Esempio n. 1
0
def index():
    for row in _data:
        issns = []
        if row[_ISSN]: issns.append(row[_ISSN])
        if row[_EISSN]: issns.append(row[_EISSN])

        jnames = []
        if row[_TITLE]: jnames.append(row[_TITLE])
        if row[_TITLE_ALT] and row[
            _TITLE_ALT] not in jnames: jnames.append(row[_TITLE_ALT])

        eissn = []
        if row[_EISSN]: eissn.append(row[_EISSN])

        publisher = []
        if row[_PUBLISHER]: publisher.append(row[_PUBLISHER])

        Journal.add(issn=issns, electronic_issn=eissn,
                    journal_title=jnames, publisher_name=publisher)
Esempio n. 2
0
def extract_data(filepath, pmidfile):
    fn = os.path.split(filepath)[1]

    # extract the xml from the zip
    z = zipfile.ZipFile(filepath)
    inf = z.filelist[0]
    f = z.open(inf)

    # parse the xml
    tree = cetree.parse(f)
    root = tree.getroot()

    pmids = []
    records = []
    for mlc in root.findall("MedlineCitation"):
        record = {"electronic_issn": [], "print_issn": [], "issn": [], "journal_title": [], "journal_abbr": []}
        has_data = False

        # record any pubmed ids that we encounter
        mypmid = None
        pmidels = mlc.findall("PMID")
        for e in pmidels:
            mypmid = e.text
            if e.text not in pmids:
                pmids.append(e.text)

        article = mlc.find("Article")
        journal = article.find("Journal")

        # record any ISSNs in their appropriate type field
        issnels = journal.findall("ISSN")
        for e in issnels:
            has_data = True
            if e.get("IssnType") == "Electronic":
                if e.text not in record["electronic_issn"]:
                    record["electronic_issn"].append(e.text)
                if e.text in record["issn"]:
                    record["issn"].remove(e.text)
            elif e.get("IssnType") == "Print":
                if e.text not in record["print_issn"]:
                    record["print_issn"].append(e.text)
                if e.text in record["issn"]:
                    record["issn"].remove(e.text)
            else:
                if e.text not in record["issn"]:
                    record["issn"].append(e.text)

        # add journal titles
        titlels = journal.findall("Title")
        for e in titlels:
            has_data = True
            if e.text not in record["journal_title"]:
                record["journal_title"].append(e.text)

        # add journal abbreviations
        isoels = journal.findall("ISOAbbreviation")
        for e in isoels:
            has_data = True
            if e.text not in record["journal_abbr"]:
                record["journal_abbr"].append(e.text)

        info = mlc.find("MedlineJournalInfo")

        # record medline's version of the name (which may well be the iso abbreviation)
        taels = info.findall("MedlineTA")
        for e in taels:
            has_data = True
            if e.text not in record["journal_title"] and e.text not in record["journal_abbr"]:
                record["journal_abbr"].append(e.text)

        # record the medline knowledge of this other issn - we don't necessarily know what type it is
        links = info.findall("ISSNLinking")
        for e in links:
            has_data = True
            if (
                e.text not in record["electronic_issn"]
                and e.text not in record["print_issn"]
                and e.text not in record["issn"]
            ):
                record["issn"].append(e.text)

        # now write it to the ACAT via catflap
        if has_data:
            jnames = record.get("journal_title", [])
            for a in record.get("journal_abbr", []):
                if a not in jnames:
                    jnames.append(a)
            source = "medline " + fn
            if mypmid is not None:
                source += " " + mypmid
            Journal.add(
                issn=record.get("issn", []) + record.get("electronic_issn", []) + record.get("print_issn", []),
                journal_title=jnames,
                electronic_issn=record.get("electronic_issn", []),
                print_issn=record.get("print_issn", []),
                journal_abbreviation=record.get("journal_abbr", []),
            )

    # save the pmids found in this file
    save_pmids(pmidfile, pmids)