def _setAttributes(self): ### Sets Attributes of Object
'''Sets Attributes of Object.'''
### ~ Basics ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ###
self.strlist = ['BackBase', 'PrevBase']
self.boollist = []
self.intlist = []
self.numlist = []
self.filelist = []
self.listlist = ['Output']
self.dictlist = []
self.objlist = []
### ~ Defaults ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ###
self._setDefaults(str='None',
bool=False,
int=0,
num=0.0,
obj=None,
setlist=True,
setdict=True,
setfile=True)
self.baseFile('slimsuite')
self.setStr({
'BackBase': 'slimsuite.%s' % rje.dateTime(dateonly=True),
'PrevBase': 'slimsuite'
})
self.setBool({})
self.setInt({})
self.setNum({})
self.list['Output'] = string.split(
'release,history,updates,readme,dependencies', ',')
### ~ Other Attributes ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ###
self._setForkAttributes() # Delete if no forking
def rmdHead(self,title=None,author=None,date=None,extra=[],setup=True,toc=True): ### Generate Rmd output file
'''
Generate Rmd output file. Call self.rmdKnit(rmdfile) to convert to another format.
>> rmdfile:str [self.str['RmdFile']] = Full/relative path to Rmd output file.
>> header:dict {} = Dictionary of Rmd header elements. Will default to self.log.obj['Info'] and HTML.
>> elements:list [] = List of tuples (type,content) to output into file. For R code, content will be a dictionary
This method puts together the basic elements of an R markdown file into a text document that can be knitted into
HTML or PDF using self.rmdKnit().
'''
try:### ~ [1] Setup ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ###
rcode = '---\n'
if not title: title = '%s - %s' % (self.prog(),self.basefile())
rcode += 'title: "%s"\n' % title
if not author: author = self.log.obj['Info'].author
rcode += 'author: "%s"\n' % author
if not date: date = rje.dateTime(dateonly=True)
rcode += 'date: "%s"\n' % date #07/02/2019
for (key,value) in extra:
rcode += '%s: "%s"\n' % (key,value)
rcode += 'output:\n html_document:\n css: http://www.slimsuite.unsw.edu.au/stylesheets/slimhtml.css\n'
if toc: rcode += string.join([' toc: true',' toc_float: true',' toc_collapsed: false',' toc_depth: 3',' number_sections: true',''],'\n')
rcode += '---\n\n'
if setup:
rcode += '%s\n\n<a name="Top" />\n\n' % setupTest
self.debug(rcode)
return rcode
except: self.errorLog('%s.rmdOutput error' % self.prog())
def _setAttributes(self): ### Sets Attributes of Object
'''Sets Attributes of Object.'''
### ~ Basics ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ###
self.strlist = ['BackBase','PrevBase']
self.boollist = []
self.intlist = []
self.numlist = []
self.filelist = []
self.listlist = ['Output']
self.dictlist = []
self.objlist = []
### ~ Defaults ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ###
self._setDefaults(str='None',bool=False,int=0,num=0.0,obj=None,setlist=True,setdict=True,setfile=True)
self.baseFile('slimsuite')
self.setStr({'BackBase':'slimsuite.%s' % rje.dateTime(dateonly=True),'PrevBase':'slimsuite'})
self.setBool({})
self.setInt({})
self.setNum({})
self.list['Output'] = string.split('release,history,updates,readme,dependencies',',')
### ~ Other Attributes ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ###
self._setForkAttributes() # Delete if no forking
def saveXGMML(
self,
filename=None,
format='Cytoscape'): ### Saves object data to file in XGMML format
'''
Saves object data to file in XGMML format.
>> filename:str [None] = Output file. Will use name.xgmml if None.
>> format:str [Cytoscape] = Target for output file
'''
try: ### ~ [1] Setup ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ###
if not filename or filename.lower() == 'none':
filename = '%s.xgmml' % self.info['Name']
self.log.printLog('#XGMML',
'Output of XGMML file %s for %s...' %
(filename, format),
log=False,
newline=False)
rje.backup(self, filename)
date = rje.dateTime()
OUT = open(filename, 'w')
### ~ [2] Output headers ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ###
OUT.write(
'<?xml version="1.0" encoding="UTF-8" standalone="yes"?>\n')
OUT.write(
'<graph label="%s" id="%s" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns="http://www.cs.rpi.edu/XGMML" xmlns:xlink="http://www.w3.org/1999/xlink" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">\n'
% (self.info['Name'], self.info['Name']))
OUT.write(' <att name="documentVersion" value="1.0"/>\n')
## ~ [2a] Cytoscape format ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ##
OUT.write(' <att name="networkMetadata">\n')
OUT.write(' <rdf:RDF>\n')
OUT.write(
' <rdf:Description rdf:about="http://www.cytoscape.org/">\n'
)
OUT.write(' <dc:source>RJE_XGMML</dc:source>\n')
OUT.write(
' <dc:format>Cytoscape-XGMML</dc:format>\n')
OUT.write(' <dc:description>%s</dc:description>\n' %
self.info['Description'])
OUT.write(' <dc:date>%s</dc:date>\n' % date)
OUT.write(' <dc:type>%s</dc:type>\n' %
self.info['Type'])
OUT.write(' <dc:identifier>N/A</dc:identifier>\n')
OUT.write(' <dc:title>%s</dc:title>\n' %
self.info['Name'])
OUT.write(' </rdf:Description>\n')
OUT.write(' </rdf:RDF>\n')
OUT.write(' </att>\n\n')
### ~ [3] Output Nodes ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ###
size = 35.0
nodelist = rje.sortKeys(self.dict['Node'])
(n, x, y) = (int(math.sqrt(len(nodelist))), 0, 0)
for node in nodelist:
try:
## ~ [3a] Basic node attributes ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ##
OUT.write(' <node label="%s" id="%d">\n' %
(node, nodelist.index(node)))
except:
self.errorLog('!')
continue
try:
for att in rje.sortKeys(self.dict['Node'][node]):
if att not in self.dict['NodeAtt']: continue
type = self.dict['NodeAtt'][att]
value = string.replace(
'%s' % self.dict['Node'][node][att], '&', 'and')
OUT.write(
' <att type="%s" name="%s" label="%s" value="%s"/>\n'
% (type, att, att, value))
### ~ [3b] Graphics ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ##
#!# Add control for these at some point! #!#
if node in self.dict['NodePos']:
(nx, ny) = self.dict['NodePos'][node]
try:
nx * size
except:
self.errorLog('%s nodepos X = %s' % (node, nx))
nx = x
try:
ny * size
except:
self.errorLog('%s nodepos Y = %s' % (node, ny))
ny = y
else:
[nx, ny] = [x, y]
if self.getBool('XGMMLAtt'):
OUT.write(
' <graphics w="%.1f" h="%.1f" width="1" type="ellipse" outline="#000000" fill="#ff9999" y="%.1f" x="%.1f">\n'
% (size, size, ny * 2 * size, nx * 2 * size))
OUT.write(
' <att name="cytoscapeNodeGraphicsAttributes">\n'
)
OUT.write(
' <att name="nodeTransparency" value="1.0"/>\n'
)
#OUT.write(' <att name="nodeLabelFont" value="Default-0-12"/>\n')
OUT.write(
' <att name="borderLineType" value="solid"/>\n'
)
OUT.write(' </att>\n')
else:
OUT.write(' <graphics y="%.1f" x="%.1f">\n' %
(ny * 2 * size, nx * 2 * size))
OUT.write(' </graphics>\n')
x += 1
if x > n: (x, y) = (0, y + 1)
### ~ [3c] Finish ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ##
except:
self.errorLog('!')
OUT.write(' </node>\n')
### ~ [4] Output Edges ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ###
for etype in rje.sortKeys(self.dict['Edge']):
for edge in rje.sortKeys(self.dict['Edge'][etype]):
try:
## ~ [3a] Basic edge attributes ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ##
id = '%s (%s) %s' % (edge[0], etype, edge[1])
OUT.write(
' <edge label="%s" id="%s" target="%d" source="%d">\n'
% (id, id, nodelist.index(
edge[1]), nodelist.index(edge[0])))
except:
self.errorLog('!')
continue
try:
OUT.write(
' <att type="string" name="canonicalName" label="canonicalName" value="%s"/>\n'
% id)
OUT.write(
' <att type="string" name="TYPE" label="TYPE" value="%s"/>\n'
% etype)
if 'interaction' not in self.dict['EdgeAtt']:
OUT.write(
' <att type="string" name="interaction" label="interaction" value="%s"/>\n'
% etype)
OUT.write(
' <att type="string" name="EDGE_TYPE" label="EDGE_TYPE" value="DefaultEdge"/>\n'
)
for att in self.dict['Edge'][etype][edge]:
if att.lower() == 'type': continue
if att not in self.dict['EdgeAtt']: continue
type = self.dict['EdgeAtt'][att]
value = string.replace(
'%s' % self.dict['Edge'][etype][edge][att],
'&', 'and')
OUT.write(
' <att type="%s" name="%s" label="%s" value="%s"/>\n'
% (type, att, att, value))
### ~ [3b] Graphics ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ##
#!# Update these at some point! #!#
#OUT.write(' <graphics width="1" fill="#0000ff">\n')
#OUT.write(' <att name="cytoscapeEdgeGraphicsAttributes">\n')
#OUT.write(' <att name="sourceArrow" value="0"/>\n')
#OUT.write(' <att name="targetArrow" value="0"/>\n')
#OUT.write(' <att name="edgeLabelFont" value="Default-0-10"/>\n')
#OUT.write(' <att name="edgeLineType" value="SOLID"/>\n')
#OUT.write(' <att name="sourceArrowColor" value="#000000"/>\n')
#OUT.write(' <att name="targetArrowColor" value="#000000"/>\n')
#OUT.write(' <att name="curved" value="STRAIGHT_LINES"/>\n')
#OUT.write(' </att>\n')
#OUT.write(' </graphics>\n')
### ~ [3c] Finish ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ##
except:
self.errorLog('!')
OUT.write(' </edge>\n')
### ~ [5] Finish ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ###
OUT.write('</graph>\n')
OUT.close()
self.log.printLog(
'\r#XGMML', 'Output of XGMML file %s for %s complete.' %
(filename, format))
except:
self.log.errorLog(rje_zen.Zen().wisdom())
def makeHistory(self): ### Extracts history information from docstrings.
'''Extracts history information from docstrings.'''
try: ### ~ [0] Setup ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ###
hdb = self.db('history')
mdb = self.db('Module')
pydoc = self.obj['PyDoc']
uhtml = [] # Update HTML text
udir = ''
### ~ [1] Work through python modules ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ###
for mkey in mdb.dataKeys():
entry = mdb.data(mkey)
pyfile = entry['File']
mod = entry['Module']
prev = '-'
lastv = ''
## ~ [1a] Parse out history text ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ##
history = [] # History lines
updates = [] # Version number entries
for mentry in self.db('Method').indexEntries('File', pyfile):
if mentry['Method'] == 'history':
try:
history = string.split(mentry['DocString'], '\n')
break
except:
history = []
self.errorLog('History parsing problem: %s' %
mentry,
printerror=False)
for dline in history:
if rje.matchExp('# (\d+\.\d+\.?\d*)\s?-\s(\S.+)$', dline):
(v,
text) = rje.matchExp('# (\d\.\d+\.?\d*)\s?-\s(\S.+)$',
dline)
if v == lastv: # Continuation of update
if prev == lastv: continue # In previous release
updates[-1]['Update'] += ' %s' % text
continue
lastv = v
ventry = {
'Dir': entry['SourceDir'],
'Module': mod,
'Version': v,
'Update': text,
'Release': rje.dateTime(dateonly=True)
}
vkey = hdb.makeKey(ventry)
if hdb.data(vkey): prev = v
else: updates.append(ventry)
## ~ [1b] Assess/report updates ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ##
if prev != lastv:
if entry['SourceDir'] != udir:
uhtml.append('<h2>Updates in %s/:</h2>\n' %
entry['SourceDir'])
udir = entry['SourceDir']
if prev == '-' and lastv:
self.printLog(
'#VNUM',
'%s: Creation -> Version %s' % (mod, entry['Version']))
uhtml.append(
'<p><b>• %s:</b> <i>Created/Renamed/moved.</i>' %
mod)
elif prev not in ['-', lastv]:
self.printLog(
'#VNUM', '%s: Version %s -> Version %s' %
(mod, prev, entry['Version']))
uhtml.append(
'<p><b>• %s:</b> <i>Updated from Version %s.</i>'
% (mod, prev))
for ventry in updates:
self.printLog('#V%s' % ventry['Version'], ventry['Update'])
uhtml.append('<br>→ Version %s: %s' %
(ventry['Version'], ventry['Update']))
hdb.addEntry(ventry)
if uhtml and uhtml[-1] != '</p>': uhtml.append('</p>')
if lastv != entry['Version']:
self.warnLog(
'Module %s Version %s but history() ends at %s' %
(mod, entry['Version'], lastv))
self.deBug('>>>')
if 'history' in self.list['Output']: hdb.saveToFile(backup=False)
### ~ [2] Make updates.html file ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ###
if 'updates' in self.list['Output']:
htmlfile = '%s.updates.html' % self.basefile()
title = 'SLiMSuite updates'
stylesheets = []
for css in pydoc.list['StyleSheets']:
stylesheets.append(pydoc.getStr('StylePath') + css)
htmlhead = rje_html.htmlHead(
title,
stylesheets,
tabber=True,
frontpage=False,
nobots=False,
keywords=pydoc.list['Keywords'],
javascript=pydoc.getStr('StylePath'))
htmlbody = string.join(['<h1>SLiMSuite updates</h1>'] + uhtml,
'\n')
htmltail = rje_html.htmlTail(
'%s %s' %
(pydoc.getStr('Author'),
string.split(time.asctime(time.localtime(
time.time())))[-1]))
open(htmlfile, 'w').write(htmlhead + htmlbody + htmltail)
self.printLog('#HTML',
'HTML update summary output to %s' % (htmlfile))
except:
self.errorLog('Error in %s.makeHistory()' % self.prog())
def makeHistory(self): ### Extracts history information from docstrings.
'''Extracts history information from docstrings.'''
try:### ~ [0] Setup ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ###
hdb = self.db('history')
mdb = self.db('Module')
pydoc = self.obj['PyDoc']
uhtml = [] # Update HTML text
udir = ''
### ~ [1] Work through python modules ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ###
for mkey in mdb.dataKeys():
entry = mdb.data(mkey)
pyfile = entry['File']
mod = entry['Module']
prev = '-'
lastv = ''
## ~ [1a] Parse out history text ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ##
history = [] # History lines
updates = [] # Version number entries
for mentry in self.db('Method').indexEntries('File',pyfile):
if mentry['Method'] == 'history':
try: history = string.split(mentry['DocString'],'\n'); break
except:
history = []
self.errorLog('History parsing problem: %s' % mentry,printerror=False)
for dline in history:
if rje.matchExp('# (\d+\.\d+\.?\d*)\s?-\s(\S.+)$',dline):
(v,text) = rje.matchExp('# (\d\.\d+\.?\d*)\s?-\s(\S.+)$',dline)
if v == lastv: # Continuation of update
if prev == lastv: continue # In previous release
updates[-1]['Update'] += ' %s' % text
continue
lastv = v
ventry = {'Dir':entry['SourceDir'],'Module':mod,'Version':v,'Update':text,'Release':rje.dateTime(dateonly=True)}
vkey = hdb.makeKey(ventry)
if hdb.data(vkey): prev = v
else: updates.append(ventry)
## ~ [1b] Assess/report updates ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ##
if prev != lastv:
if entry['SourceDir'] != udir: uhtml.append('<h2>Updates in %s/:</h2>\n' % entry['SourceDir']); udir = entry['SourceDir']
if prev == '-' and lastv:
self.printLog('#VNUM','%s: Creation -> Version %s' % (mod,entry['Version']))
uhtml.append('<p><b>• %s:</b> <i>Created/Renamed/moved.</i>' % mod)
elif prev not in ['-',lastv]:
self.printLog('#VNUM','%s: Version %s -> Version %s' % (mod,prev,entry['Version']))
uhtml.append('<p><b>• %s:</b> <i>Updated from Version %s.</i>' % (mod,prev))
for ventry in updates:
self.printLog('#V%s' % ventry['Version'],ventry['Update'])
uhtml.append('<br>→ Version %s: %s' % (ventry['Version'],ventry['Update']))
hdb.addEntry(ventry)
if uhtml and uhtml[-1] != '</p>': uhtml.append('</p>')
if lastv != entry['Version']: self.warnLog('Module %s Version %s but history() ends at %s' % (mod,entry['Version'],lastv))
self.deBug('>>>')
if 'history' in self.list['Output']: hdb.saveToFile(backup=False)
### ~ [2] Make updates.html file ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ###
if 'updates' in self.list['Output']:
htmlfile = '%s.updates.html' % self.basefile()
title = 'SLiMSuite updates'
stylesheets = []
for css in pydoc.list['StyleSheets']: stylesheets.append(pydoc.getStr('StylePath')+css)
htmlhead = rje_html.htmlHead(title,stylesheets,tabber=True,frontpage=False,nobots=False,keywords=pydoc.list['Keywords'],javascript=pydoc.getStr('StylePath'))
htmlbody = string.join(['<h1>SLiMSuite updates</h1>'] + uhtml,'\n')
htmltail = rje_html.htmlTail('%s %s' % (pydoc.getStr('Author'),string.split(time.asctime(time.localtime(time.time())))[-1]))
open(htmlfile,'w').write(htmlhead+htmlbody+htmltail)
self.printLog('#HTML','HTML update summary output to %s' % (htmlfile))
except: self.errorLog('Error in %s.makeHistory()' % self.prog())
def saveXGMML(self,filename=None,format='Cytoscape'): ### Saves object data to file in XGMML format
'''
Saves object data to file in XGMML format.
>> filename:str [None] = Output file. Will use name.xgmml if None.
>> format:str [Cytoscape] = Target for output file
'''
try:### ~ [1] Setup ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ###
if not filename or filename.lower() == 'none': filename = '%s.xgmml' % self.info['Name']
self.log.printLog('#XGMML','Output of XGMML file %s for %s...' % (filename,format),log=False,newline=False)
rje.backup(self,filename)
date = rje.dateTime()
OUT = open(filename,'w')
### ~ [2] Output headers ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ###
OUT.write('<?xml version="1.0" encoding="UTF-8" standalone="yes"?>\n')
OUT.write('<graph label="%s" id="%s" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns="http://www.cs.rpi.edu/XGMML" xmlns:xlink="http://www.w3.org/1999/xlink" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">\n' % (self.info['Name'],self.info['Name']))
OUT.write(' <att name="documentVersion" value="1.0"/>\n')
## ~ [2a] Cytoscape format ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ##
OUT.write(' <att name="networkMetadata">\n')
OUT.write(' <rdf:RDF>\n')
OUT.write(' <rdf:Description rdf:about="http://www.cytoscape.org/">\n')
OUT.write(' <dc:source>RJE_XGMML</dc:source>\n')
OUT.write(' <dc:format>Cytoscape-XGMML</dc:format>\n')
OUT.write(' <dc:description>%s</dc:description>\n' % self.info['Description'])
OUT.write(' <dc:date>%s</dc:date>\n' % date)
OUT.write(' <dc:type>%s</dc:type>\n' % self.info['Type'])
OUT.write(' <dc:identifier>N/A</dc:identifier>\n')
OUT.write(' <dc:title>%s</dc:title>\n' % self.info['Name'])
OUT.write(' </rdf:Description>\n')
OUT.write(' </rdf:RDF>\n')
OUT.write(' </att>\n\n')
### ~ [3] Output Nodes ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ###
size = 35.0
nodelist = rje.sortKeys(self.dict['Node'])
(n,x,y) = (int(math.sqrt(len(nodelist))),0,0)
for node in nodelist:
try:
## ~ [3a] Basic node attributes ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ##
OUT.write(' <node label="%s" id="%d">\n' % (node,nodelist.index(node)))
except: self.errorLog('!'); continue
try:
for att in rje.sortKeys(self.dict['Node'][node]):
if att not in self.dict['NodeAtt']: continue
type = self.dict['NodeAtt'][att]
value = string.replace('%s' % self.dict['Node'][node][att],'&','and')
OUT.write(' <att type="%s" name="%s" label="%s" value="%s"/>\n' % (type,att,att,value))
### ~ [3b] Graphics ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ##
#!# Add control for these at some point! #!#
if node in self.dict['NodePos']:
(nx,ny) = self.dict['NodePos'][node]
try: nx * size
except: self.errorLog('%s nodepos X = %s' % (node,nx)); nx = x
try: ny * size
except: self.errorLog('%s nodepos Y = %s' % (node,ny)); ny = y
else: [nx,ny] = [x,y]
if self.getBool('XGMMLAtt'):
OUT.write(' <graphics w="%.1f" h="%.1f" width="1" type="ellipse" outline="#000000" fill="#ff9999" y="%.1f" x="%.1f">\n' % (size,size,ny*2*size,nx*2*size))
OUT.write(' <att name="cytoscapeNodeGraphicsAttributes">\n')
OUT.write(' <att name="nodeTransparency" value="1.0"/>\n')
#OUT.write(' <att name="nodeLabelFont" value="Default-0-12"/>\n')
OUT.write(' <att name="borderLineType" value="solid"/>\n')
OUT.write(' </att>\n')
else:
OUT.write(' <graphics y="%.1f" x="%.1f">\n' % (ny*2*size,nx*2*size))
OUT.write(' </graphics>\n')
x += 1
if x > n: (x,y) = (0,y+1)
### ~ [3c] Finish ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ##
except: self.errorLog('!')
OUT.write(' </node>\n')
### ~ [4] Output Edges ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ###
for etype in rje.sortKeys(self.dict['Edge']):
for edge in rje.sortKeys(self.dict['Edge'][etype]):
try:
## ~ [3a] Basic edge attributes ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ##
id = '%s (%s) %s' % (edge[0],etype,edge[1])
OUT.write(' <edge label="%s" id="%s" target="%d" source="%d">\n' % (id,id,nodelist.index(edge[1]),nodelist.index(edge[0])))
except: self.errorLog('!'); continue
try:
OUT.write(' <att type="string" name="canonicalName" label="canonicalName" value="%s"/>\n' % id)
OUT.write(' <att type="string" name="TYPE" label="TYPE" value="%s"/>\n' % etype)
if 'interaction' not in self.dict['EdgeAtt']: OUT.write(' <att type="string" name="interaction" label="interaction" value="%s"/>\n' % etype)
OUT.write(' <att type="string" name="EDGE_TYPE" label="EDGE_TYPE" value="DefaultEdge"/>\n')
for att in self.dict['Edge'][etype][edge]:
if att.lower() == 'type': continue
if att not in self.dict['EdgeAtt']: continue
type = self.dict['EdgeAtt'][att]
value = string.replace('%s' % self.dict['Edge'][etype][edge][att],'&','and')
OUT.write(' <att type="%s" name="%s" label="%s" value="%s"/>\n' % (type,att,att,value))
### ~ [3b] Graphics ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ##
#!# Update these at some point! #!#
#OUT.write(' <graphics width="1" fill="#0000ff">\n')
#OUT.write(' <att name="cytoscapeEdgeGraphicsAttributes">\n')
#OUT.write(' <att name="sourceArrow" value="0"/>\n')
#OUT.write(' <att name="targetArrow" value="0"/>\n')
#OUT.write(' <att name="edgeLabelFont" value="Default-0-10"/>\n')
#OUT.write(' <att name="edgeLineType" value="SOLID"/>\n')
#OUT.write(' <att name="sourceArrowColor" value="#000000"/>\n')
#OUT.write(' <att name="targetArrowColor" value="#000000"/>\n')
#OUT.write(' <att name="curved" value="STRAIGHT_LINES"/>\n')
#OUT.write(' </att>\n')
#OUT.write(' </graphics>\n')
### ~ [3c] Finish ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ##
except: self.errorLog('!')
OUT.write(' </edge>\n')
### ~ [5] Finish ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ###
OUT.write('</graph>\n')
OUT.close()
self.log.printLog('\r#XGMML','Output of XGMML file %s for %s complete.' % (filename,format))
except: self.log.errorLog(rje_zen.Zen().wisdom())