def _extract_metrics(self, page, status_code=200, id=None):
if status_code != 200:
if status_code == 404:
return {}
else:
raise(self._get_error(status_code))
if ("subjectseeker" not in page) and ("Recent Posts" not in page):
raise ProviderContentMalformedError
(doc, lookup_function) = provider._get_doc_from_xml(page)
if not doc:
return {}
try:
feed_doc = doc.getElementsByTagName("feed")
entry_docs = feed_doc[0].getElementsByTagName("entry")
number_blog_posts = len(entry_docs)
except (KeyError, IndexError, TypeError):
return {}
if number_blog_posts:
metrics_dict = {'scienceseeker:blog_posts': number_blog_posts}
else:
metrics_dict = {}
return metrics_dict
def _extract_metrics(self, page, status_code=200, id=None):
if status_code != 200:
if status_code == 404:
return {}
else:
raise (self._get_error(status_code))
if ("subjectseeker" not in page) and ("Recent Posts" not in page):
raise ProviderContentMalformedError
(doc, lookup_function) = provider._get_doc_from_xml(page)
if not doc:
return {}
try:
feed_doc = doc.getElementsByTagName("feed")
entry_docs = feed_doc[0].getElementsByTagName("entry")
number_blog_posts = len(entry_docs)
except (KeyError, IndexError, TypeError):
return {}
if number_blog_posts:
metrics_dict = {'scienceseeker:blog_posts': number_blog_posts}
else:
metrics_dict = {}
return metrics_dict
def _extract_aliases_from_pmid(self, page, pmid):
(doc, lookup_function) = provider._get_doc_from_xml(page)
doi = None
pmc = None
try:
articleidlist = doc.getElementsByTagName("ArticleIdList")[0]
for articleid in articleidlist.getElementsByTagName("ArticleId"):
if (articleid.getAttribute("IdType") == u"doi"):
doi = articleid.firstChild.data
if (articleid.getAttribute("IdType") == u"pmc"):
pmc = articleid.firstChild.data
if not doi:
#give it another try, in another part of the xml
# see http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&id=23682040&retmode=xml&[email protected]&tool=total-impact
article = doc.getElementsByTagName("Article")[0]
for elocationid in article.getElementsByTagName("ELocationID"):
if (elocationid.getAttribute("EIdType") == u"doi"):
if (elocationid.getAttribute("ValidYN") == u"Y"):
doi = elocationid.firstChild.data
except (IndexError, TypeError):
pass
#sometimes no doi, or PMID has a doi-fragment in the doi field:
aliases_list = []
if doi:
if "10." in doi:
aliases_list += [("doi", doi), ("url", "http://dx.doi.org/"+doi)]
if pmc:
aliases_list += [("pmc", pmc), ("url", "http://www.ncbi.nlm.nih.gov/pmc/articles/"+pmc)]
return aliases_list
def _extract_metrics(self, page, status_code=200, id=None):
#logger.info(u"_extract_metrics with %s, %i,\n%s\n" % (id, status_code, page))
if status_code != 200:
if (status_code == 404):
return {}
else:
raise (self._get_error(status_code))
(doc, lookup_function) = provider._get_doc_from_xml(page)
try:
searchinfo = doc.getElementsByTagName('searchinfo')
totalhits = int(searchinfo[0].attributes['totalhits'].value)
except (TypeError, IndexError):
raise ProviderContentMalformedError(
"No searchinfo in response document")
if totalhits:
metrics_dict = {"wikipedia:mentions": totalhits}
else:
metrics_dict = {}
#logger.info(u"_extract_metrics returns metrics_dict %s" % (str(metrics_dict)))
return metrics_dict
def _extract_metrics(self, page, status_code=200, id=None):
if status_code != 200:
if status_code == 404:
return {}
else:
raise (self._get_error(status_code))
if "<pmc-web-stat>" not in page:
raise ProviderContentMalformedError
(doc, lookup_function) = provider._get_doc_from_xml(page)
if not doc:
return {}
try:
articles = doc.getElementsByTagName("article")
for article in articles:
print article
metrics_dict = {}
meta_data = article.getElementsByTagName("meta-data")[0]
pmid = meta_data.getAttribute("pubmed-id")
if id == pmid:
metrics = article.getElementsByTagName("usage")[0]
pdf_downloads = int(metrics.getAttribute("pdf"))
if pdf_downloads:
metrics_dict.update(
{'pmc:pdf_downloads': pdf_downloads})
abstract_views = int(metrics.getAttribute("abstract"))
if abstract_views:
metrics_dict.update(
{'pmc:abstract_views': abstract_views})
fulltext_views = int(metrics.getAttribute("full-text"))
if fulltext_views:
metrics_dict.update(
{'pmc:fulltext_views': fulltext_views})
unique_ip_views = int(metrics.getAttribute("unique-ip"))
if unique_ip_views:
metrics_dict.update(
{'pmc:unique_ip_views': unique_ip_views})
figure_views = int(metrics.getAttribute("figure"))
if figure_views:
metrics_dict.update({'pmc:figure_views': figure_views})
suppdata_views = int(metrics.getAttribute("supp-data"))
if suppdata_views:
metrics_dict.update(
{'pmc:suppdata_views': suppdata_views})
return metrics_dict
except (KeyError, IndexError, TypeError):
pass
return {}
def _extract_citing_pmcids(self, page):
if (not "PubMedToPMCcitingformSET" in page):
raise ProviderContentMalformedError()
dict_of_keylists = {"pubmed:pmc_citations": ["PubMedToPMCcitingformSET", "REFORM"]}
(doc, lookup_function) = provider._get_doc_from_xml(page)
try:
pmcid_doms = doc.getElementsByTagName("PMCID")
pmcids = [pmcid_dom.firstChild.data for pmcid_dom in pmcid_doms]
except TypeError:
logger.warning(u"%20s no PMCID xml tags for %s" % (self.provider_name, id))
pmcids = []
return pmcids
def _extract_metrics(self, page, status_code=200, id=None):
if status_code != 200:
if status_code == 404:
return {}
else:
raise(self._get_error(status_code))
if "<pmc-web-stat>" not in page:
raise ProviderContentMalformedError
(doc, lookup_function) = provider._get_doc_from_xml(page)
if not doc:
return {}
try:
articles = doc.getElementsByTagName("article")
for article in articles:
print article
metrics_dict = {}
meta_data = article.getElementsByTagName("meta-data")[0]
pmid = meta_data.getAttribute("pubmed-id")
if id == pmid:
metrics = article.getElementsByTagName("usage")[0]
pdf_downloads = int(metrics.getAttribute("pdf"))
if pdf_downloads:
metrics_dict.update({'pmc:pdf_downloads': pdf_downloads})
abstract_views = int(metrics.getAttribute("abstract"))
if abstract_views:
metrics_dict.update({'pmc:abstract_views': abstract_views})
fulltext_views = int(metrics.getAttribute("full-text"))
if fulltext_views:
metrics_dict.update({'pmc:fulltext_views': fulltext_views})
unique_ip_views = int(metrics.getAttribute("unique-ip"))
if unique_ip_views:
metrics_dict.update({'pmc:unique_ip_views': unique_ip_views})
figure_views = int(metrics.getAttribute("figure"))
if figure_views:
metrics_dict.update({'pmc:figure_views': figure_views})
suppdata_views = int(metrics.getAttribute("supp-data"))
if suppdata_views:
metrics_dict.update({'pmc:suppdata_views': suppdata_views})
return metrics_dict
except (KeyError, IndexError, TypeError):
pass
return {}
def _filter(self, id, citing_pmcids, filter_ptype):
pmcids_string = " OR ".join(["PMC"+pmcid for pmcid in citing_pmcids])
query_string = filter_ptype + "[ptyp] AND (" + pmcids_string + ")"
pmcid_filter_url = self.metrics_pmc_filter_url_template %query_string
page = self._get_eutils_page(pmcid_filter_url, id)
(doc, lookup_function) = provider._get_doc_from_xml(page)
try:
id_docs = doc.getElementsByTagName("Id")
pmids = [id_doc.firstChild.data for id_doc in id_docs]
except TypeError:
logger.warning(u"%20s no Id xml tags for %s" % (self.provider_name, id))
pmids = []
return pmids
def _extract_aliases_from_pmid(self, page, pmid):
dict_of_keylists = {"doi": ["PubmedData", "ArticleIdList"]}
(doc, lookup_function) = provider._get_doc_from_xml(page)
doi = None
try:
articleidlist = doc.getElementsByTagName("ArticleIdList")[0]
for articleid in articleidlist.getElementsByTagName("ArticleId"):
if (articleid.getAttribute("IdType") == u"doi"):
doi = articleid.firstChild.data
except (IndexError, TypeError):
pass
#sometimes no doi, or PMID has a doi-fragment in the doi field:
aliases_list = []
if doi:
if "10." in doi:
aliases_list = [("doi", doi)]
return aliases_list
def _extract_metrics(self, page, status_code=200, id=None):
#logger.info(u"_extract_metrics with %s, %i,\n%s\n" % (id, status_code, page))
if status_code != 200:
if (status_code == 404):
return {}
else:
raise(self._get_error(status_code))
(doc, lookup_function) = provider._get_doc_from_xml(page)
try:
searchinfo = doc.getElementsByTagName('searchinfo')
totalhits = int(searchinfo[0].attributes['totalhits'].value)
except (TypeError, IndexError):
raise ProviderContentMalformedError("No searchinfo in response document")
if totalhits:
metrics_dict = {"wikipedia:mentions": totalhits}
else:
metrics_dict = {}
#logger.info(u"_extract_metrics returns metrics_dict %s" % (str(metrics_dict)))
return metrics_dict
