def OnBlipSubmitted(properties, context):
blip = context.GetBlipById(properties['blipId'])
contents = blip.GetDocument().GetText()
key = '(chem)'
leftdelim = '\\['
query = '([a-zA-Z0-9-]{1,20})'
image = '(;image)'
rightdelim = '\\]'
compiledregex = re.compile(key+leftdelim+query+image+rightdelim, re.IGNORECASE|re.DOTALL)
chemicallist = compiledregex.finditer(contents)
if chemicallist != None:
for chemicalname in chemicallist: # Just pull off first one in list
r = document.Range(0,0)
r.start = chemicalname.start()
r.end = chemicalname.end() + 1
query = chemicalname.group(2)
compound = ChemSpiPy.simplesearch(query) # obtain chemspider ID
chemspiderlink = 'http://www.chemspider.com/Chemical-Structure.%s.html' % compound
#insert the gadget
gadgeturl = 'http://www.danhagon.me.uk/Wave/ChemSpiderDoodleGadgetMVCDev.xml'
gadget = document.Gadget(gadgeturl) # setup gadget instance
blip.GetDocument().InsertElement(r.start, gadget) # insert gadget
delta = {'molfile' : compound.getMolFile()} # set state with molfile for CSID
blip.GetDocument().GadgetSubmitDelta(gadget, delta) # submit the delta
#cleaning up text and insert link
blip.GetDocument().SetTextInRange(r, query) # remove markup
r.start = blip.GetDocument().GetText().find(query) #re-find range of query
r.end = r.start + len(query)
blip.GetDocument().SetAnnotation(r, 'link/manual', chemspiderlink) #link to CS
def chemify(text):
"""Accepts a text string and returns dictionary of information and annotations
Text string is parsed and sent to chemspider to return chemspider ID, image url,
and molecular weight information that makes it feasible to convert weight to
moles and similar. Returns a dictionary that contains at a minimum the keys
'replacementtext', 'imageurl', and 'annotations' which is a tuple of dictionaries
containing the keys 'text', 'annotation', 'value', 'offset', 'length' for each
of the annotations required
test = {'replacementtext':'chemchemchem',
'imageurl' :'http://www.chemspider.com/ImagesHandler.ashx?id=236',
'annotations' :[{'text' :'chem',
'annotation':'link/manual',
'value' :'http://www.chemspider.com',
'offset' :4,
'length' :4},
{'text' :'chem',
'annotation':'chemspidey.appspot.com/csid',
'value' :'666',
'offset' :8,
'length' :4}
]
}
"""
# Set up the dictionary to be returned
chemified = {'replacementtext' : 'chemchem',
'originaltext' : text,
'imageurl' : 'none',
'annotations' : []
}
# Parse the text using chemparse which returns a dictionary
parsed = ChemParsing.chemparse(text)
# Create local variables for the relevant returned information
parsedname = parsed.get('name', None)
quantity = parsed.get('amount', None)
quantityunits = parsed.get('units', None)
role = parsed.get('role', None)
# Obtain chemspider ID and other information via ChemSpider simple search
try:
chemspiderID = ChemSpiPy.simplesearch(parsedname)
logging.debug('Success connecting to ChemSpider')
except IndexError, ie:
errorstring = "Sorry I can't find %s in ChemSpider - try a different name?" % parsedname
chemified['replacementtext'] = errorstring
chemified['error'] = 'IndexError'
logging.debug('Failed to find a match in simplesearch')
return chemified
def OnBlipSubmitted(properties, context):
blip = context.GetBlipById(properties['blipId'])
contents = blip.GetDocument().GetText()
key = '(chem)'
leftdelim = '\\['
query = '([a-zA-Z0-9-]{1,20})'
optintspacer = ';?'
optfloat = '\\s?(\\d{0,5}\\.?\\d{0,5})?'
optunits = '\\s?([mgl]{1,2})?'
optional = optintspacer + optfloat + optunits
rightdelim = '\\]'
compiledregex = re.compile(key+leftdelim+query+optional+rightdelim, re.IGNORECASE|re.DOTALL)
chemicallist = compiledregex.finditer(contents)
if chemicallist != None:
count = 0
changeslist = []
for chemicalname in chemicallist:
r = doc.Range(0,0)
r.start = chemicalname.start()
r.end = chemicalname.end() + 1
query = chemicalname.group(2)
compound = ChemSpiPy.simplesearch(query)
url = "http://www.chemspider.com/Chemical-Structure.%s.html" % compound
insert = query + " (csid:" + compound
if chemicalname.group(3) != None and chemicalname.group(4) == 'mg':
nanomoles = 1000*(float(chemicalname.group(3))/compound.molweight())
nanomoles = round(nanomoles, 2)
insert = insert + ", " + chemicalname.group(3) + 'mg, ' + str(nanomoles) + " nanomoles"
if chemicalname.group(3) != None and chemicalname.group(4) == 'g':
millimoles = 1000*(float(chemicalname.group(3))/compound.molweight())
millimoles = round(millimoles, 2)
insert = insert + ", " + chemicalname.group(3) + 'g, ' + str(millimoles) + " millimoles"
insert = insert + ") "
changeslist.append([r, insert, compound, url])
count = count + 1
while count != 0:
count = count - 1
blip.GetDocument().SetTextInRange(changeslist[count][0], changeslist[count][1])
SetManualLink(blip, changeslist[count][2], changeslist[count][3])
SetManualLink(blip, changeslist[count][1], 'chem', 'lang')
