refactor elastic transform into CLI tool

1 files changed, 204 insertions, 0 deletions

diff --git a/fatcat_covid19/transform.py b/fatcat_covid19/transform.py
new file mode 100644
index 0000000..c31c9f4
--- /dev/null
+++ b/fatcat_covid19/transform.py
@@ -0,0 +1,204 @@
+
+import sys
+import json
+import argparse
+import datetime
+
+from fatcat_covid19.common import *
+
+
+def fulltext_to_elasticsearch(row, force_bool=True):
+    """
+    Converts from fulltext content and release model/schema to elasticsearch
+    oriented schema.
+
+    Returns: dict
+    Raises exception on error (never returns None)
+    """
+
+    if not 'fatcat_release' in row:
+        # skip papers that don't match to a fatcat release
+        return None
+
+    release = row['fatcat_release']
+
+    abstracts = []
+    abstract_langs = []
+
+    # first, easy fatcat metadata
+    t = {
+        'fatcat_ident': release['ident'],
+        'fatcat_revision': release['revision'],
+        'fulltext': dict(),
+    }
+    BIBLIO_KEYS = [
+        'work_id',
+        'title',
+        'subtitle',
+        'original_title',
+        'release_type',
+        'release_stage',
+        'release_year',
+        'release_date',
+        'withdrawn_status',
+        'language',
+        'volume',
+        'issue',
+        'pages',
+        'number',
+        'license',
+    ]
+    EXT_IDS = [
+        'doi',
+        'pmid',
+        'pmcid',
+        'isbn13',
+        'wikidata_qid',
+        'arxiv_id',
+        'jstor_id',
+        'mag_id',
+    ]
+    for key in BIBLIO_KEYS:
+        t[key] = release.get(key) or None
+    for key in EXT_IDS:
+        t[key] = release['ext_ids'].get(key) or None
+
+    t['contrib_count'] = len(release['contribs'] or [])
+
+    if release.get('abstracts'):
+        for a in release['abstracts']:
+            abstracts.append(a['content'])
+            abstract_langs.append(a['lang'])
+
+    contrib_names = []
+    contrib_affiliations = []
+    creator_ids = []
+    for c in (release['contribs'] or []):
+        if c.get('raw_name'):
+            contrib_names.append(c['raw_name'])
+        elif c.get('surname'):
+            contrib_names.append(c['surname'])
+        if c.get('creator_id'):
+            creator_ids.append(c['creator_id'])
+        if c.get('raw_affiliation'):
+            contrib_affiliations.append(c['raw_affiliation'])
+    t['contrib_names'] = contrib_names
+    t['creator_ids'] = creator_ids
+    t['affiliations'] = contrib_affiliations
+
+    container = release.get('container')
+    if container:
+        t['publisher'] = container.get('publisher')
+        t['container_name'] = container.get('name')
+        t['container_original_name'] = container.get('original_name')
+        # this is container.ident, not release.container_id, because there may
+        # be a redirect involved
+        t['container_id'] = container['ident']
+        t['container_issnl'] = container.get('issnl')
+        t['container_type'] = container.get('container_type')
+        if container.get('extra'):
+            c_extra = container['extra']
+            if c_extra.get('country'):
+                t['country_code'] = c_extra['country']
+                t['country_code_upper'] = c_extra['country'].upper()
+
+    # fall back to release-level container metadata if container not linked or
+    # missing context
+    if not t.get('publisher'):
+        t['publisher'] = release.get('publisher')
+    if not t.get('container_name') and release.get('extra'):
+        t['container_name'] = release['extra'].get('container_name')
+
+    extra = release['extra'] or dict()
+    if extra:
+        if not t.get('container_name'):
+            t['container_name'] = extra.get('container_name')
+        # backwards compatible subtitle fetching
+        if not t['subtitle'] and extra.get('subtitle'):
+            if type(extra['subtitle']) == list:
+                t['subtitle'] = extra['subtitle'][0]
+            else:
+                t['subtitle'] = extra['subtitle']
+
+    t['first_page'] = None
+    if release.get('pages'):
+        first = release['pages'].split('-')[0]
+        first = first.replace('p', '')
+        if first.isdigit():
+            t['first_page'] = first
+        # TODO: non-numerical first pages
+
+    t['doi_registrar'] = None
+    if extra and t['doi']:
+        for k in ('crossref', 'datacite', 'jalc'):
+            if k in extra:
+                t['doi_registrar'] = k
+        if not 'doi_registrar' in t:
+            t['doi_registrar'] = 'crossref'
+
+    if t['doi']:
+        t['doi_prefix'] = t['doi'].split('/')[0]
+
+    # then the fulltext stuff
+    t['fulltext']['status'] = row.get('fulltext_status', 'none')
+    if 'fulltext_file' in row:
+        full = row['fulltext_file']
+        t['fulltext']['sha1'] = full['sha1']
+        t['fulltext']['pdf_url'] = "/" + full['pdf_path']
+        if full.get('pdftotext_path'):
+            t['fulltext']['pdftotext_url'] = "/" + full['pdftotext_path']
+        if full.get('thumbnail_path'):
+            t['fulltext']['thumbnail_url'] = "/" + full['thumbnail_path']
+        if full.get('grobid_xml_path'):
+            t['fulltext']['grobid_xml_url'] = "/" + full['grobid_xml_path']
+
+    if 'fulltext_grobid' in row:
+        grobid = row['fulltext_grobid']
+        if grobid.get('abstract'):
+            abstracts.append(grobid['abstract'])
+            abstract_langs.append(grobid['language_code'])
+        t['fulltext']['abstract'] = grobid.get('abstract', None)
+        t['fulltext']['body'] = grobid.get('body', None)
+        t['fulltext']['acknowledgement'] = grobid.get('acknowledgement', None)
+        t['fulltext']['annex'] = grobid.get('annex', None)
+        t['fulltext']['lang'] = grobid.get('language_code', None)
+    elif 'fulltext_pdftotext' in row:
+        pdftotext = row['fulltext_pdftotext']
+        t['fulltext']['body'] = pdftotext.get('body', None)
+
+    # then other metadata stuff
+    if row.get('source_tags'):
+        # will get set-uniq at the end
+        t['source_tags'] = row['source_tags']
+    else:
+        t['source_tags'] = []
+
+    if 'cord19_paper' in row:
+        t['source_tags'].append('cord19')
+        paper = row['cord19_paper']
+        t['cord19_uid'] = paper['cord_uid']
+        if paper.get('who_covidence_id'):
+            t['who_covidence_id'] = paper['who_covidence_id']
+            t['source_tags'].append('who')
+        if paper.get('abstract') and not abstracts:
+            abstracts.append(paper['abstract'])
+        if not t['license']:
+            t['license'] = paper.get('license') or None
+    
+    t['abstract'] = abstracts
+    t['abstract_lang'] = list(set(abstract_langs))
+
+    t['source_tags'] = list(set(t['source_tags']))
+
+    return t
+
+def transform_es_file(json_input, json_output):
+    """
+    Takes *enriched* JSON objects which include fatcat metadata and fulltext
+    content, and outputs JSON lines in fatcat_fulltext schema.
+    """
+    for l in json_input:
+        l = json.loads(l)
+        result = fulltext_to_elasticsearch(l, args)
+        if result:
+            print(json.dumps(result, sort_keys=True), file=json_output)