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########################################################################################
# #
# Author: Herve Menager, #
# Organization:'Biological Software and Databases' Group, Institut Pasteur, Paris. #
# Distributed under GPLv2 Licence. Please refer to the COPYING.LIB document. #
# #
########################################################################################
import os
import logging
from lxml import etree
from Mobyle.ConfigManager import Config
from Mobyle.Utils import indent
_cfg = Config()
log = logging.getLogger('mobyle.registry' )
class InterfacePreprocessor(object):
"""
InterfacePreprocessor is a component that generates the pre-computed parts of the MobylePortal interface, i.e., form and
job pages, workflow graphs, etc.
"""
def __init__(self):
self.load_xsl_pipe()
def load_xsl_pipe(self):
"""
Preload all necessary xsl files and define the xsl processing pipeline
"""
self.XslPipe = []
local_categories_path = os.path.join(_cfg.mobylehome() , "Local", "categories.xml")
if os.path.exists(local_categories_path):
local_categories_url = os.path.join("file://",local_categories_path)
style0 = etree.parse(os.path.join(_cfg.portal_path(), "xsl", "localize.xsl"))
self.localize_style = etree.XSLT(style0)
self.XslPipe.append((self.localize_style, {'localCategoriesUrl':"'"+local_categories_url+"'"}))
style1bis = etree.parse(os.path.join(_cfg.portal_path(), "xsl", "clean_import.xsl"))
self.clean_style = etree.XSLT(style1bis)
style1 = etree.parse(os.path.join(_cfg.portal_path(), "xsl", "parameters.xsl"))
self.param_style = etree.XSLT(style1)
style2 = etree.parse(os.path.join(_cfg.portal_path(), "xsl", "layout.xsl"))
self.layout_style = etree.XSLT(style2)
style3 = etree.parse(os.path.join(_cfg.portal_path(), "xsl", "annotate.xsl"))
self.ann_style = etree.XSLT(style3)
style4 = etree.parse(os.path.join(_cfg.portal_path(), "xsl", "results.xsl"))
self.res_style = etree.XSLT(style4)
style5 = etree.parse(os.path.join(_cfg.portal_path(), "xsl", "graphviz_simplify.xsl"))
self.gvz_style = etree.XSLT(style5)
self.XslPipe += [
(self.clean_style, {}),
(self.param_style, {'previewDataLimit':str(_cfg.previewDataLimit()),'programUri':''}),
(self.layout_style, {'type':"'form'",'programUri':''}),
(self.layout_style, {'type':"'viewer'",'programUri':''}),
(self.res_style, {'previewDataLimit':str(_cfg.previewDataLimit())}),
(self.ann_style, {}),
(self.gvz_style, {}),
(self.layout_style, {'type':"'job_input'"}),
(self.layout_style, {'type':"'job_output'"})
]
def process_interface(self, programpath):
"""
Pre-process the xsl on program xml definitions
@param programpath : xml path file to process
@type programpath : string
@return: if the processing run well or not
@rtype: boolean
"""
doc = etree.parse(programpath)
if doc.getroot().tag=='workflow':
from Mobyle.Workflow import Parser
from Mobyle.WorkflowLayout import layout
p = Parser()
w = p.parse(programpath)
i_l_s = layout(w) # graph layout as an svg string
i_l_e = etree.XML(i_l_s) # graph layout as an element
h = w.find("head")
if h is None:
h = etree.SubElement(w,'head') # graph interface container element
g_i = w.find("head/interface[@type='graph']")
if g_i is None:
g_i = etree.SubElement(w.find('head'),'interface') # graph interface container element
g_i.clear()
g_i.set("type","graph")
g_i.append(i_l_e)
fileResult = open(programpath,"w")
fileResult.write(etree.tostring(w, pretty_print=True))
fileResult.close()
doc = etree.parse(programpath)
for style, params in self.XslPipe:
for p in params.keys():
if p == 'programUri':
params[p] = "'"+programpath+"'"
log.debug('programUri=%s' % programpath)
result = style(doc, **params)
doc = result
#write the result on the xml itself
try:
fileResult = open(programpath,"w")
indent(doc.getroot())
fileResult.write(str(doc))
fileResult.close()
return True
except IOError, ex:
log.error("Problem with the html generation: %s." % ex)
return False
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