory( name, help, default=val, type=type, choices=choices,
required=required, flag=flag, group=group, display_name=display_name ))
......
#
# Copyright (C) 2009 INRA
# Copyright (C) 2015 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
......
#
# Copyright (C) 2012 INRA
# Copyright (C) 2015 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
......
#
# Copyright (C) 2012 INRA
# Copyright (C) 2015 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
......
#
# Copyright (C) 2012 INRA
# Copyright (C) 2015 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
......
......@@ -64,30 +64,13 @@ class tx_nG6_pi1 extends tslib_pibase {
$GLOBALS['TSFE']->additionalHeaderData[$this->prefixId] = '
<script type="text/javascript" src="'.t3lib_extMgm::siteRelPath($this->extKey).'res/js/jquery.min.js"></script>
<script type="text/javascript" src="'.t3lib_extMgm::siteRelPath($this->extKey).'res/js/jquery.dataTables.min.js"></script>
<script type="text/javascript" src="'.t3lib_extMgm::siteRelPath($this->extKey).'res/js/jquery.tmpl.min.js"></script>
<script type="text/javascript" src="'.t3lib_extMgm::siteRelPath($this->extKey).'res/js/jquery.ui.widget.js"></script>
<script type="text/javascript" src="'.t3lib_extMgm::siteRelPath($this->extKey).'res/js/jquery.iframe-transport.js"></script>
<script type="text/javascript" src="'.t3lib_extMgm::siteRelPath($this->extKey).'res/js/jquery.fileupload.js"></script>
<script type="text/javascript" src="'.t3lib_extMgm::siteRelPath($this->extKey).'res/js/jquery.fileupload-process.js"></script>
<script type="text/javascript" src="'.t3lib_extMgm::siteRelPath($this->extKey).'res/js/jquery.fileupload-validate.js"></script>
<script type="text/javascript" src="'.t3lib_extMgm::siteRelPath($this->extKey).'res/js/jquery.validate.js"></script>
<script type="text/javascript" src="'.t3lib_extMgm::siteRelPath($this->extKey).'res/js/wysihtml5-0.3.0.min.js"></script>
<script type="text/javascript" src="'.t3lib_extMgm::siteRelPath($this->extKey).'res/js/bootstrap.min.js"></script>
<script type="text/javascript" src="'.t3lib_extMgm::siteRelPath($this->extKey).'res/js/bootstrap-editable.min.js"></script>
<script type="text/javascript" src="'.t3lib_extMgm::siteRelPath($this->extKey).'res/js/bootstrap-datepicker.js"></script>
<script type="text/javascript" src="'.t3lib_extMgm::siteRelPath($this->extKey).'res/js/bootstrap3-wysihtml5.all.min.js"></script>
<script type="text/javascript" src="'.t3lib_extMgm::siteRelPath($this->extKey).'res/js/dataTables.bootstrap.js"></script>
<script type="text/javascript" src="'.t3lib_extMgm::siteRelPath($this->extKey).'res/js/cytoscape-2.3.7.js"></script>
<script type="text/javascript" src="'.t3lib_extMgm::siteRelPath($this->extKey).'res/js/cytoscape.js-panzoom.js"></script>
<script type="text/javascript" src="'.t3lib_extMgm::siteRelPath($this->extKey).'res/js/dagre.js"></script>
<script type="text/javascript" src="'.t3lib_extMgm::siteRelPath($this->extKey).'res/js/ZeroClipboard.min.js"></script>
<script type="text/javascript" src="'.t3lib_extMgm::siteRelPath($this->extKey).'res/js/typeahead.bundle.js"></script>
<script type="text/javascript" src="'.t3lib_extMgm::siteRelPath($this->extKey).'res/js/handsontable.full.min.js"></script>
<script type="text/javascript" src="'.t3lib_extMgm::siteRelPath($this->extKey).'res/js/jflow-activewf.js"></script>
<script type="text/javascript" src="'.t3lib_extMgm::siteRelPath($this->extKey).'res/js/jflow-availablewf.js"></script>
<script type="text/javascript" src="'.t3lib_extMgm::siteRelPath($this->extKey).'res/js/jflow-wfform.js"></script>
<script type="text/javascript" src="'.t3lib_extMgm::siteRelPath($this->extKey).'res/js/jflow-wfoutputs.js"></script>
<script type="text/javascript" src="'.t3lib_extMgm::siteRelPath($this->extKey).'res/js/jflow-wfstatus.js"></script>
<script type="text/javascript" src="'.t3lib_extMgm::siteRelPath($this->extKey).'res/js/jflow.min.js"></script>
<script type="text/javascript" src="'.t3lib_extMgm::siteRelPath($this->extKey).'res/js/tx_nG6_pi1.js"></script>
<script type="text/javascript" src="'.t3lib_extMgm::siteRelPath($this->extKey).'res/js/tx_nG6_utils.js"></script>
......@@ -95,11 +78,8 @@ class tx_nG6_pi1 extends tslib_pibase {
<link type="text/css" rel="stylesheet" media="screen" href="'.t3lib_extMgm::siteRelPath($this->extKey).'res/css/dataTables.bootstrap.css"/>
<link type="text/css" rel="stylesheet" media="screen" href="'.t3lib_extMgm::siteRelPath($this->extKey).'res/css/bootstrap-editable.css"/>
<link type="text/css" rel="stylesheet" media="screen" href="'.t3lib_extMgm::siteRelPath($this->extKey).'res/css/typeaheadjs.css"/>
<link type="text/css" rel="stylesheet" media="screen" href="'.t3lib_extMgm::siteRelPath($this->extKey).'res/css/datepicker.css"/>
<link type="text/css" rel="stylesheet" media="screen" href="'.t3lib_extMgm::siteRelPath($this->extKey).'res/css/cytoscape.js-panzoom.css"/>
<link type="text/css" rel="stylesheet" media="screen" href="'.t3lib_extMgm::siteRelPath($this->extKey).'res/css/font-awesome.css"/>
<link type="text/css" rel="stylesheet" media="screen" href="'.t3lib_extMgm::siteRelPath($this->extKey).'res/css/handsontable.full.min.css"/>
<link type="text/css" rel="stylesheet" media="screen" href="'.t3lib_extMgm::siteRelPath($this->extKey).'res/css/jflow.css"/>
<link type="text/css" rel="stylesheet" media="screen" href="'.t3lib_extMgm::siteRelPath($this->extKey).'res/css/jflow.min.css"/>
<link type="text/css" rel="stylesheet" media="screen" href="'.t3lib_extMgm::siteRelPath($this->extKey).'res/css/tx_nG6.css"/>';
tx_nG6_db::check_db_rights_level();
......
......@@ -60,8 +60,8 @@ class tx_nG6_pi5 extends tslib_pibase {
// Add the jquery libs + the tree plugins and its css
$GLOBALS['TSFE']->additionalHeaderData[$this->prefixId] = '
<script type="text/javascript" src="'.t3lib_extMgm::siteRelPath($this->extKey).'res/js/jquery.min.js"></script>
<script type="text/javascript" src="'.t3lib_extMgm::siteRelPath($this->extKey).'res/js/jquery.validate.js"></script>
<script type="text/javascript" src="'.t3lib_extMgm::siteRelPath($this->extKey).'res/js/jquery.jstree.min.js"></script>
<script type="text/javascript" src="'.t3lib_extMgm::siteRelPath($this->extKey).'res/js/jflow.min.js"></script>
<script type="text/javascript" src="'.t3lib_extMgm::siteRelPath($this->extKey).'res/js/bootstrap.min.js"></script>
<script type="text/javascript" src="'.t3lib_extMgm::siteRelPath($this->extKey).'res/js/tx_nG6_pi5.js"></script>
......
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