diff options
24 files changed, 350 insertions, 120 deletions
diff --git a/CHANGELOG.md b/CHANGELOG.md index a3562271..29814b6a 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -31,9 +31,13 @@ this release. ### Fixed - pubmed importer `text` vs. `get_text()` for HTML tags +- fatcat-python-client package now works with Python 3.7, with removal of + `async` keyword ### Changed +- fatcat-python-client re-code-generated using openapi generator instead of + swagger tooling - minimum rust version now 1.36 - Switch from swagger-codegen to openapi-generator for python client generation - switch python Kafka code from pykafka to confluent-kafka diff --git a/python/fatcat_tools/importers/common.py b/python/fatcat_tools/importers/common.py index 99c330a6..eafc6546 100644 --- a/python/fatcat_tools/importers/common.py +++ b/python/fatcat_tools/importers/common.py @@ -458,7 +458,8 @@ class EntityImporter: creator_id = rv.ident except ApiException as ae: # If anything other than a 404 (not found), something is wrong - assert ae.status == 404 + if ae.status != 404: + raise ae self._orcid_id_map[orcid] = creator_id # might be None return creator_id @@ -479,7 +480,8 @@ class EntityImporter: release_id = rv.ident except ApiException as ae: # If anything other than a 404 (not found), something is wrong - assert ae.status == 404 + if ae.status != 404: + raise ae self._doi_id_map[doi] = release_id # might be None return release_id @@ -495,7 +497,8 @@ class EntityImporter: release_id = rv.ident except ApiException as ae: # If anything other than a 404 (not found), something is wrong - assert ae.status == 404 + if ae.status != 404: + raise ae self._pmid_id_map[pmid] = release_id # might be None return release_id @@ -512,7 +515,8 @@ class EntityImporter: container_id = rv.ident except ApiException as ae: # If anything other than a 404 (not found), something is wrong - assert ae.status == 404 + if ae.status != 404: + raise ae self._issnl_id_map[issnl] = container_id # might be None return container_id diff --git a/python/fatcat_tools/importers/datacite.py b/python/fatcat_tools/importers/datacite.py index 81f00876..d998f266 100644 --- a/python/fatcat_tools/importers/datacite.py +++ b/python/fatcat_tools/importers/datacite.py @@ -496,10 +496,12 @@ class DataciteImporter(EntityImporter): if not desc.get('descriptionType') == 'Abstract': continue - # Description maybe a string or list. + # Description maybe a string, int or list. text = desc.get('description', '') if not text: continue + if isinstance(text, int): + text = '{}'.format(text) if isinstance(text, list): try: text = "\n".join(text) @@ -758,6 +760,14 @@ class DataciteImporter(EntityImporter): given_name = clean(given_name) if surname: surname = clean(surname) + + # Perform a final assertion that name does not reduce to zero + # (e.g. whitespace only name). + if name: + name = name.strip() + if not name: + continue + if raw_affiliation == '': continue diff --git a/python/fatcat_tools/importers/ingest.py b/python/fatcat_tools/importers/ingest.py index 4772bfaa..6cf1604b 100644 --- a/python/fatcat_tools/importers/ingest.py +++ b/python/fatcat_tools/importers/ingest.py @@ -19,6 +19,7 @@ class IngestFileResultImporter(EntityImporter): editgroup_description=eg_desc, editgroup_extra=eg_extra, **kwargs) + self.use_glutton_match = False self.default_link_rel = kwargs.get("default_link_rel", "web") assert self.default_link_rel self.require_grobid = require_grobid @@ -107,9 +108,10 @@ class IngestFileResultImporter(EntityImporter): elif err.status == 400: self.counts['warn-extid-invalid'] += 1 continue + raise err release_ident = release.ident break - if not release_ident and row.get('grobid'): + if self.use_glutton_match and not release_ident and row.get('grobid'): # try biblio-glutton extracted hit if row['grobid'].get('fatcat_release'): release_ident = row['grobid']['fatcat_release'].split('_')[-1] @@ -197,8 +199,7 @@ class IngestFileResultImporter(EntityImporter): if not existing: return True - # the following checks all assume there is an existing item - + # NOTE: the following checks all assume there is an existing item if (fe.release_ids[0] in existing.release_ids) and existing.urls: # TODO: could still, in theory update with the new URL? self.counts['exists'] += 1 diff --git a/python/fatcat_tools/importers/pubmed.py b/python/fatcat_tools/importers/pubmed.py index abcb21d9..3d3e3a8c 100644 --- a/python/fatcat_tools/importers/pubmed.py +++ b/python/fatcat_tools/importers/pubmed.py @@ -782,6 +782,7 @@ class PubmedImporter(EntityImporter): # NOTE: API behavior might change in the future? if "release_edit_editgroup_id_ident_id_key" in err.body: self.counts['skip-update-conflict'] += 1 + return False else: raise err finally: diff --git a/python/fatcat_tools/workers/elasticsearch.py b/python/fatcat_tools/workers/elasticsearch.py index 525f372b..e58b3da1 100644 --- a/python/fatcat_tools/workers/elasticsearch.py +++ b/python/fatcat_tools/workers/elasticsearch.py @@ -19,7 +19,7 @@ class ElasticsearchReleaseWorker(FatcatWorker): def __init__(self, kafka_hosts, consume_topic, poll_interval=10.0, offset=None, elasticsearch_backend="http://localhost:9200", elasticsearch_index="fatcat", - batch_size=200): + batch_size=200, api_host="https://api.fatcat.wiki/v0"): super().__init__(kafka_hosts=kafka_hosts, consume_topic=consume_topic) self.consumer_group = "elasticsearch-updates3" @@ -30,9 +30,11 @@ class ElasticsearchReleaseWorker(FatcatWorker): self.entity_type = ReleaseEntity self.elasticsearch_document_name = "release" self.transform_func = release_to_elasticsearch + self.api_host = api_host def run(self): ac = ApiClient() + api = public_api(self.api_host) def fail_fast(err, partitions): if err is not None: @@ -103,13 +105,20 @@ class ElasticsearchReleaseWorker(FatcatWorker): if entity_dict.get('name') and not entity_dict.get('title'): continue entity = entity_from_json(json_str, self.entity_type, api_client=ac) + if self.elasticsearch_document_name == "changelog": + key = entity.index + # might need to fetch from API + if not (entity.editgroup and entity.editgroup.editor): + entity = api.get_changelog_entry(entity.index) + else: + key = entity.ident # TODO: handle deletions from index bulk_actions.append(json.dumps({ - "index": { "_id": entity.ident, }, + "index": { "_id": key, }, })) bulk_actions.append(json.dumps( self.transform_func(entity))) - print("Upserting, eg, {} (of {} releases in elasticsearch)".format(entity.ident, len(batch))) + print("Upserting, eg, {} (of {} {} in elasticsearch)".format(key, len(batch), self.elasticsearch_document_name)) elasticsearch_endpoint = "{}/{}/{}/_bulk".format( self.elasticsearch_backend, self.elasticsearch_index, diff --git a/python/fatcat_web/routes.py b/python/fatcat_web/routes.py index 8583d255..58f4b7e0 100644 --- a/python/fatcat_web/routes.py +++ b/python/fatcat_web/routes.py @@ -707,6 +707,8 @@ def generic_search(): def release_search(): query = request.args.get('q') + if not query: + query = '*' fulltext_only = bool(request.args.get('fulltext_only')) issnl = request.args.get('container_issnl') @@ -731,6 +733,8 @@ def release_search(): def container_search(): query = request.args.get('q') + if not query: + query = '*' offset = request.args.get('offset', '0') offset = max(0, int(offset)) if offset.isnumeric() else 0 diff --git a/python/fatcat_web/templates/container_search.html b/python/fatcat_web/templates/container_search.html index 1a089643..1a804595 100644 --- a/python/fatcat_web/templates/container_search.html +++ b/python/fatcat_web/templates/container_search.html @@ -9,6 +9,7 @@ {% endif %} {% endblock %} + {% block fullmain %} <div class="ui vertical stripe segment" style="background-color: #EEE; padding-top: 4.5em;"> @@ -17,8 +18,7 @@ <form class="" role="search" action="/container/search" method="get"> <div class="ui form"> <div class="ui action input huge fluid"> - <input type="text" placeholder="Query..." name="q" value="{% if query %}{{ query }}{% endif %}" aria-label="search container metadata"> - <button class="ui button">Search</button> + <input type="text" placeholder="Query..." name="q" value="{% if query %}{{ query }}{% endif %}" aria-label="search container metadata"> <button class="ui button">Search</button> </div> <br>Can also lookup by <b><a href="/container/lookup">identifier</a></b> or search <b><a href="/release/search?q={{ query or "" }}">releases</a></b>. </div> @@ -30,49 +30,56 @@ <br> {% if found %} -{% if found.results %} - {{ entity_macros.top_results(found) }} + {% if found.results %} -{% for entity in found.results %} -<div> - <h4 style="margin-top: 1em; margin-bottom: 4px; font-size: 1.1em;"> - <a href="/container/{{ entity.ident }}" style="color: #2224c7;">{{ entity['name'] }}</a> - {% if entity.is_oa %}<i class="icon unlock orange small"></i>{% endif %} - </h4> - {% if entity.publisher %} - <h5 style="margin-top: 4px; margin-bottom: 4px; font-size: 1em;">{{ entity.publisher }}</h5> - {% endif %} - {% if entity.issnl %} - <a href="https://portal.issn.org/resource/ISSN/{{entity.issnl }}" style="color: green;">issn:{{ entity.issnl }}</a> - {% endif %} - {% if entity.container_type %} - {{ entity.container_type }} - {% endif %} -</div> -{% endfor %} -{% if found.results|length > 8 %} - <div class="ui divider"></div> - <div style="text-align: center"> - {{ entity_macros.bottom_results(found, endpoint='container_search')}} - </div> -{% endif %} -{% else %} + {{ entity_macros.top_results(found) }} -Raw query was: <i>{{ found.query.q }}</i> + {% for entity in found.results %} + <div> + <h4 style="margin-top: 1em; margin-bottom: 4px; font-size: 1.1em;"> + <a href="/container/{{ entity.ident }}" style="color: #2224c7;">{{ entity['name'] }}</a> + {% if entity.is_oa %}<i class="icon unlock orange small"></i>{% endif %} + </h4> + {% if entity.publisher %} + <h5 style="margin-top: 4px; margin-bottom: 4px; font-size: 1em;">{{ entity.publisher }}</h5> + {% endif %} + {% if entity.issnl %} + <a href="https://portal.issn.org/resource/ISSN/{{entity.issnl }}" style="color: green;">issn:{{ entity.issnl }}</a> + {% endif %} + {% if entity.container_type %} + {{ entity.container_type }} + {% endif %} + </div> + {% endfor %} + + {% if found.results|length > 8 %} + <div class="ui divider"></div> + <div style="text-align: center"> + {{ entity_macros.bottom_results(found, endpoint='container_search') }} + </div> + {% endif %} -<div class="ui centered stackable grid" style="padding-top: 15%;"> - <div class="row"> - <div class="four wide column"> - <img src="/static/paper_man_confused.gif" alt="confused paper man"> + {% else %} + + Raw query was: <i>{{ found.query.q }}</i> + + <div class="ui centered stackable grid" style="padding-top: 15%;"> + <div class="row"> + <div class="four wide column"> + <img src="/static/paper_man_confused.gif" alt="confused paper man"> + </div> + <div class="six wide column"> + <h2>No results found!</h2> + <p>You could try elsewhere:</p> + <ul> + <li>Search <a href="https://scholar.google.com/scholar?q={{ found.query.q | urlencode }}">Google Scholar</a></li> + </ul> + </div> + </div> </div> - <div class="six wide column"> - <h2>No results found!</h2> - <p>You could try elsewhere:</p> - <ul> - <li>Search <a href="https://scholar.google.com/scholar?q={{ found.query.q | urlencode }}">Google Scholar</a></li> - </ul> -</div> -{% endif %} + + {% endif %} + {% endif %} </div> diff --git a/python/fatcat_web/templates/container_view.html b/python/fatcat_web/templates/container_view.html index 8d7c4cae..cf444956 100644 --- a/python/fatcat_web/templates/container_view.html +++ b/python/fatcat_web/templates/container_view.html @@ -23,6 +23,7 @@ Published by {{ container.publisher }} {% endif %} +{% if container.state == "active" %} <h3>Search Releases from this Container</h3> <form class="" role="search" action="/release/search" method="get"> <div class="ui form"> @@ -33,6 +34,7 @@ </div> </div> </form> +{% endif %} {% if container._random_releases %} <h3>Example Publications</h3> diff --git a/python/fatcat_web/templates/entity_macros.html b/python/fatcat_web/templates/entity_macros.html index 7c5436c6..c22eb106 100644 --- a/python/fatcat_web/templates/entity_macros.html +++ b/python/fatcat_web/templates/entity_macros.html @@ -54,10 +54,12 @@ </a> </div> +{% if entity.ident %} <div class="two ui buttons bottom attached"> <a href="{% if editgroup %}/editgroup/{{ editgroup.editgroup_id }}{% endif %}/{{ entity_type }}/{{ entity.ident }}/edit" class="ui blue button">Edit Metadata</a> <a href="/{{ entity_type }}/{{ entity.ident }}/history" class="ui button">View History</a> </div> +{% endif %} {%- endmacro %} @@ -156,17 +158,35 @@ [blank] {% endif %} </a> + + {# release type suffix #} + {% if paper.release_type in ("article-journal", "paper-conference") %} + {# pass #} + {% elif paper.release_type in ("book", "chapter", "dataset") %} + <b style="text-transform: uppercase;">[{{ paper.release_type }}]</b> + {% elif not paper.release_type %} + <b style="text-transform: uppercase; color: black;">[unknown-media]</b> + {% else %} + <b style="text-transform: uppercase;">[{{ paper.release_type }}]</b> + {% endif %} + + {# show original_title #} + {% if paper.original_title and paper.title != paper.original_title %} + <br> + <i style="font-weight: normal;"> + {{ paper.original_title[:512] }} {% if paper.original_title|length > 512 %}...{% endif %} + </i> + {% endif %} + </h4> + {% if paper.best_pdf_url %} <div style="float: right; padding: 4px;"> <a href="{{ paper.best_pdf_url }}" class="ui violet tag label"><i class="file icon"></i>fulltext</a> </div> {% endif %} - {# - <h5 style="margin-top: 4px; margin-bottom: 4px; font-size: 1em;">{{ ", ".join(paper.contrib_names[:12]) }} - {% if paper.contrib_names|length > 12 %}<i>(+{{ paper.contrib_names|length - 12 }} others)</i>{% endif %} - </h5> - #} + + {# ### AUTHOR ROW #} {% if paper.contrib_names %} <div style="margin-top: 0px; margin-bottom: 0px; font-size: 1em;"> <b> @@ -175,25 +195,14 @@ </b> </div> {% endif %} + + + {# ### JOURNAL ROW #} {% if paper.release_year %} {{ paper.release_year }} {% endif %} - {% if paper.release_type %} - {% if paper.release_type in ("article-journal", "paper-conference") %} - <span class="ui black basic label small">{{ paper.release_type }}</span> - {% elif paper.release_type in ("book") %} - <span class="ui brown basic label small">{{ paper.release_type }}</span> - {% else %} - <span class="ui grey basic label small">{{ paper.release_type }}</span> - {% endif %} - {% endif %} - {% if paper.withdrawn_status %} - <span class="ui red label small">{{ paper.withdrawn_status }}</span> - {% endif %} - {% if paper.release_stage and paper.release_stage != "published" %} - <span class="ui pink basic label small">{{ paper.release_stage }}</span> - {% elif not paper.release_stage %} - <span class="ui red basic label small">unknown</span> + {% if paper.release_year and paper.container_name %} + | {% endif %} {% if paper.container_name %} {% if paper.container_id %} @@ -203,8 +212,22 @@ {% endif %} {% if paper.container_is_oa %}<i class="icon unlock orange small"></i>{% endif %} {% endif %} - {% if paper.doi or paper.pmid or paper.arxiv_id or paper.jstor_id %} - <br> + {% if paper.withdrawn_status %} + <b style="color: red;"><code>[{{ paper.withdrawn_status }}]</code></b> + {% endif %} + {% if paper.release_stage == "accepted" %} + <b style="color: darkmagenta;"><code>[{{ paper.release_stage }} manuscript]</code></b> + {% elif paper.release_stage == "submitted" %} + <b style="color: magenta;"><code>[pre-print]</code></b> + {% elif paper.release_stage and paper.release_stage != "published" %} + <b style="color: magenta;"><code>[{{ paper.release_stage }}]</code></b> + {% elif not paper.release_stage %} + <b style="color: red;"><code>[unpublished?]</code></b> + {% endif %} + + {# ### IDENTIFIERS #} + {% if paper.doi or paper.pmid or paper.arxiv_id or paper.jstor_id or paper.pmcid %} + <br> {% endif %} {% if paper.doi %} <a href="https://doi.org/{{paper.doi }}" style="color: green;">doi:{{ paper.doi }}</a> @@ -212,13 +235,18 @@ {% if paper.pmid %} <a href="https://www.ncbi.nlm.nih.gov/pubmed/{{paper.pmid }}" style="color: green;">pmid:{{ paper.pmid }}</a> {% endif %} + {% if paper.pmcid %} + <a href="https://pubmed.ncbi.nlm.nih.gov/{{paper.pmcid }}/" style="color: green;">pmcid:{{ paper.pmcid }}</a> + {% endif %} {% if paper.arxiv_id %} <a href="https://arxiv.org/abs/{{paper.arxiv_id }}" style="color: green;">arXiv:{{ paper.arxiv_id }}</a> {% endif %} - {% if False %} {# XXX: elastic release work grouping searches #} + +{# WIP: elastic release work grouping searches <br> <a href="/work/{{ paper.work_id }}"><i class="sitemap icon"></i> and 5 other versions of the same work!</a> - {% endif %} +#} + </div> {% endmacro %} diff --git a/python/fatcat_web/templates/release_search.html b/python/fatcat_web/templates/release_search.html index 47f4330a..70c46c0a 100644 --- a/python/fatcat_web/templates/release_search.html +++ b/python/fatcat_web/templates/release_search.html @@ -35,37 +35,44 @@ <br> {% if found %} -{% if found.results %} + {% if found.results %} + {{ entity_macros.top_results(found) }} - {% for paper in found.results %} - {{ entity_macros.release_search_result_row(paper) }} -{% endfor %} -{% if found.results|length > 8 %} - <div class="ui divider"></div> - <div style="text-align: center"> - {{ entity_macros.bottom_results(found)}} - </div> -{% endif %} -{% else %} + {% for paper in found.results %} + {{ entity_macros.release_search_result_row(paper) }} + {% endfor %} + + {% if found.results|length > 8 %} + <div class="ui divider"></div> + <div style="text-align: center"> + {{ entity_macros.bottom_results(found, endpoint='release_search') }} + </div> + {% endif %} + + {% else %} -Raw query was: <i>{{ found.query.q }}</i> + Raw query was: <i>{{ found.query.q }}</i> -<div class="ui centered stackable grid" style="padding-top: 15%;"> - <div class="row"> - <div class="four wide column"> - <img src="/static/paper_man_confused.gif" alt="confused paper man"> + <div class="ui centered stackable grid" style="padding-top: 15%;"> + <div class="row"> + <div class="four wide column"> + <img src="/static/paper_man_confused.gif" alt="confused paper man"> + </div> + <div class="six wide column"> + <h2>No results found!</h2> + <p>You could try elsewhere:</p> + <ul> + <li>Search <a href="https://dissem.in/search?q={{ found.query.q | urlencode }}">dissem.in</a></li> + <li>Search <a href="https://www.base-search.net/Search/Results?lookfor={{ found.query.q | urlencode }}">BASE</a></li> + <li>Search <a href="https://scholar.google.com/scholar?q={{ found.query.q | urlencode }}">Google Scholar</a></li> + </ul> + </div> + </div> </div> - <div class="six wide column"> - <h2>No results found!</h2> - <p>You could try elsewhere:</p> - <ul> - <li>Search <a href="https://dissem.in/search?q={{ found.query.q | urlencode }}">dissem.in</a></li> - <li>Search <a href="https://www.base-search.net/Search/Results?lookfor={{ found.query.q | urlencode }}">BASE</a></li> - <li>Search <a href="https://scholar.google.com/scholar?q={{ found.query.q | urlencode }}">Google Scholar</a></li> - </ul> -</div> -{% endif %} + + {% endif %} + {% endif %} </div> diff --git a/python/fatcat_web/templates/release_view.html b/python/fatcat_web/templates/release_view.html index d7c4e76e..60e4624e 100644 --- a/python/fatcat_web/templates/release_view.html +++ b/python/fatcat_web/templates/release_view.html @@ -3,9 +3,9 @@ {% import "entity_macros.html" as entity_macros %} {% extends "entity_base.html" %} -{# HTML metadata embeddings #} -{% if release and release.status == "active" %} - {% block extra_head %} +{% block extra_head %} + {% if release and release.state == "active" %} + {# HTML metadata embeddings #} <link rel="canonical" href="https://{{ config.FATCAT_DOMAIN }}/release/{{ entity.ident }}"> <meta name="twitter:card" content="summary"> @@ -70,8 +70,8 @@ <meta name="citation_pdf_url" content="{{ url.url }}"> {% endif %} {% endfor %}{% endfor %} - {% endblock %} -{% endif %} + {% endif %} +{% endblock %} {% block main_extra_attr %}itemscope itemtype="http://schema.org/ScholarlyArticle" itemid="#release"{% endblock %} @@ -388,7 +388,7 @@ accessible version. <br>grouping other versions (eg, pre-print) and variants of this release </div> -{% if release._can_citeproc %} +{% if release.state == "active" and release._can_citeproc %} <div class="ui segment attached accordion"> <div class="title" style="padding: 0px;"> <i class="dropdown icon"></i><b>Cite This Release</b> diff --git a/python/tests/files/datacite/datacite_doc_31.json b/python/tests/files/datacite/datacite_doc_31.json new file mode 100644 index 00000000..83af3e4d --- /dev/null +++ b/python/tests/files/datacite/datacite_doc_31.json @@ -0,0 +1,53 @@ +{ + "id": "10.17912/micropub.biology.000143", + "type": "dois", + "attributes": { + "doi": "10.17912/micropub.biology.000143", + "identifiers": null, + "creators": [ + { + "raw_name": " ", + "givenName": "", + "familyName": "", + "affiliation": [], + "role": "author" + } + ], + "titles": [ + { + "title": "Sample" + } + ], + "publisher": "microPublication Biology", + "publicationYear": 2019, + "types": { + "resourceTypeGeneral": "DataPaper" + }, + "relatedIdentifiers": [], + "sizes": [], + "formats": [], + "version": null, + "rightsList": [], + "descriptions": [ + { + "description": "Biological liquid-liquid phase separation", + "descriptionType": "Abstract" + } + ], + "geoLocations": [], + "fundingReferences": [], + "url": "https://www.micropublication.org/journals/biology/micropub.biology.000143", + "created": "2019-08-19T14:43:08.000Z", + "registered": "2019-08-19T14:43:09.000Z", + "published": "2019", + "updated": "2019-11-09T12:32:02.000Z" + }, + "relationships": { + "client": { + "data": { + "id": "caltech.micropub", + "type": "clients" + } + } + } +} diff --git a/python/tests/files/datacite/datacite_doc_32.json b/python/tests/files/datacite/datacite_doc_32.json new file mode 100644 index 00000000..7ea7e873 --- /dev/null +++ b/python/tests/files/datacite/datacite_doc_32.json @@ -0,0 +1,53 @@ +{ + "id": "10.17912/micropub.biology.000143", + "type": "dois", + "attributes": { + "doi": "10.17912/micropub.biology.000143", + "identifiers": null, + "creators": [ + { + "raw_name": " ", + "givenName": "", + "familyName": "", + "affiliation": [], + "role": "author" + } + ], + "titles": [ + { + "title": "Sample" + } + ], + "publisher": "microPublication Biology", + "publicationYear": 2019, + "types": { + "resourceTypeGeneral": "DataPaper" + }, + "relatedIdentifiers": [], + "sizes": [], + "formats": [], + "version": null, + "rightsList": [], + "descriptions": [ + { + "description": 1234567890, + "descriptionType": "Abstract" + } + ], + "geoLocations": [], + "fundingReferences": [], + "url": "https://www.micropublication.org/journals/biology/micropub.biology.000143", + "created": "2019-08-19T14:43:08.000Z", + "registered": "2019-08-19T14:43:09.000Z", + "published": "2019", + "updated": "2019-11-09T12:32:02.000Z" + }, + "relationships": { + "client": { + "data": { + "id": "caltech.micropub", + "type": "clients" + } + } + } +} diff --git a/python/tests/files/datacite/datacite_result_31.json b/python/tests/files/datacite/datacite_result_31.json new file mode 100644 index 00000000..193104b0 --- /dev/null +++ b/python/tests/files/datacite/datacite_result_31.json @@ -0,0 +1,24 @@ +{ + "abstracts": [ + { + "content": "Biological liquid-liquid phase separation", + "lang": "fr", + "mimetype": "text/plain" + } + ], + "contribs": [], + "ext_ids": { + "doi": "10.17912/micropub.biology.000143" + }, + "extra": { + "datacite": { + "resourceTypeGeneral": "DataPaper" + }, + "container_name": "microPublication Biology" + }, + "refs": [], + "release_stage": "published", + "release_year": 2019, + "publisher": "microPublication Biology", + "title": "Sample" +} diff --git a/python/tests/files/datacite/datacite_result_32.json b/python/tests/files/datacite/datacite_result_32.json new file mode 100644 index 00000000..1a84a043 --- /dev/null +++ b/python/tests/files/datacite/datacite_result_32.json @@ -0,0 +1,23 @@ +{ + "abstracts": [ + { + "content": "1234567890", + "mimetype": "text/plain" + } + ], + "contribs": [], + "ext_ids": { + "doi": "10.17912/micropub.biology.000143" + }, + "extra": { + "datacite": { + "resourceTypeGeneral": "DataPaper" + }, + "container_name": "microPublication Biology" + }, + "refs": [], + "release_stage": "published", + "release_year": 2019, + "publisher": "microPublication Biology", + "title": "Sample" +} diff --git a/python/tests/import_datacite.py b/python/tests/import_datacite.py index 15650375..c9210ea4 100644 --- a/python/tests/import_datacite.py +++ b/python/tests/import_datacite.py @@ -287,7 +287,7 @@ def test_datacite_conversions(datacite_importer): for now. """ datacite_importer.debug = True - for i in range(31): + for i in range(33): src = 'tests/files/datacite/datacite_doc_{0:02d}.json'.format(i) dst = 'tests/files/datacite/datacite_result_{0:02d}.json'.format(i) with open(src, 'r') as f: diff --git a/python_openapi_client/README.md b/python_openapi_client/README.md index 4682a596..fd739e5b 100644 --- a/python_openapi_client/README.md +++ b/python_openapi_client/README.md @@ -4,7 +4,7 @@ Fatcat is a scalable, versioned, API-oriented catalog of bibliographic entities This Python package is automatically generated by the [OpenAPI Generator](https://openapi-generator.tech) project: - API version: 0.3.1 -- Package version: 0.3.1 +- Package version: 0.3.2 - Build package: org.openapitools.codegen.languages.PythonClientCodegen For more information, please visit [https://fatcat.wiki](https://fatcat.wiki) diff --git a/python_openapi_client/codegen_python_client.sh b/python_openapi_client/codegen_python_client.sh index 80a7f698..0f70db74 100755 --- a/python_openapi_client/codegen_python_client.sh +++ b/python_openapi_client/codegen_python_client.sh @@ -20,7 +20,7 @@ docker run \ --input-spec /tmp/swagger/api.yml \ --output /tmp/swagger/ \ --package-name=fatcat_openapi_client \ - -p packageVersion="0.3.1" + -p packageVersion="0.3.2" sudo chown -R `whoami`:`whoami` $OUTPUT mkdir -p fatcat_openapi_client diff --git a/python_openapi_client/fatcat_openapi_client/__init__.py b/python_openapi_client/fatcat_openapi_client/__init__.py index 82ea68f7..5d05953b 100644 --- a/python_openapi_client/fatcat_openapi_client/__init__.py +++ b/python_openapi_client/fatcat_openapi_client/__init__.py @@ -15,7 +15,7 @@ from __future__ import absolute_import -__version__ = "0.3.1" +__version__ = "0.3.2" # import apis into sdk package from fatcat_openapi_client.api.default_api import DefaultApi diff --git a/python_openapi_client/fatcat_openapi_client/__version__.py b/python_openapi_client/fatcat_openapi_client/__version__.py index 0c7a00a9..e855ccb2 100644 --- a/python_openapi_client/fatcat_openapi_client/__version__.py +++ b/python_openapi_client/fatcat_openapi_client/__version__.py @@ -1,3 +1,3 @@ -VERSION = (0, 3, 1) # eg, (0, 2, '0dev0') +VERSION = (0, 3, 2) # eg, (0, 2, '0dev0') __version__ = '.'.join(map(str, VERSION)) diff --git a/python_openapi_client/fatcat_openapi_client/api/default_api.py b/python_openapi_client/fatcat_openapi_client/api/default_api.py index bb6ffbac..43ca78c1 100644 --- a/python_openapi_client/fatcat_openapi_client/api/default_api.py +++ b/python_openapi_client/fatcat_openapi_client/api/default_api.py @@ -484,7 +484,7 @@ class DefaultApi(object): def create_container(self, editgroup_id, entity, **kwargs): # noqa: E501 """create_container # noqa: E501 - Create a single Container entity as part of an existing editgroup. Editgroup must be mutable (aka, not accepted) and editor must have permission (aka, have created the editgrou p or have `admin` role). # noqa: E501 + Create a single Container entity as part of an existing editgroup. Editgroup must be mutable (aka, not accepted) and editor must have permission (aka, have created the editgroup or have `admin` role). # noqa: E501 This method makes a synchronous HTTP request by default. To make an asynchronous HTTP request, please pass async_req=True >>> thread = api.create_container(editgroup_id, entity, async_req=True) @@ -510,7 +510,7 @@ class DefaultApi(object): def create_container_with_http_info(self, editgroup_id, entity, **kwargs): # noqa: E501 """create_container # noqa: E501 - Create a single Container entity as part of an existing editgroup. Editgroup must be mutable (aka, not accepted) and editor must have permission (aka, have created the editgrou p or have `admin` role). # noqa: E501 + Create a single Container entity as part of an existing editgroup. Editgroup must be mutable (aka, not accepted) and editor must have permission (aka, have created the editgroup or have `admin` role). # noqa: E501 This method makes a synchronous HTTP request by default. To make an asynchronous HTTP request, please pass async_req=True >>> thread = api.create_container_with_http_info(editgroup_id, entity, async_req=True) @@ -9986,7 +9986,7 @@ class DefaultApi(object): def update_container(self, editgroup_id, ident, entity, **kwargs): # noqa: E501 """update_container # noqa: E501 - Updates an existing entity as part of a specific (existing) editgroup. The editgroup must be open for updates (aka, not accepted/merged), and the editor making the requiest must have permissions (aka, must have created the editgroup or have `admin` role). This method can also be used to update an existing entity edit as part of an editgroup. For example, if an entity was created in this editgroup, an editor could make changes to the new entity's metadata before merging. # noqa: E501 + Updates an existing entity as part of a specific (existing) editgroup. The editgroup must be open for updates (aka, not accepted/merged), and the editor making the request must have permissions (aka, must have created the editgroup or have `admin` role). This method can also be used to update an existing entity edit as part of an editgroup. For example, if an entity was created in this editgroup, an editor could make changes to the new entity's metadata before merging. # noqa: E501 This method makes a synchronous HTTP request by default. To make an asynchronous HTTP request, please pass async_req=True >>> thread = api.update_container(editgroup_id, ident, entity, async_req=True) @@ -10013,7 +10013,7 @@ class DefaultApi(object): def update_container_with_http_info(self, editgroup_id, ident, entity, **kwargs): # noqa: E501 """update_container # noqa: E501 - Updates an existing entity as part of a specific (existing) editgroup. The editgroup must be open for updates (aka, not accepted/merged), and the editor making the requiest must have permissions (aka, must have created the editgroup or have `admin` role). This method can also be used to update an existing entity edit as part of an editgroup. For example, if an entity was created in this editgroup, an editor could make changes to the new entity's metadata before merging. # noqa: E501 + Updates an existing entity as part of a specific (existing) editgroup. The editgroup must be open for updates (aka, not accepted/merged), and the editor making the request must have permissions (aka, must have created the editgroup or have `admin` role). This method can also be used to update an existing entity edit as part of an editgroup. For example, if an entity was created in this editgroup, an editor could make changes to the new entity's metadata before merging. # noqa: E501 This method makes a synchronous HTTP request by default. To make an asynchronous HTTP request, please pass async_req=True >>> thread = api.update_container_with_http_info(editgroup_id, ident, entity, async_req=True) diff --git a/python_openapi_client/fatcat_openapi_client/api_client.py b/python_openapi_client/fatcat_openapi_client/api_client.py index 12cb98ca..d156560a 100644 --- a/python_openapi_client/fatcat_openapi_client/api_client.py +++ b/python_openapi_client/fatcat_openapi_client/api_client.py @@ -77,7 +77,7 @@ class ApiClient(object): self.default_headers[header_name] = header_value self.cookie = cookie # Set default User-Agent. - self.user_agent = 'OpenAPI-Generator/0.3.1/python' + self.user_agent = 'OpenAPI-Generator/0.3.2/python' def __del__(self): if self._pool: diff --git a/python_openapi_client/fatcat_openapi_client/configuration.py b/python_openapi_client/fatcat_openapi_client/configuration.py index b4aeff09..cf75cc8a 100644 --- a/python_openapi_client/fatcat_openapi_client/configuration.py +++ b/python_openapi_client/fatcat_openapi_client/configuration.py @@ -268,7 +268,7 @@ class Configuration(object): "OS: {env}\n"\ "Python Version: {pyversion}\n"\ "Version of the API: 0.3.1\n"\ - "SDK Package Version: 0.3.1".\ + "SDK Package Version: 0.3.2".\ format(env=sys.platform, pyversion=sys.version) def get_host_settings(self): |