diff options
Diffstat (limited to 'python/fatcat_tools/transforms/ingest.py')
| -rw-r--r-- | python/fatcat_tools/transforms/ingest.py | 45 |
1 files changed, 28 insertions, 17 deletions
diff --git a/python/fatcat_tools/transforms/ingest.py b/python/fatcat_tools/transforms/ingest.py index c2ae6e0f..e08d56b8 100644 --- a/python/fatcat_tools/transforms/ingest.py +++ b/python/fatcat_tools/transforms/ingest.py @@ -1,7 +1,7 @@ from .elasticsearch import release_to_elasticsearch -def release_ingest_request(release, oa_only=False, ingest_request_source='fatcat'): +def release_ingest_request(release, oa_only=False, ingest_request_source='fatcat', ingest_type=None): """ Takes a full release entity object and returns an ingest request (as dict), or None if it seems like this release shouldn't be ingested. @@ -12,7 +12,7 @@ def release_ingest_request(release, oa_only=False, ingest_request_source='fatcat The 'oa_only' boolean flag indicates that we should only return an ingest request if we have reason to believe this is an OA release (or, eg, in arxiv or pubmed central). Respecting this flag means we are likely to miss - a lot of "hybrid" and "bronze" content, but could reduce load + a lot of "hybrid" and "bronze" content, but could reduce crawl load significantly. The type of the ingest request may depend on release type and container @@ -25,42 +25,53 @@ def release_ingest_request(release, oa_only=False, ingest_request_source='fatcat # generate a URL where we expect to find fulltext url = None - expect_mimetypes = [] + link_source = None + link_source_id = None if release.ext_ids.arxiv: url = "https://arxiv.org/pdf/{}.pdf".format(release.ext_ids.arxiv) - expect_mimetypes = ['application/pdf'] - elif release.ext_ids.pmcid: - #url = "https://www.ncbi.nlm.nih.gov/pmc/articles/{}/pdf/".format(release.ext_ids.pmcid) - url = "http://europepmc.org/backend/ptpmcrender.fcgi?accid={}&blobtype=pdf".format(release.ext_ids.pmcid) - expect_mimetypes = ['application/pdf'] + link_source = "arxiv" + link_source_id = release.ext_ids.arxiv elif release.ext_ids.doi: url = "https://doi.org/{}".format(release.ext_ids.doi) + link_source = "doi" + link_source_id = release.ext_ids.doi + elif release.ext_ids.pmcid and release.ext_ids.pmid: + # TODO: how to tell if an author manuscript in PMC vs. published? + #url = "https://www.ncbi.nlm.nih.gov/pmc/articles/{}/pdf/".format(release.ext_ids.pmcid) + url = "http://europepmc.org/backend/ptpmcrender.fcgi?accid={}&blobtype=pdf".format(release.ext_ids.pmcid) + link_source = "pubmed" + link_source_id = release.ext_ids.pmid if not url: return None - ext_ids = dict() - for k in ('doi', 'pmid', 'pmcid', 'arxiv'): - v = getattr(release.ext_ids, k) - if v: - ext_ids[k] = v + ext_ids = release.ext_ids.to_dict() + ext_ids = dict([(k, v) for (k, v) in ext_ids.items() if v]) - if oa_only and not ext_ids.get('arxiv') and not ext_ids.get('pmcid'): + if oa_only and link_source not in ('arxiv', 'pubmed'): es = release_to_elasticsearch(release) if not es['is_oa']: return None + # TODO: infer ingest type based on release_type or container metadata? + if not ingest_type: + ingest_type = 'pdf' + ingest_request = { - 'ingest_type': 'file', + 'ingest_type': ingest_type, 'ingest_request_source': ingest_request_source, 'base_url': url, + 'release_stage': release.release_stage, 'fatcat': { - 'release_stage': release.release_stage, 'release_ident': release.ident, 'work_ident': release.work_id, }, 'ext_ids': ext_ids, - 'expect_mimetypes': expect_mimetypes or None, } + + if link_source and link_source_id: + ingest_request['link_source'] = link_source + ingest_request['link_source_id'] = link_source_id + return ingest_request |