move scripts/ to bin/

4 files changed, 543 insertions, 0 deletions

diff --git a/bin/cord19_fatcat_enrich.py b/bin/cord19_fatcat_enrich.py
new file mode 100755
index 0000000..a911007
--- /dev/null
+++ b/bin/cord19_fatcat_enrich.py
@@ -0,0 +1,104 @@
+#!/usr/bin/env python3
+
+"""
+Takes a JSON-transformed CORD-19 *metadata* file and enriches it with fatcat
+metadata.
+"""
+
+import sys
+import json
+import argparse
+import datetime
+
+import requests
+from requests.adapters import HTTPAdapter
+from requests.packages.urllib3.util.retry import Retry # pylint: disable=import-error
+
+
+def requests_retry_session(retries=10, backoff_factor=3,
+        status_forcelist=(500, 502, 504), session=None):
+    """
+    From: https://www.peterbe.com/plog/best-practice-with-retries-with-requests
+    """
+    session = session or requests.Session()
+    retry = Retry(
+        total=retries,
+        read=retries,
+        connect=retries,
+        backoff_factor=backoff_factor,
+        status_forcelist=status_forcelist,
+    )
+    adapter = HTTPAdapter(max_retries=retry)
+    session.mount('http://', adapter)
+    session.mount('https://', adapter)
+    return session
+
+
+def do_line(row, args):
+
+    pubmed_id = row.get('pubmed_id') or None
+    pmcid = row.get('pmcid') or None
+    doi = row.get('doi') or None
+    fatcat_release = None
+
+    if doi == '0.1126/science.abb7331':
+        doi = '10.1126/science.abb7331'
+
+    if not fatcat_release and pmcid:
+        resp = args.session.get('https://api.fatcat.wiki/v0/release/lookup',
+            params={
+                'pmcid': pmcid,
+                'expand': 'container,files,filesets,webcaptures',
+                'hide': 'abstracts,references',
+        })
+        if resp.status_code == 200:
+            fatcat_release = resp.json()
+    if not fatcat_release and doi:
+        resp = args.session.get('https://api.fatcat.wiki/v0/release/lookup',
+            params={
+                'doi': doi,
+                'expand': 'container,files,filesets,webcaptures',
+                'hide': 'abstracts,references',
+        })
+        if resp.status_code == 200:
+            fatcat_release = resp.json()
+    if not fatcat_release and pubmed_id:
+        resp = args.session.get('https://api.fatcat.wiki/v0/release/lookup',
+            params={
+                'pmid': pubmed_id,
+                'expand': 'container,files,filesets,webcaptures',
+                'hide': 'abstracts,references',
+        })
+        if resp.status_code == 200:
+            fatcat_release = resp.json()
+
+    obj = dict(
+        cord19_paper=row,
+    )
+    if fatcat_release:
+        obj['fatcat_release'] = fatcat_release
+        obj['release_id'] = fatcat_release['ident']
+        obj['fatcat_url'] = "https://fatcat.wiki/release/{}".format(obj['release_id'])
+    print(json.dumps(obj, sort_keys=True))
+
+def run(args):
+    for l in args.json_file:
+        l = json.loads(l)
+        do_line(l, args)
+
+def main():
+    parser = argparse.ArgumentParser(
+        formatter_class=argparse.ArgumentDefaultsHelpFormatter)
+    parser.add_argument('json_file',
+        help="CORD-19 parsed JSON file",
+        type=argparse.FileType('r'))
+    subparsers = parser.add_subparsers()
+
+    args = parser.parse_args()
+    args.session = requests_retry_session()
+
+    run(args)
+
+if __name__ == '__main__':
+    main()
+
diff --git a/bin/deliver_file2disk.py b/bin/deliver_file2disk.py
new file mode 100755
index 0000000..f54ecb3
--- /dev/null
+++ b/bin/deliver_file2disk.py
@@ -0,0 +1,225 @@
+#!/usr/bin/env python3
+"""
+Tool for downloading fatcat release PDFs to disk (assuming there is at least
+one accessible PDF file entity for each release).
+
+Behavior:
+- if no file, or not accessible, skip release
+- filter files, then iterate through:
+    - if already exists locally on disk, skip
+    - try downloading from any archive.org or web.archive.org URLs
+    - verify SHA-1
+    - write out to disk
+"""
+
+# XXX: some broken MRO thing going on in here due to python3 object wrangling
+# in `wayback` library. Means we can't run pylint.
+# pylint: skip-file
+
+import os
+import sys
+import json
+import magic
+import hashlib
+import argparse
+import requests
+from requests.adapters import HTTPAdapter
+from requests.packages.urllib3.util.retry import Retry # pylint: disable=import-error
+from collections import Counter
+
+
+def gen_file_metadata(blob):
+    """
+    Takes a file blob (bytestream) and returns hashes and other metadata.
+
+    Returns a dict: size_bytes, md5hex, sha1hex, sha256hex, mimetype
+    """
+    assert blob
+    mimetype = magic.Magic(mime=True).from_buffer(blob)
+    hashes = [
+        hashlib.sha1(),
+        hashlib.sha256(),
+        hashlib.md5(),
+    ]
+    for h in hashes:
+        h.update(blob)
+    return dict(
+        size_bytes=len(blob),
+        sha1hex=hashes[0].hexdigest(),
+        sha256hex=hashes[1].hexdigest(),
+        md5hex=hashes[2].hexdigest(),
+        mimetype=mimetype,
+    )
+
+def requests_retry_session(retries=2, backoff_factor=3,
+        status_forcelist=(500, 502, 504), session=None):
+    """
+    From: https://www.peterbe.com/plog/best-practice-with-retries-with-requests
+    """
+    session = session or requests.Session()
+    retry = Retry(
+        total=retries,
+        read=retries,
+        connect=retries,
+        backoff_factor=backoff_factor,
+        status_forcelist=status_forcelist,
+    )
+    adapter = HTTPAdapter(max_retries=retry)
+    session.mount('http://', adapter)
+    session.mount('https://', adapter)
+    return session
+
+
+class DeliverFatcatDisk:
+
+    def __init__(self, disk_dir, **kwargs):
+        self.count = Counter()
+        self.disk_dir = disk_dir
+        self.disk_prefix = kwargs.get('disk_prefix', 'pdf/')
+        self.disk_suffix = kwargs.get('disk_suffix', '.pdf')
+        self.session = requests_retry_session()
+        self.session.headers.update({
+            'User-Agent': 'Mozilla/5.0 fatcat.DeliverFatcatDisk',
+        })
+
+    def run(self, release_json_file):
+        sys.stderr.write("Ensuring all 256 base directories exist...\n")
+        for i in range(256):
+            fpath = "{}/{}{:02x}".format(
+                    self.disk_dir,
+                    self.disk_prefix,
+                    i)
+            os.makedirs(fpath, exist_ok=True)
+        sys.stderr.write("Starting...\n")
+        for line in release_json_file:
+            self.count['total'] += 1
+            if not line.startswith('{'):
+                self.count['skip-no-release'] += 1
+                continue
+            #print(line)
+            release = json.loads(line)
+            assert 'ident' in release
+            self.fetch_release(release)
+        sys.stderr.write("{}\n".format(self.count))
+
+    def blob_path(self, sha1hex):
+        fpath = "{}/{}{}/{}{}".format(
+                self.disk_dir,
+                self.disk_prefix,
+                sha1hex[0:2],
+                sha1hex,
+                self.disk_suffix)
+        return fpath
+
+    def does_file_already_exist(self, sha1hex):
+        return os.path.isfile(self.blob_path(sha1hex))
+
+    def filter_files(self, files):
+        """
+        Takes a list of file entities and only returns the ones which are PDFs
+        we can download.
+        """
+        good = []
+        for f in files:
+            if f['mimetype'] and not 'pdf' in f['mimetype'].lower():
+                continue
+            for url in f['urls']:
+                if 'archive.org/' in url['url']:
+                    good.append(f)
+                    break
+        return good
+
+    def fetch_content(self, url):
+        """
+        Returns tuple: (str:status, content)
+        Content contains bytes only if status is "success", otherwise None
+        """
+        if '://web.archive.org/' in url:
+            # add id_ to URL to avoid wayback re-writing
+            l = url.split('/')
+            if l[2] == 'web.archive.org' and l[3] == 'web' and not '_' in l[4]:
+                l[4] = l[4] + 'id_'
+            url = '/'.join(l)
+
+        try:
+            resp = self.session.get(url)
+        except requests.exceptions.RetryError:
+            return ('wayback-error', None)
+        except requests.exceptions.TooManyRedirects:
+            return ('too-many-redirects', None)
+        if resp.status_code != 200:
+            return ('fetch:{}'.format(resp.status_code), None)
+        else:
+            return ('success', resp.content)
+
+    def fetch_file(self, f):
+        """
+        Returns tuple: (status, sha1hex, file_meta)
+
+        file_meta is a dict on success, or None otherwise
+        """
+        sha1hex = f['sha1']
+        if self.does_file_already_exist(sha1hex):
+            return ('exists', sha1hex, None)
+        status = None
+        for url in f['urls']:
+            url = url['url']
+            if not 'archive.org' in url:
+                continue
+            status, content = self.fetch_content(url)
+            if status == 'success':
+                # TODO: verify sha1hex
+                file_meta = gen_file_metadata(content)
+                if file_meta['sha1hex'] != sha1hex:
+                    status = 'sha1-mismatch'
+                    continue
+                with open(self.blob_path(sha1hex), 'wb') as outf:
+                    outf.write(content)
+                return ('success', sha1hex, file_meta)
+        if status:
+            return (status, sha1hex, None)
+        else:
+            return ('no-urls', sha1hex, None)
+
+    def fetch_release(self, release):
+        good_files = self.filter_files(release['files'])
+        status = 'no-file'
+        sha1hex = None
+        for f in good_files:
+            status, sha1hex, file_meta = self.fetch_file(f)
+            if status in ('success', 'exists'):
+                break
+            else:
+                continue
+        if sha1hex:
+            print("{}\t{}".format(status, sha1hex))
+        else:
+            print(status)
+        self.count[status] += 1
+
+def main():
+
+    parser = argparse.ArgumentParser()
+    parser.add_argument('--disk-dir',
+                        required=True,
+                        type=str,
+                        help='local base directory to save into')
+    parser.add_argument('--disk-prefix',
+                        type=str,
+                        default="pdf/",
+                        help='directory prefix for items created in bucket')
+    parser.add_argument('--disk-suffix',
+                        type=str,
+                        default=".pdf",
+                        help='file suffix for created files')
+    parser.add_argument('release_json_file',
+                        help="JSON manifest of fatcat release entities",
+                        default=sys.stdin,
+                        type=argparse.FileType('r'))
+    args = parser.parse_args()
+
+    worker = DeliverFatcatDisk(**args.__dict__)
+    worker.run(args.release_json_file)
+
+if __name__ == '__main__': # pragma: no cover
+    main()
diff --git a/bin/grobid2json.py b/bin/grobid2json.py
new file mode 100755
index 0000000..39ab222
--- /dev/null
+++ b/bin/grobid2json.py
@@ -0,0 +1,199 @@
+#!/usr/bin/env python3
+
+"""
+NB: adapted to work as a library for PDF extraction. Will probably be
+re-written eventually to be correct, complete, and robust; this is just a
+first iteration.
+
+This script tries to extract everything from a GROBID TEI XML fulltext dump:
+
+- header metadata
+- affiliations
+- references (with context)
+- abstract
+- fulltext
+- tables, figures, equations
+
+A flag can be specified to disable copyright encumbered bits (--no-emcumbered):
+
+- abstract
+- fulltext
+- tables, figures, equations
+
+Prints JSON to stdout, errors to stderr
+"""
+
+import io
+import json
+import argparse
+import xml.etree.ElementTree as ET
+
+xml_ns = "http://www.w3.org/XML/1998/namespace"
+ns = "http://www.tei-c.org/ns/1.0"
+
+def all_authors(elem):
+    names = []
+    for author in elem.findall('.//{%s}author' % ns):
+        pn = author.find('./{%s}persName' % ns)
+        if not pn:
+            continue
+        given_name = pn.findtext('./{%s}forename' % ns) or None
+        surname = pn.findtext('./{%s}surname' % ns) or None
+        full_name = ' '.join(pn.itertext())
+        obj = dict(name=full_name)
+        if given_name:
+            obj['given_name'] = given_name
+        if surname:
+            obj['surname'] = surname
+        ae = author.find('./{%s}affiliation' % ns)
+        if ae:
+            affiliation = dict()
+            for on in ae.findall('./{%s}orgName' % ns):
+                affiliation[on.get('type')] = on.text
+            addr_e = ae.find('./{%s}address' % ns)
+            if addr_e:
+                address = dict()
+                for t in addr_e.getchildren():
+                    address[t.tag.split('}')[-1]] = t.text
+                if address:
+                    affiliation['address'] = address
+                #affiliation['address'] = {
+                #    'post_code': addr.findtext('./{%s}postCode' % ns) or None,
+                #    'settlement': addr.findtext('./{%s}settlement' % ns) or None,
+                #    'country': addr.findtext('./{%s}country' % ns) or None,
+                #}
+            obj['affiliation'] = affiliation
+        names.append(obj)
+    return names
+
+
+def journal_info(elem):
+    journal = dict()
+    journal['name'] = elem.findtext('.//{%s}monogr/{%s}title' % (ns, ns))
+    journal['publisher'] = elem.findtext('.//{%s}publicationStmt/{%s}publisher' % (ns, ns))
+    if journal['publisher'] == '':
+        journal['publisher'] = None
+    journal['issn'] = elem.findtext('.//{%s}idno[@type="ISSN"]' % ns)
+    journal['eissn'] = elem.findtext('.//{%s}idno[@type="eISSN"]' % ns)
+    journal['volume'] = elem.findtext('.//{%s}biblScope[@unit="volume"]' % ns)
+    journal['issue'] = elem.findtext('.//{%s}biblScope[@unit="issue"]' % ns)
+    keys = list(journal.keys())
+
+    # remove empty/null keys
+    for k in keys:
+        if not journal[k]:
+            journal.pop(k)
+    return journal
+
+
+def biblio_info(elem):
+    ref = dict()
+    ref['id'] = elem.attrib.get('{http://www.w3.org/XML/1998/namespace}id')
+    # Title stuff is messy in references...
+    ref['title'] = elem.findtext('.//{%s}analytic/{%s}title' % (ns, ns))
+    other_title = elem.findtext('.//{%s}monogr/{%s}title' % (ns, ns))
+    if other_title:
+        if ref['title']:
+            ref['journal'] = other_title
+        else:
+            ref['journal'] = None
+            ref['title'] = other_title
+    ref['authors'] = all_authors(elem)
+    ref['publisher'] = elem.findtext('.//{%s}publicationStmt/{%s}publisher' % (ns, ns))
+    if ref['publisher'] == '':
+        ref['publisher'] = None
+    date = elem.find('.//{%s}date[@type="published"]' % ns)
+    ref['date'] = (date != None) and date.attrib.get('when')
+    ref['volume'] = elem.findtext('.//{%s}biblScope[@unit="volume"]' % ns)
+    ref['issue'] = elem.findtext('.//{%s}biblScope[@unit="issue"]' % ns)
+    el = elem.find('.//{%s}ptr[@target]' % ns)
+    if el is not None:
+        ref['url'] = el.attrib['target']
+        # Hand correction
+        if ref['url'].endswith(".Lastaccessed"):
+            ref['url'] = ref['url'].replace(".Lastaccessed", "")
+    else:
+        ref['url'] = None
+    return ref
+
+
+def teixml2json(content, encumbered=True):
+
+    if type(content) == str:
+        content = io.StringIO(content)
+    elif type(content) == bytes:
+        content = io.BytesIO(content)
+
+    info = dict()
+
+    #print(content)
+    #print(content.getvalue())
+    tree = ET.parse(content)
+    tei = tree.getroot()
+
+    header = tei.find('.//{%s}teiHeader' % ns)
+    if header is None:
+        raise ValueError("XML does not look like TEI format")
+    application_tag = header.findall('.//{%s}appInfo/{%s}application' % (ns, ns))[0]
+    info['grobid_version'] = application_tag.attrib['version'].strip()
+    info['grobid_timestamp'] = application_tag.attrib['when'].strip()
+    info['title'] = header.findtext('.//{%s}analytic/{%s}title' % (ns, ns))
+    info['authors'] = all_authors(header.find('.//{%s}sourceDesc/{%s}biblStruct' % (ns, ns)))
+    info['journal'] = journal_info(header)
+    date = header.find('.//{%s}date[@type="published"]' % ns)
+    info['date'] = (date != None) and date.attrib.get('when')
+    info['fatcat_release'] = header.findtext('.//{%s}idno[@type="fatcat"]' % ns)
+    info['doi'] = header.findtext('.//{%s}idno[@type="DOI"]' % ns)
+    if info['doi']:
+        info['doi'] = info['doi'].lower()
+
+    refs = []
+    for (i, bs) in enumerate(tei.findall('.//{%s}listBibl/{%s}biblStruct' % (ns, ns))):
+        ref = biblio_info(bs)
+        ref['index'] = i
+        refs.append(ref)
+    info['citations'] = refs
+
+    text = tei.find('.//{%s}text' % (ns))
+    #print(text.attrib)
+    if text.attrib.get('{%s}lang' % xml_ns):
+        info['language_code'] = text.attrib['{%s}lang' % xml_ns]  # xml:lang
+
+    if encumbered:
+        el = tei.find('.//{%s}profileDesc/{%s}abstract' % (ns, ns))
+        info['abstract'] = (el or None) and " ".join(el.itertext()).strip()
+        el = tei.find('.//{%s}text/{%s}body' % (ns, ns))
+        info['body'] = (el or None) and " ".join(el.itertext()).strip()
+        el = tei.find('.//{%s}back/{%s}div[@type="acknowledgement"]' % (ns, ns))
+        info['acknowledgement'] = (el or None) and " ".join(el.itertext()).strip()
+        el = tei.find('.//{%s}back/{%s}div[@type="annex"]' % (ns, ns))
+        info['annex'] = (el or None) and " ".join(el.itertext()).strip()
+
+    # remove empty/null keys
+    keys = list(info.keys())
+    for k in keys:
+        if not info[k]:
+            info.pop(k)
+    return info
+
+def main():   # pragma no cover
+    parser = argparse.ArgumentParser(
+        formatter_class=argparse.ArgumentDefaultsHelpFormatter,
+        description="GROBID TEI XML to JSON",
+        usage="%(prog)s [options] <teifile>...")
+    parser.add_argument("--no-encumbered",
+        action="store_true",
+        help="don't include ambiguously copyright encumbered fields (eg, abstract, body)")
+    parser.add_argument("teifiles", nargs='+')
+
+    args = parser.parse_args()
+
+    for filename in args.teifiles:
+        content = open(filename, 'r')
+        print(json.dumps(
+            teixml2json(content,
+               encumbered=(not args.no_encumbered)),
+            sort_keys=True))
+
+if __name__=='__main__':   # pragma no cover
+    main()
diff --git a/bin/parse_cord19_csv.py b/bin/parse_cord19_csv.py
new file mode 100755
index 0000000..536e5d3
--- /dev/null
+++ b/bin/parse_cord19_csv.py
@@ -0,0 +1,15 @@
+#!/usr/bin/env python3
+
+import sys
+import csv
+import json
+
+CSVFILE = sys.argv[1]
+
+with open(CSVFILE, newline='') as csvfile:
+    reader = csv.DictReader(csvfile)
+    for row in reader:
+        row = dict(row)
+        row['mag_id'] = row.pop('Microsoft Academic Paper ID')
+        row['who_covidence_id'] = row.pop('WHO #Covidence').replace('#', '')
+        print(json.dumps(row, sort_keys=True))