def getMedlineList(pmids):
"""
This function takes a list of article-ids and returns a list of
MedLine articles that contains an abstract.
"""
records = []
cleaned_records = []
listLength = len(pmids)
Entrez.email = '*****@*****.**'
for i in range(0, listLength, 650):
tempList = pmids[i:i + 650]
handle = Entrez.efetch(db='pubmed', id=tempList,rettype='medline', retmode='text')
try:
records.extend(list(Medline.parse(handle)))
except:
IOmodule.writeOutTxt(_mainFolder+'/'+'errordir_medline_records', pmids[i], '')
print 'Downloaded',len(records),'MedLine articles.',str(listLength-len(records)),'remaining...'
for article in records:
if 'AB' in article:
cleaned_records.append(article)
print 'Returned',len(cleaned_records),'MedLine articles containing an abstract.'
return cleaned_records
def gatherOfAllThings(startIndex=0,stopIndex=None):
# Get the number of diseases, based on start and stop. If
# stopIndex = None, then it returns the whole range
numberOfRareDiseases = len(_readDiseases(startIndex,stopIndex))
# Default number per chuck, before writeout
numberToGet = 1
# Calculate the numbers of steps, for looping.
steps = int(math.ceil(numberOfRareDiseases / numberToGet))
# Default directory to save information files in.
directory = 'medline_records'
_path_medlinerecords+=_mainFolder+'/'+directory
if not os.path.isDir(_path_medlinerecords):
os.mkdir(_path_medlinerecords)
# Read in the range of diseases we want to get information about,
# in a list, it needs to be sorted to support resume.
d=_readDiseases(startIndex,stopIndex)
for i in range(steps):
# Read in the a chuck of diseases in a list
diseaseList = d[i * numberToGet:i * numberToGet + numberToGet]
diseaseDictionary = {}
for i in range(len(diseaseList)):
# Transfer the ordered disease list into an unordered
# dictionary
diseaseDictionary[diseaseList[i].keys()[0]] = diseaseList[i].values()[0]
dictionary = {}
# Runs through the disease dictionary and gets all the PMIDs
# for each disease
diseaseDictionary = getArticleIDs(diseaseDictionary)
for disease in diseaseDictionary:
dictionary[disease] = {}
dictionary[disease]['records']=[]
dictionary[disease]['description'] = diseaseDictionary[disease]['description']
dictionary[disease]['records'].extend(getMedlineList(diseaseDictionary[disease]['PMIDs']))
IOmodule.writeOutTxt(_path_medlinerecords, disease, dictionary[disease], 'w')
def fetchPubmedDiseaseTerms(pages):
"""
Takes a URL-list of pages to crawl for pubmed terms, uids and optional
describtions.
Returns a dictionary on the form:
{DiseaseName:{db='',terms:'',syn=[],uid:'',desc:''}}
"""
pubmedURLs={}
printvar=0
pagenumber=0
desccounter=0
for page in pages:
pagenumber+=1
# Open the page.
for i in range(3):
try:
c=urllib2.urlopen(page)
except:
print "Could not open %s" % page
print "Attempt",str(i+1),"out of 3"
sleep(5)
if i==2:
print "Could not open page. Terminating.."
raise StopIteration()
try:
soup=BeautifulSoup(c.read())
except HTMLParseError:
print 'Experienced difficulties opening %s' % page
IOmodule.writeOutTxt(_subFolder+"/"+diseaseFolder+'/'+errorFolder,strftime('%H%M%S'),page)
continue
# Get disease name.
title=soup.html.head.title.string
# Some pages are 'officially' not working. Catch them here.
if title=='NIH Office of Rare Diseases Research (ORDR) - Error':
IOmodule.writeOutTxt(_subFolder+"/"+diseaseFolder+'/'+errorFolder,'Page error'+strftime('%H%M%S'),page)
print 'Page Error on %s' % page
continue
# Allocate dictionary.
pubmedURLs[title]={}
pubmedURLs[title]['db']='pubmed' # ..database to search in (pubmed by default)
pubmedURLs[title]['terms']='' # ..handcrafted search term
pubmedURLs[title]['syn']=[] # ..disease synonyms
pubmedURLs[title]['uid']='' # ..search id
pubmedURLs[title]['desc']='' # ..optional disease description
# Check for PubMed direct links.
links=soup('a')
found=False
for link in links:
if (link.contents):
if ((link.contents[0] == 'PubMed')) & ('href' in dict(link.attrs)):
urlString = link['href'].lower()
# If there is a PubMed direct link and it's an id:
if ('uid=' in urlString) | ('uids=' in urlString) | ('idsfromresult=' in urlString):
tokens = _parseURL(urlString)
uid = tokens['from_uid']
pubmedURLs[title]['uid'] = uid
pubmedURLs[title]['db'] = tokens['db']
printvar += 1
found = True
print 'Found', str(printvar), 'PubMed terms/uids.', title
continue
# If there is a PubMed direct link and it's a handcrafted term:
elif ('term=' in urlString):
tokens = _parseURL(urlString)
terms = tokens['term']
pubmedURLs[title]['terms'] = terms
pubmedURLs[title]['db'] = tokens['db']
printvar += 1
found = True
print 'Found', str(printvar), 'PubMed terms/uids.', title
continue
# Special case 1: If there is a PubMed direct link but the uid is not part of the tokens.
elif ('/entrez/' not in urlString):
start = urlString.find('/pubmed/') + 8
if '?' in urlString:
end = urlString.find('?')
uid = urlString[start:end]
else:
uid = urlString[start:]
print uid
pubmedURLs[title]['uid'] = uid
printvar += 1
found = True
print 'Found', str(printvar), 'PubMed terms/uids.', title, '. (Special case 1: No tokens)'
# Special case 2: If there is a webenv, the url is (by experience) not working but the disease name is still valuable for a pbumed search.
elif '&webenv=' in urlString:
printvar += 1
found = True
print 'Found', str(printvar), 'PubMed terms/uids.', title, '. (Special case 2: WebEnv)'
# Terminate if an unexpected url shows up
if link.contents:
if (not found) & (link.contents[0]=='PubMed'):
print 'Could not fetch url'
raise StopIteration()
# A simple addition to the printouts.
if not found:
printvar+=1
print 'Found',str(printvar),'Diseases.',title,'(no uid or term).'
# Notify if an unexpected database shows up.
if ((pubmedURLs[title]['db']!='')&(pubmedURLs[title]['db']!='omim')&(pubmedURLs[title]['db']!='pubmed')):
print "*****Found different db:",pubmedURLs[title]['db']
print 'Could not fetch url'
raise StopIteration()
# Disease synonyms are also added to the term list.
lis=soup('li')
for li in lis:
if ('synonym' in str(li.parent)):
synonym=li.contents[0]
if (',') in str(synonym):
aditionalSynonyms=synonym.split(',')
for syn in aditionalSynonyms:
pubmedURLs[title]['syn'].append(syn)
print ' ' + syn
else:
pubmedURLs[title]['syn'].append(synonym)
print ' ' + synonym
# Look for a optional disease description on rarediseases.info.nih.gov.
descs=soup('span')
for desc in descs:
if ('id' in dict(desc.attrs)):
idString=desc['id'].lower()
if (('descriptionquestion' in idString) & ('#003366' not in str(desc))):
desc=_cleanString(str(desc))
pubmedURLs[title]['desc']=desc
desccounter+=1
print ' *Found optional disease description'
print ''
if ((pagenumber%20)==0):
# Print status report
print '*****************************************************'
print 'Total pages looked in:',str(pagenumber),'\nPages found:',str(printvar),'\nRemaining in total:',(len(pages)-printvar),'out of',len(pages),'\nDescriptions found:',str(desccounter)
print '*****************************************************'
print 'Writing to files...'
# Write out and flush dictionary
for disease in pubmedURLs:
# Remove some problematic tokens from the file name
content=pubmedURLs[disease]
disease=removeSlashes.sub(' ',disease)
disease=removeCommas.sub(' ',disease)
# Write out
IOmodule.writeOutTxt(diseaseFolder,disease,content)
pubmedURLs={}
print 'Wrote successfully. Dictionary flushed.'