From 28d2d94a9100c1a809955cde93fdbb7a36263057 Mon Sep 17 00:00:00 2001 From: Bryan Newbold Date: Thu, 5 Sep 2019 18:49:36 -0700 Subject: refactor all python source for client lib name --- python/fatcat_tools/importers/pubmed.py | 32 ++++++++++++++++---------------- 1 file changed, 16 insertions(+), 16 deletions(-) (limited to 'python/fatcat_tools/importers/pubmed.py') diff --git a/python/fatcat_tools/importers/pubmed.py b/python/fatcat_tools/importers/pubmed.py index 4bfbbc79..80cf986c 100644 --- a/python/fatcat_tools/importers/pubmed.py +++ b/python/fatcat_tools/importers/pubmed.py @@ -7,7 +7,7 @@ import warnings from bs4 import BeautifulSoup from bs4.element import NavigableString -import fatcat_client +import fatcat_openapi_client from .common import EntityImporter, clean, LANG_MAP_MARC # from: https://www.ncbi.nlm.nih.gov/books/NBK3827/table/pubmedhelp.T.publication_types/?report=objectonly @@ -508,7 +508,7 @@ class PubmedImporter(EntityImporter): and container_name): # name, type, publisher, issnl # extra: issnp, issne, original_name, languages, country - ce = fatcat_client.ContainerEntity( + ce = fatcat_openapi_client.ContainerEntity( name=container_name, container_type='journal', #NOTE: publisher not included @@ -532,7 +532,7 @@ class PubmedImporter(EntityImporter): primary_abstract = medline.find("Abstract") if primary_abstract and primary_abstract.AbstractText.get('NlmCategory'): joined = "\n".join([m.get_text() for m in primary_abstract.find_all("AbstractText")]) - abst = fatcat_client.ReleaseAbstract( + abst = fatcat_openapi_client.ReleaseAbstract( content=joined, mimetype="text/plain", lang="en", @@ -541,7 +541,7 @@ class PubmedImporter(EntityImporter): abstracts.append(abst) elif primary_abstract: for abstract in primary_abstract.find_all("AbstractText"): - abst = fatcat_client.ReleaseAbstract( + abst = fatcat_openapi_client.ReleaseAbstract( content=abstract.get_text().strip(), mimetype="text/plain", lang="en", @@ -549,7 +549,7 @@ class PubmedImporter(EntityImporter): if abst.content: abstracts.append(abst) if abstract.find('math'): - abst = fatcat_client.ReleaseAbstract( + abst = fatcat_openapi_client.ReleaseAbstract( # strip the tags content=str(abstract)[14:-15], mimetype="application/mathml+xml", @@ -562,7 +562,7 @@ class PubmedImporter(EntityImporter): lang = "en" if other.get('Language'): lang = LANG_MAP_MARC.get(other['Language']) - abst = fatcat_client.ReleaseAbstract( + abst = fatcat_openapi_client.ReleaseAbstract( content=other.AbstractText.get_text().strip(), mimetype="text/plain", lang=lang, @@ -617,7 +617,7 @@ class PubmedImporter(EntityImporter): if author.find("EqualContrib"): # TODO: schema for this? contrib_extra['equal'] = True - contribs.append(fatcat_client.ReleaseContrib( + contribs.append(fatcat_openapi_client.ReleaseContrib( raw_name=raw_name, given_name=given_name, surname=surname, @@ -628,7 +628,7 @@ class PubmedImporter(EntityImporter): )) if medline.AuthorList['CompleteYN'] == 'N': - contribs.append(fatcat_client.ReleaseContrib(raw_name="et al.")) + contribs.append(fatcat_openapi_client.ReleaseContrib(raw_name="et al.")) for i, contrib in enumerate(contribs): if contrib.raw_name != "et al.": @@ -659,7 +659,7 @@ class PubmedImporter(EntityImporter): ref_extra['unstructured'] = ref_raw.string if not ref_extra: ref_extra = None - refs.append(fatcat_client.ReleaseRef( + refs.append(fatcat_openapi_client.ReleaseRef( target_release_id=ref_release_id, extra=ref_extra, )) @@ -682,7 +682,7 @@ class PubmedImporter(EntityImporter): if not title: return None - re = fatcat_client.ReleaseEntity( + re = fatcat_openapi_client.ReleaseEntity( work_id=None, title=title, original_title=clean(original_title), @@ -691,7 +691,7 @@ class PubmedImporter(EntityImporter): release_date=release_date, release_year=release_year, withdrawn_status=withdrawn_status, - ext_ids=fatcat_client.ReleaseExtIds( + ext_ids=fatcat_openapi_client.ReleaseExtIds( doi=doi, pmid=pmid, pmcid=pmcid, @@ -717,7 +717,7 @@ class PubmedImporter(EntityImporter): existing = None try: existing = self.api.lookup_release(pmid=re.ext_ids.pmid) - except fatcat_client.rest.ApiException as err: + except fatcat_openapi_client.rest.ApiException as err: if err.status != 404: raise err @@ -725,7 +725,7 @@ class PubmedImporter(EntityImporter): if not existing and re.ext_ids.doi: try: existing = self.api.lookup_release(doi=re.ext_ids.doi) - except fatcat_client.rest.ApiException as err: + except fatcat_openapi_client.rest.ApiException as err: if err.status != 404: raise err if existing and existing.ext_ids.pmid and existing.ext_ids.pmid != re.ext_ids.pmid: @@ -751,7 +751,7 @@ class PubmedImporter(EntityImporter): try: self.api.update_release(self.get_editgroup_id(), existing.ident, existing) self.counts['update'] += 1 - except fatcat_client.rest.ApiException as err: + except fatcat_openapi_client.rest.ApiException as err: # there is a code path where we try to update the same release # twice in a row; if that happens, just skip # NOTE: API behavior might change in the future? @@ -765,8 +765,8 @@ class PubmedImporter(EntityImporter): return True def insert_batch(self, batch): - self.api.create_release_auto_batch(fatcat_client.ReleaseAutoBatch( - editgroup=fatcat_client.Editgroup( + self.api.create_release_auto_batch(fatcat_openapi_client.ReleaseAutoBatch( + editgroup=fatcat_openapi_client.Editgroup( description=self.editgroup_description, extra=self.editgroup_extra), entity_list=batch)) -- cgit v1.2.3