User:BogBot/Source code/Task 03: Difference between revisions

Revision as of 02:00, 14 August 2011

Revision as of 02:33, 16 August 2011

Line 192:

regexp_ref_tag_end = re.compile(r"</ref>")

regexp_citation_template = re.compile(r"\{\{[C|c]ite\s*?(?P<TEMPLATE>.*?)\}\}")

# href='/monograph/maprotiline-hydrochloride.html'

regexp_monograph_url = re.compile("href='/monograph/(?P<STEM>.*?)\.html'", re.DOTALL)

def Allowbots(text):

Line 588 ⟶ 591:

"KEGG" in current_parameters or "ChEBI" in current_parameters or "ChEMBL" in current_parameters):

new_drugbox += "\n<!--Identifiers-->\n"

if current_parameters.has_key("CASNo_RefCAS_number_Ref"): new_drugbox += "| CASNo_RefCAS_number_Ref = " + current_parameters['CASNo_RefCAS_number_Ref'] + "\n"

if current_parameters.has_key("CASNo_Ref"): new_drugbox += "| CASNo_Ref = " + current_parameters['CASNo_Ref'] + "\n"

if current_parameters.has_key("CAS_number"): new_drugbox += "| CAS_number = " + current_parameters['CAS_number'] + "\n"

if current_parameters.has_key("CAS_supplemental"): new_drugbox += "| CAS_supplemental = " + current_parameters['CAS_supplemental'] + "\n"

Line 598 ⟶ 602:

if current_parameters.has_key("PubChemSubstance"): new_drugbox += "| PubChemSubstance = " + current_parameters['PubChemSubstance'] + "\n"

if current_parameters.has_key("IUPHAR_ligand"): new_drugbox += "| IUPHAR_ligand = " + current_parameters['IUPHAR_ligand'] + "\n"

if current_parameters.has_key("DrugBank_Ref"): new_drugbox += "| DrugBank_Ref = " + current_parameters['DrugBank_Ref'] + "\n"

if current_parameters.has_key("DrugBank"): new_drugbox += "| DrugBank = " + current_parameters['DrugBank'] + "\n"

if current_parameters.has_key("ChemSpiderID_Ref"): new_drugbox += "| ChemSpiderID_Ref = " + current_parameters['ChemSpiderID_Ref'] + "\n"

Line 650 ⟶ 655:

if current_parameters.has_key("InChI_Ref"): new_drugbox += "| InChI_Ref = " + current_parameters['InChI_Ref'] + "\n"

if current_parameters.has_key("InChI"): new_drugbox += "| InChI = " + current_parameters['InChI'] + "\n"

if current_parameters.has_key("InChIKey"): new_drugbox += "| InChIKey = " + current_parameters['InChIKey'] + "\n"

if current_parameters.has_key("StdInChI_Ref"): new_drugbox += "| StdInChI_Ref = " + current_parameters['StdInChI_Ref'] + "\n"

if current_parameters.has_key("StdInChI"): new_drugbox += "| StdInChI = " + current_parameters['StdInChI'] + "\n"

Line 753 ⟶ 759:

else:

stems.append(drugname)

# also try common salts

stems.append(drugname + "-hydrochloride")

stems.append(drugname + "-sulfate")

stems.append(drugname + "-chloride")

stems.append(drugname + "-sodium")

stems.append(drugname + "-bromide")

stems.append(drugname + "-maleate")

stems.append(drugname + "-citrate")

if drugbank_drugs_com:

if (string.find(drugbank_drugs_com, "http://www.drugs.com/") > -1):

Line 768 ⟶ 782:

if urllib.urlopen(link).getcode() == 200: # test link status to make sure it is good before assigning parameter

# print "passed link: ", link

link = "{{drugs.com|" +if root[0] + "|" + stem +== "}}monograph":

raise StopIteration() link = "{{drugs.com|" + root[0] + "|" + stem + "}}"

raise StopIteration()

else:

opener = urllib.FancyURLopener({})

f = opener.open(link)

text = f.read()

result = regexp_monograph_url.search(text)

if result:

stem = result.group('STEM')

link = "{{drugs.com|" + roots[0][0] + "|" + stem + "}}"

raise StopIteration()

else:

link = ""

Line 799 ⟶ 823:

return False

def savepage(page, text, summary = '', minor = False, log_string = ""):

"""Save text to a page and log exceptions."""

if summary != '':

Line 805 ⟶ 829:

try:

page.put(text, minorEdit = minor)

wikipedia.output('%s \03{green}saving %s' % (log_string, page.title()) )

return ''

except wikipedia.LockedPage:

wikipedia.output('%s \03{red}cannot save %s because it is locked\03{default}' % (log_string, page.title()) )

return '# %s: page was locked\n' % page.aslink()

except wikipedia.EditConflict:

wikipedia.output('%s \03{red}cannot save %s because of edit conflict\03{default}' % (log_string, page.title()) )

return '# %s: edit conflict occurred\n' % page.aslink()

except wikipedia.SpamfilterError, error:

wikipedia.output('%s \03{red}cannot save %s because of spam blacklist entry %s\03{default}' % ((log_string, page.title(), error.url)) )

return '# %s: spam blacklist entry\n' % page.aslink()

except:

wikipedia.output('%s \03{red}unknown error on saving %s\03{default}' % (log_string, page.title()) )

return '# %s: unknown error occurred\n' % page.aslink()

Line 846 ⟶ 870:

new_drugbox = ""

log_string = "* [[" + article + "]], "

print log_string,

site = wikipedia.getSite()

Line 859 ⟶ 882:

if begin:

parameters = text[begin:end]

log_string = ", article: " + article

print log_string,

else:

log_string = ", article: " + articlelog_string + "drugbox not found!"

print log_string

continue

Line 871 ⟶ 892:

if unbalanced(parameters):

log_string = ", article: " + articlelog_string + ", unmatched brackets found, article skipped!"

print log_string

continue

Line 896 ⟶ 917:

db_data = drugbank_data[INN]

elif "DrugBank" in current_parameters and current_parameters['DrugBank'] in DrugBank_ID_INN:

printlog_string = log_string + "INN reset from ", INN,

INN = DrugBank_ID_INN[current_parameters['DrugBank']]

printlog_string = log_string + "to ", + INN, ", ",

db_data = drugbank_data[INN]

if not "drug_name" in current_parameters:

Line 907 ⟶ 928:

if "DrugBank" in current_parameters and current_parameters['DrugBank'] in DrugBank_ID_INN:

if DrugBank_ID_INN[current_parameters['DrugBank']] == INN:

printlog_string = log_string + "DrugBankID/INN OK!, ",

else:

printlog_string = log_string + "DrugBankID/INN NOT OK!, ",

else:

if db_data:

if db_data[8]:

current_parameters['if not "DrugBank']" =in db_data[8]current_parameters:

current_parameters['DrugBank'] = db_data[8]

Line 970 ⟶ 992:

new_text = text[:begin] + build_new_drugbox(current_parameters) + text[end:]

# print build_new_drugbox(current_parameters)

# print current_parameters

# print new_text

Line 975 ⟶ 999:

if current_parameters:

comment='populated new fields in drugbox and reordered per [[Wikipedia:Bots/Requests_for_approval/BogBot_2|bot approval]]'

status = savepage(page, new_text, comment, minorFalse, = Falselog_string)

print ", ", status

else:

print ", page not updated"

Line 983 ⟶ 1,006:

run()

</source>