diff options
Diffstat (limited to 'python')
| -rwxr-xr-x | python/fatcat_tools/importers/cdl_dash_dat.py | 8 | ||||
| -rw-r--r-- | python/fatcat_tools/importers/crossref.py | 26 | ||||
| -rw-r--r-- | python/fatcat_tools/importers/grobid_metadata.py | 1 | ||||
| -rw-r--r-- | python/fatcat_tools/transforms/csl.py | 8 | ||||
| -rw-r--r-- | python/fatcat_tools/transforms/elasticsearch.py | 21 | ||||
| -rw-r--r-- | python/fatcat_web/forms.py | 24 | ||||
| -rw-r--r-- | python/fatcat_web/routes.py | 2 | ||||
| -rw-r--r-- | python/fatcat_web/templates/entity_macros.html | 6 | ||||
| -rw-r--r-- | python/fatcat_web/templates/release_edit.html | 4 | ||||
| -rw-r--r-- | python/fatcat_web/templates/release_view.html | 56 |
10 files changed, 86 insertions, 70 deletions
diff --git a/python/fatcat_tools/importers/cdl_dash_dat.py b/python/fatcat_tools/importers/cdl_dash_dat.py index 1a21194d..e1252b6d 100755 --- a/python/fatcat_tools/importers/cdl_dash_dat.py +++ b/python/fatcat_tools/importers/cdl_dash_dat.py @@ -96,7 +96,9 @@ def cdl_dash_release(meta, extra=None): )) r = ReleaseEntity( - doi=doi, + ext_ids=ReleaseEntityExtIds( + doi=doi, + ), title=clean(meta['title'], force_xml=True), publisher=clean(meta['publisher']), release_year=int(meta['publicationYear']), @@ -170,9 +172,9 @@ def auto_cdl_dash_dat(api, dat_path, release_id=None, editgroup_id=None): agent="fatcat_tools.auto_cdl_dash_dat"))) editgroup_id = eg.editgroup_id - if not release_id and release.doi: + if not release_id and release.ext_ids.doi: try: - r = api.lookup_release(doi=release.doi) + r = api.lookup_release(doi=release.ext_ids.doi) release_id = r.ident except fatcat_client.rest.ApiException: pass diff --git a/python/fatcat_tools/importers/crossref.py b/python/fatcat_tools/importers/crossref.py index 722f93aa..999ce13f 100644 --- a/python/fatcat_tools/importers/crossref.py +++ b/python/fatcat_tools/importers/crossref.py @@ -355,10 +355,10 @@ class CrossrefImporter(EntityImporter): # release status if obj['type'] in ('journal-article', 'conference-proceeding', 'book', 'dissertation', 'book-chapter'): - release_status = "published" + release_stage = "published" else: # unknown - release_status = None + release_stage = None # external identifiers extids = self.lookup_ext_ids(doi=obj['DOI'].lower()) @@ -408,18 +408,20 @@ class CrossrefImporter(EntityImporter): title=title, original_title=original_title, release_type=release_type, - release_status=release_status, + release_stage=release_stage, release_date=release_date, release_year=release_year, publisher=publisher, - doi=obj['DOI'].lower(), - pmid=extids['pmid'], - pmcid=extids['pmcid'], - wikidata_qid=extids['wikidata_qid'], - isbn13=isbn13, - core_id=extids['core_id'], - arxiv_id=extids['arxiv_id'], - jstor_id=extids['jstor_id'], + ext_ids=fatcat_client.ReleaseEntityExtIds( + doi=obj['DOI'].lower(), + pmid=extids['pmid'], + pmcid=extids['pmcid'], + wikidata_qid=extids['wikidata_qid'], + isbn13=isbn13, + core=extids['core_id'], + arxiv=extids['arxiv_id'], + jstor=extids['jstor_id'], + ), volume=clean(obj.get('volume')), issue=clean(obj.get('issue')), pages=clean(obj.get('page')), @@ -437,7 +439,7 @@ class CrossrefImporter(EntityImporter): # lookup existing DOI (don't need to try other ext idents for crossref) existing = None try: - existing = self.api.lookup_release(doi=re.doi) + existing = self.api.lookup_release(doi=re.ext_ids.doi) except fatcat_client.rest.ApiException as err: if err.status != 404: raise err diff --git a/python/fatcat_tools/importers/grobid_metadata.py b/python/fatcat_tools/importers/grobid_metadata.py index 7281a7a1..ba91d183 100644 --- a/python/fatcat_tools/importers/grobid_metadata.py +++ b/python/fatcat_tools/importers/grobid_metadata.py @@ -156,6 +156,7 @@ class GrobidMetadataImporter(EntityImporter): volume=clean(obj['journal'].get('volume')), issue=clean(obj['journal'].get('issue')), abstracts=abstracts, + ext_ids=fatcat_client.ReleaseEntityExtIds(), extra=extra) return re diff --git a/python/fatcat_tools/transforms/csl.py b/python/fatcat_tools/transforms/csl.py index 7bc026ed..079e0501 100644 --- a/python/fatcat_tools/transforms/csl.py +++ b/python/fatcat_tools/transforms/csl.py @@ -109,13 +109,13 @@ def release_to_csl(entity): container_title=entity.container and entity.container.name, #container-title-short #dimensions - DOI=entity.doi, + DOI=entity.ext_ids.doi, #edition #event #event-place #first-reference-note-number #genre - ISBN=entity.isbn13, + ISBN=entity.ext_ids.isbn13, ISSN=entity.container and entity.container.issnl, issue=entity.issue, #jurisdiction @@ -131,8 +131,8 @@ def release_to_csl(entity): #original-title # TODO: page=entity.pages, page_first=entity.pages and entity.pages.split('-')[0], - PMCID=entity.pmcid, - PMID=entity.pmid, + PMCID=entity.ext_ids.pmcid, + PMID=entity.ext_ids.pmid, publisher=(entity.container and entity.container.publisher) or entity.publisher, #publisher-place #references diff --git a/python/fatcat_tools/transforms/elasticsearch.py b/python/fatcat_tools/transforms/elasticsearch.py index 73ac046e..971d1c11 100644 --- a/python/fatcat_tools/transforms/elasticsearch.py +++ b/python/fatcat_tools/transforms/elasticsearch.py @@ -45,17 +45,18 @@ def release_to_elasticsearch(entity, force_bool=True): title = release.title, original_title = release.original_title, release_type = release.release_type, - release_status = release.release_status, + release_status = release.release_stage, language = release.language, license = release.license_slug, - doi = release.doi, - pmid = release.pmid, - pmcid = release.pmcid, - isbn13 = release.isbn13, - wikidata_qid = release.wikidata_qid, - core_id = release.core_id, - arxiv_id = release.core_id, - jstor_id = release.jstor_id, + doi = release.ext_ids.doi, + pmid = release.ext_ids.pmid, + pmcid = release.ext_ids.pmcid, + isbn13 = release.ext_ids.isbn13, + wikidata_qid = release.ext_ids.wikidata_qid, + core_id = release.ext_ids.core, + arxiv_id = release.ext_ids.arxiv, + jstor_id = release.ext_ids.jstor, + # TODO: mag, ark ) is_oa = None @@ -121,7 +122,7 @@ def release_to_elasticsearch(entity, force_bool=True): else: t['publisher'] = release.publisher - if release.jstor_id or (release.doi and release.doi.startswith('10.2307/')): + if release.ext_ids.jstor or (release.ext_ids.doi and release.ext_ids.doi.startswith('10.2307/')): in_jstor = True files = release.files or [] diff --git a/python/fatcat_web/forms.py b/python/fatcat_web/forms.py index 79365687..e22476ce 100644 --- a/python/fatcat_web/forms.py +++ b/python/fatcat_web/forms.py @@ -9,7 +9,7 @@ from wtforms import SelectField, DateField, StringField, IntegerField, \ HiddenField, FormField, FieldList, validators from fatcat_client import ContainerEntity, CreatorEntity, FileEntity, \ - ReleaseEntity, ReleaseContrib, FileEntityUrls + ReleaseEntity, ReleaseContrib, FileEntityUrls, ReleaseEntityExtIds release_type_options = [ ('', 'Unknown'), @@ -21,7 +21,7 @@ release_type_options = [ ('dataset', 'Dataset'), ('stub', 'Invalid/Stub'), ] -release_status_options = [ +release_stage_options = [ ('', 'Unknown'), ('draft', 'Draft'), ('submitted', 'Submitted'), @@ -62,9 +62,10 @@ class ReleaseContribForm(FlaskForm): default='author') RELEASE_SIMPLE_ATTRS = ['title', 'original_title', 'work_id', 'container_id', - 'release_type', 'release_status', 'release_date', 'doi', 'wikidata_qid', - 'isbn13', 'pmid', 'pmcid', 'volume', 'issue', 'pages', 'publisher', - 'language', 'license_slug'] + 'release_type', 'release_stage', 'release_date', 'volume', 'issue', + 'pages', 'publisher', 'language', 'license_slug'] + +RELEASE_EXTID_ATTRS = ['doi', 'wikidata_qid', 'isbn13', 'pmid', 'pmcid'] class ReleaseEntityForm(EntityEditForm): """ @@ -85,7 +86,7 @@ class ReleaseEntityForm(EntityEditForm): [validators.DataRequired()], choices=release_type_options, default='') - release_status = SelectField(choices=release_status_options) + release_stage = SelectField(choices=release_stage_options) release_date = DateField('Release Date', [validators.Optional(True)]) #release_year @@ -118,6 +119,9 @@ class ReleaseEntityForm(EntityEditForm): for simple_attr in RELEASE_SIMPLE_ATTRS: a = getattr(ref, simple_attr) a.data = getattr(re, simple_attr) + for extid_attr in RELEASE_EXTID_ATTRS: + a = getattr(ref, extid_attr) + a.data = getattr(re.ext_ids, extid_attr) for i, c in enumerate(re.contribs): rcf = ReleaseContribForm() rcf.prev_index = i @@ -128,7 +132,7 @@ class ReleaseEntityForm(EntityEditForm): def to_entity(self): assert(self.title.data) - entity = ReleaseEntity(title=self.title.data) + entity = ReleaseEntity(title=self.title.data, ext_ids=ReleaseEntityExtIds()) self.update_entity(entity) return entity @@ -145,6 +149,12 @@ class ReleaseEntityForm(EntityEditForm): if a == '': a = None setattr(re, simple_attr, a) + for extid_attr in RELEASE_EXTID_ATTRS: + a = getattr(self, simple_attr).data + # special case blank strings + if a == '': + a = None + setattr(re.ext_ids, simple_attr, a) # bunch of complexity here to preserve old contrib metadata (eg, # affiliation and extra) not included in current forms # TODO: this may be broken; either way needs tests diff --git a/python/fatcat_web/routes.py b/python/fatcat_web/routes.py index 633cbb22..a61c7c6d 100644 --- a/python/fatcat_web/routes.py +++ b/python/fatcat_web/routes.py @@ -239,7 +239,7 @@ def webcapture_view(ident): @app.route('/release/lookup', methods=['GET']) def release_lookup(): extid = None - for key in ('doi', 'wikidata_qid', 'pmid', 'pmcid', 'isbn13', 'core_id'): + for key in ('doi', 'wikidata_qid', 'pmid', 'pmcid', 'isbn13', 'core', 'ark', 'mag'): if request.args.get(key): extid = key break diff --git a/python/fatcat_web/templates/entity_macros.html b/python/fatcat_web/templates/entity_macros.html index cefb0378..d1bf86c3 100644 --- a/python/fatcat_web/templates/entity_macros.html +++ b/python/fatcat_web/templates/entity_macros.html @@ -60,12 +60,12 @@ {% if release.release_date %}{{ release.release_date }}{% elif release.release_year %}{{ release.release_year }}{% else %}<i>unknown</i>{% endif %} <td class=""> <b><a href="/release/{{ release.ident }}">{{ release.title }}</a></b> - <br><small>{{ release.release_status or "unknown status" }} + <br><small>{{ release.release_stage or "unknown status" }} | {{ release.release_type or "unknown type" }} {% if release.license_slug %} | {{ release.license_slug }}{% endif %} </small> - {% if release.doi %} - <br><a href="https://doi.org/{{ release.doi }}" style="color:green;">doi:{{ release.doi }}</a> + {% if release.ext_ids.doi %} + <br><a href="https://doi.org/{{ release.ext_ids.doi }}" style="color:green;">doi:{{ release.ext_ids.doi }}</a> {% endif %} {% endfor %} </tbody> diff --git a/python/fatcat_web/templates/release_edit.html b/python/fatcat_web/templates/release_edit.html index 7bd4a00a..b3beec2b 100644 --- a/python/fatcat_web/templates/release_edit.html +++ b/python/fatcat_web/templates/release_edit.html @@ -20,7 +20,7 @@ <div class="twelve wide column" style="padding-bottom: 0px;"> <div class="ui equal width fields"> {{ edit_macros.form_field_basic(form.release_type, "required") }} - {{ edit_macros.form_field_basic(form.release_status) }} + {{ edit_macros.form_field_basic(form.release_stage) }} </div> </div> <div class="one wide column" style="padding-bottom: 0px;"></div> @@ -133,7 +133,7 @@ $(document).ready(function() { // these javascript dropdowns hide the original <input>, which breaks browser // form focusing (eg, for required fields) :( //$('#release_type').dropdown(); - //$('#release_status').dropdown(); + //$('#release_stage').dropdown(); $('.ui.accordion').accordion(); var fixup_contrib_numbering = function(group_item) { diff --git a/python/fatcat_web/templates/release_view.html b/python/fatcat_web/templates/release_view.html index 403af653..820c2797 100644 --- a/python/fatcat_web/templates/release_view.html +++ b/python/fatcat_web/templates/release_view.html @@ -55,13 +55,13 @@ <meta name="DC.citation.spage" content="{{ release.pages }}"> <meta name="citation_first_page" content="{{ release.pages }}"> {% endif %} - {% if release.doi %} - <meta name="DC.identifier" content="doi:{{ release.doi }}"> - <meta name="citation_doi" content="{{ release.doi }}"> + {% if release.ext_ids.doi %} + <meta name="DC.identifier" content="doi:{{ release.ext_ids.doi }}"> + <meta name="citation_doi" content="{{ release.ext_ids.doi }}"> {% endif %} - {% if release.isbn13 %} - <meta name="DC.identifier" content="isbn:{{ release.isbn13}}"> - <meta name="citation_isbn" content="{{ release.isbn13}}"> + {% if release.ext_ids.isbn13 %} + <meta name="DC.identifier" content="isbn:{{ release.ext_ids.isbn13}}"> + <meta name="citation_isbn" content="{{ release.ext_ids.isbn13}}"> {% endif %} {% for file in (entity.files or [])[:10] %}{% for url in (file.urls or [])[:10] %} {% if '//web.archive.org/web/' in url.url %} @@ -101,7 +101,7 @@ <div class="ui accordion"> <div class="title" itemprop="isPartOf" itemscope itemtype="http://schema.org/Periodical" itemid="#container"> - {% if release.release_status == 'published' %} + {% if release.release_stage == 'published' %} <i class="dropdown icon"></i>Published in <a href="/container/{{ container.ident }}"><span itemprop="name">{{ container.name }}</span></a> {% else %} <i class="dropdown icon"></i>Released as a <i>{{ release.release_type }}</i> @@ -323,13 +323,13 @@ <span class="ui top attached fluid huge grey button"><i class="file cross icon"></i>No Full Text Available</span> {% endif %} -{% if release.release_type or release.release_status or release.release_year %} +{% if release.release_type or release.release_stage or release.release_year %} <div class="ui segment attached"> {% if release.release_type %} <b>Type</b> <code>{{ release.release_type }}</code><br> {% endif %} - {% if release.release_status %} - <b>Status</b> <code>{{ release.release_status or 'unknown' }}</code><br> + {% if release.release_stage %} + <b>Status</b> <code>{{ release.release_stage or 'unknown' }}</code><br> {% endif %} {% if release.release_date %} <meta itemprop="datePublished" content="{{ release.release_date }}"> @@ -341,22 +341,22 @@ </div> {% endif %} -{% if release.doi or release.pmid or release.pmcid or release.wikidata_qid %} +{% if release.ext_ids.doi or release.ext_ids.pmid or release.ext_ids.pmcid or release.ext_ids.wikidata_qid %} <div class="ui segment attached" style="word-wrap: break-word;"> -{% if release.doi %} - <b>DOI </b> <a href="https://doi.org/{{ release.doi }}" title="{{ release.doi }}" itemprop="sameAs">{{ release.doi }}</a><br> +{% if release.ext_ids.doi %} + <b>DOI </b> <a href="https://doi.org/{{ release.ext_ids.doi }}" title="{{ release.ext_ids.doi }}" itemprop="sameAs">{{ release.ext_ids.doi }}</a><br> {% endif %} -{% if release.pmid != None %} - <b>PubMed</b> <a href="https://www.ncbi.nlm.nih.gov/pubmed/{{ release.pmid }}"> <code>{{ release.pmid }}</code></a><br> +{% if release.ext_ids.pmid != None %} + <b>PubMed</b> <a href="https://www.ncbi.nlm.nih.gov/pubmed/{{ release.ext_ids.pmid }}"> <code>{{ release.ext_ids.pmid }}</code></a><br> {% endif %} -{% if release.pmcid != None %} - <b>PMC</b> <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/{{ release.pmcid }}"> <code>{{ release.pmcid }}</code></a><br> +{% if release.ext_ids.pmcid != None %} + <b>PMC</b> <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/{{ release.ext_ids.pmcid }}"> <code>{{ release.ext_ids.pmcid }}</code></a><br> {% endif %} -{% if release.wikidata_qid != None %} - <b>Wikidata</b> <a href="https://www.wikidata.org/wiki/{{ release.wikidata_qid }}"> <code>{{ release.wikidata_qid }}</code></a><br> +{% if release.ext_ids.wikidata_qid != None %} + <b>Wikidata</b> <a href="https://www.wikidata.org/wiki/{{ release.ext_ids.wikidata_qid }}"> <code>{{ release.ext_ids.wikidata_qid }}</code></a><br> {% endif %} -{% if release.isbn13 != None %} - <b>ISBN-13 </b> <code>{{ release.isbn13 }}</code> +{% if release.ext_ids.isbn13 != None %} + <b>ISBN-13 </b> <code>{{ release.ext_ids.isbn13 }}</code> {% endif %} </div> {% endif %} @@ -429,17 +429,17 @@ {% if container != None and container.issnl != None %} <a href="http://www.sherpa.ac.uk/romeo/issn/{{ container.issnl }}/">SHERPA/RoMEO</a> (journal policies)<br/> {% endif %} - {% if container != None and container.doi != None %} - <a href="https://oadoi.org/{{ release.doi }}">oaDOI/unpaywall</a><br/> + {% if release != None and release.ext_ids.doi != None %} + <a href="https://oadoi.org/{{ release.ext_ids.doi }}">oaDOI/unpaywall</a><br/> {% endif %} - {% if release.isbn13 != None %} - <a href="https://openlibrary.org/search?isbn={{ release.isbn13 }}">Open Library</a><br> - <a href="http://www.worldcat.org/search?q=bn%3A{{ release.isbn13 }}">Worldcat</a><br> + {% if release.ext_ids.isbn13 != None %} + <a href="https://openlibrary.org/search?isbn={{ release.ext_ids.isbn13 }}">Open Library</a><br> + <a href="http://www.worldcat.org/search?q=bn%3A{{ release.ext_ids.isbn13 }}">Worldcat</a><br> {% else %} <a href="http://www.worldcat.org/search?qt=worldcat_org_art&q={{ release.title|urlencode }}">Worldcat</a><br> {% endif %} - {% if release.doi %} - <a href="https://api.crossref.org/v1/works/http://dx.doi.org/{{ release.doi }}">Crossref Metadata</a> (via API)<br> + {% if release.ext_ids.doi %} + <a href="https://api.crossref.org/v1/works/http://dx.doi.org/{{ release.ext_ids.doi }}">Crossref Metadata</a> (via API)<br> {% endif %} <a href="https://www.wikidata.org/w/index.php?search={{ release.title|urlencode }}">wikidata.org</a><br> <a href="https://core.ac.uk/search?q={{ release.title|urlencode }}">CORE.ac.uk</a><br> |