commonmeta-py 0.23__py3-none-any.whl → 0.24__py3-none-any.whl

commonmeta/resources/styles/vancouver.csl

@@ -0,0 +1,376 @@
+<?xml version="1.0" encoding="utf-8"?>
+<style xmlns="http://purl.org/net/xbiblio/csl" class="in-text" version="1.0" demote-non-dropping-particle="sort-only" initialize-with-hyphen="false" page-range-format="minimal">
+  <info>
+    <title>Vancouver</title>
+    <id>http://www.zotero.org/styles/vancouver</id>
+    <link href="http://www.zotero.org/styles/vancouver" rel="self"/>
+    <link href="http://www.nlm.nih.gov/bsd/uniform_requirements.html" rel="documentation"/>
+    <author>
+      <name>Michael Berkowitz</name>
+      <email>mberkowi@gmu.edu</email>
+    </author>
+    <contributor>
+      <name>Sean Takats</name>
+      <email>stakats@gmu.edu</email>
+    </contributor>
+    <contributor>
+      <name>Sebastian Karcher</name>
+    </contributor>
+    <category citation-format="numeric"/>
+    <category field="medicine"/>
+    <summary>Vancouver style as outlined by International Committee of Medical Journal Editors Uniform Requirements for Manuscripts Submitted to Biomedical Journals: Sample References</summary>
+    <updated>2022-09-28T11:33:04+00:00</updated>
+    <rights license="http://creativecommons.org/licenses/by-sa/3.0/">This work is licensed under a Creative Commons Attribution-ShareAlike 3.0 License</rights>
+  </info>
+  <locale xml:lang="en">
+    <date form="text" delimiter=" ">
+      <date-part name="year"/>
+      <date-part name="month" form="short" strip-periods="true"/>
+      <date-part name="day"/>
+    </date>
+    <terms>
+      <term name="collection-editor" form="long">
+        <single>editor</single>
+        <multiple>editors</multiple>
+      </term>
+      <term name="presented at">presented at</term>
+      <term name="available at">available from</term>
+      <term name="section" form="short">sect.</term>
+    </terms>
+  </locale>
+  <locale xml:lang="fr">
+    <date form="text" delimiter=" ">
+      <date-part name="day"/>
+      <date-part name="month" form="short" strip-periods="true"/>
+      <date-part name="year"/>
+    </date>
+  </locale>
+  <macro name="author">
+    <names variable="author">
+      <name sort-separator=" " initialize-with="" name-as-sort-order="all" delimiter=", " delimiter-precedes-last="always"/>
+      <label form="long" prefix=", "/>
+      <substitute>
+        <text macro="webpage-title"/>
+        <names variable="editor"/>
+      </substitute>
+    </names>
+  </macro>
+  <macro name="editor">
+    <names variable="editor" suffix=".">
+      <name sort-separator=" " initialize-with="" name-as-sort-order="all" delimiter=", " delimiter-precedes-last="always"/>
+      <label form="long" prefix=", "/>
+    </names>
+  </macro>
+  <macro name="chapter-marker">
+    <choose>
+      <if type="chapter paper-conference entry-dictionary entry-encyclopedia" match="any">
+        <text term="in" text-case="capitalize-first"/>
+      </if>
+    </choose>
+  </macro>
+  <macro name="webpage-title">
+    <!--If a webpage has a container, we're assuming the citation is "part of a website" as per ch. 25 Citing Medicine https://www.ncbi.nlm.nih.gov/books/NBK7274/?report=reader -->
+    <choose>
+      <if type="webpage" variable="container-title" match="all">
+        <group delimiter=" ">
+          <text variable="container-title"/>
+          <text term="internet" prefix="[" suffix="]" text-case="capitalize-first"/>
+        </group>
+      </if>
+    </choose>
+  </macro>
+  <macro name="publisher">
+    <choose>
+      <!--discard publisher info for articles-->
+      <if type="article-journal article-magazine article-newspaper" match="none">
+        <group delimiter=": " suffix=";">
+          <choose>
+            <if type="thesis">
+              <text variable="publisher-place" prefix="[" suffix="]"/>
+            </if>
+            <else-if type="speech"/>
+            <else>
+              <text variable="publisher-place"/>
+            </else>
+          </choose>
+          <text variable="publisher"/>
+        </group>
+      </if>
+    </choose>
+  </macro>
+  <macro name="access">
+    <choose>
+      <if variable="URL">
+        <group delimiter=": ">
+          <text term="available at" text-case="capitalize-first"/>
+          <text variable="URL"/>
+        </group>
+      </if>
+    </choose>
+  </macro>
+  <macro name="accessed-date">
+    <choose>
+      <if variable="URL">
+        <group prefix="[" suffix="]" delimiter=" ">
+          <text term="cited" text-case="lowercase"/>
+          <date variable="accessed" form="text"/>
+        </group>
+      </if>
+    </choose>
+  </macro>
+  <macro name="container-title">
+    <choose>
+      <if type="article-journal article-magazine chapter paper-conference article-newspaper review review-book entry-dictionary entry-encyclopedia" match="any">
+        <group suffix="." delimiter=" ">
+          <choose>
+            <if type="article-journal review review-book" match="any">
+              <text variable="container-title" form="short" strip-periods="true"/>
+            </if>
+            <else>
+              <text variable="container-title" strip-periods="true"/>
+            </else>
+          </choose>
+          <choose>
+            <if variable="URL">
+              <text term="internet" prefix="[" suffix="]" text-case="capitalize-first"/>
+            </if>
+          </choose>
+        </group>
+        <text macro="edition" prefix=" "/>
+      </if>
+      <!--add event-name and event-place once they become available-->
+      <else-if type="bill legislation" match="any">
+        <group delimiter=", ">
+          <group delimiter=". ">
+            <text variable="container-title"/>
+            <group delimiter=" ">
+              <text term="section" form="short" text-case="capitalize-first"/>
+              <text variable="section"/>
+            </group>
+          </group>
+          <text variable="number"/>
+        </group>
+      </else-if>
+      <else-if type="speech">
+        <group delimiter=": " suffix=";">
+          <group delimiter=" ">
+            <text variable="genre" text-case="capitalize-first"/>
+            <text term="presented at"/>
+          </group>
+          <text variable="event"/>
+        </group>
+      </else-if>
+      <else>
+        <group delimiter=", " suffix=".">
+          <choose>
+            <if variable="collection-title" match="none">
+              <group delimiter=" ">
+                <label variable="volume" form="short" text-case="capitalize-first"/>
+                <text variable="volume"/>
+              </group>
+            </if>
+          </choose>
+          <text variable="container-title"/>
+        </group>
+      </else>
+    </choose>
+  </macro>
+  <macro name="title">
+    <choose>
+      <if type="webpage" variable="container-title" match="all"/>
+      <else>
+        <text variable="title"/>
+        <choose>
+          <if type="article-journal article-magazine chapter paper-conference article-newspaper review review-book entry-dictionary entry-encyclopedia" match="none">
+            <choose>
+              <if variable="URL">
+                <text term="internet" prefix=" [" suffix="]" text-case="capitalize-first"/>
+              </if>
+            </choose>
+            <text macro="edition" prefix=". "/>
+          </if>
+        </choose>
+      </else>
+    </choose>
+    <choose>
+      <if type="thesis">
+        <text variable="genre" prefix=" [" suffix="]"/>
+      </if>
+    </choose>
+  </macro>
+  <macro name="edition">
+    <choose>
+      <if is-numeric="edition">
+        <group delimiter=" ">
+          <number variable="edition" form="ordinal"/>
+          <text term="edition" form="short"/>
+        </group>
+      </if>
+      <else>
+        <text variable="edition" suffix="."/>
+      </else>
+    </choose>
+  </macro>
+  <macro name="date">
+    <choose>
+      <if type="article-journal article-magazine article-newspaper review review-book" match="any">
+        <group suffix=";" delimiter=" ">
+          <date variable="issued" form="text"/>
+          <text macro="accessed-date"/>
+        </group>
+      </if>
+      <else-if type="bill legislation" match="any">
+        <group delimiter=", ">
+          <date variable="issued" delimiter=" ">
+            <date-part name="month" form="short" strip-periods="true"/>
+            <date-part name="day"/>
+          </date>
+          <date variable="issued">
+            <date-part name="year"/>
+          </date>
+        </group>
+      </else-if>
+      <else-if type="report">
+        <date variable="issued" delimiter=" ">
+          <date-part name="year"/>
+          <date-part name="month" form="short" strip-periods="true"/>
+        </date>
+        <text macro="accessed-date" prefix=" "/>
+      </else-if>
+      <else-if type="patent">
+        <group suffix=".">
+          <group delimiter=", ">
+            <text variable="number"/>
+            <date variable="issued">
+              <date-part name="year"/>
+            </date>
+          </group>
+          <text macro="accessed-date" prefix=" "/>
+        </group>
+      </else-if>
+      <else-if type="speech">
+        <group delimiter="; ">
+          <group delimiter=" ">
+            <date variable="issued" delimiter=" ">
+              <date-part name="year"/>
+              <date-part name="month" form="short" strip-periods="true"/>
+              <date-part name="day"/>
+            </date>
+            <text macro="accessed-date"/>
+          </group>
+          <text variable="event-place"/>
+        </group>
+      </else-if>
+      <else>
+        <group suffix=".">
+          <date variable="issued">
+            <date-part name="year"/>
+          </date>
+          <text macro="accessed-date" prefix=" "/>
+        </group>
+      </else>
+    </choose>
+  </macro>
+  <macro name="pages">
+    <choose>
+      <if type="article-journal article-magazine article-newspaper review review-book" match="any">
+        <text variable="page" prefix=":"/>
+      </if>
+      <else-if type="book" match="any">
+        <text variable="number-of-pages" prefix=" "/>
+        <choose>
+          <if is-numeric="number-of-pages">
+            <label variable="number-of-pages" form="short" prefix=" " plural="never"/>
+          </if>
+        </choose>
+      </else-if>
+      <else>
+        <group prefix=" " delimiter=" ">
+          <label variable="page" form="short" plural="never"/>
+          <text variable="page"/>
+        </group>
+      </else>
+    </choose>
+  </macro>
+  <macro name="journal-location">
+    <choose>
+      <if type="article-journal article-magazine review review-book" match="any">
+        <text variable="volume"/>
+        <text variable="issue" prefix="(" suffix=")"/>
+      </if>
+    </choose>
+  </macro>
+  <macro name="webpage-part">
+    <choose>
+      <if type="webpage" variable="container-title" match="all">
+        <text variable="title"/>
+      </if>
+    </choose>
+  </macro>
+  <macro name="collection-details">
+    <choose>
+      <if type="article-journal article-magazine article-newspaper review review-book" match="none">
+        <choose>
+          <if variable="collection-title">
+            <group delimiter=" " prefix="(" suffix=")">
+              <names variable="collection-editor" suffix=".">
+                <name sort-separator=" " initialize-with="" name-as-sort-order="all" delimiter=", " delimiter-precedes-last="always"/>
+                <label form="long" prefix=", "/>
+              </names>
+              <group delimiter="; ">
+                <text variable="collection-title"/>
+                <group delimiter=" ">
+                  <label variable="volume" form="short"/>
+                  <text variable="volume"/>
+                </group>
+              </group>
+            </group>
+          </if>
+        </choose>
+      </if>
+    </choose>
+  </macro>
+  <macro name="report-details">
+    <choose>
+      <if type="report">
+        <text variable="number" prefix="Report No.: "/>
+      </if>
+    </choose>
+  </macro>
+  <citation collapse="citation-number">
+    <sort>
+      <key variable="citation-number"/>
+    </sort>
+    <layout prefix="(" suffix=")" delimiter=",">
+      <text variable="citation-number"/>
+    </layout>
+  </citation>
+  <bibliography et-al-min="7" et-al-use-first="6" second-field-align="flush">
+    <layout>
+      <text variable="citation-number" suffix="."/>
+      <group delimiter=". " suffix=". ">
+        <text macro="author"/>
+        <text macro="title"/>
+      </group>
+      <group delimiter=" " suffix=". ">
+        <group delimiter=": ">
+          <text macro="chapter-marker"/>
+          <group delimiter=" ">
+            <text macro="editor"/>
+            <text macro="container-title"/>
+          </group>
+        </group>
+        <text macro="publisher"/>
+        <group>
+          <text macro="date"/>
+          <text macro="journal-location"/>
+          <text macro="pages"/>
+        </group>
+        <text macro="webpage-part"/>
+      </group>
+      <text macro="collection-details" suffix=". "/>
+      <text macro="report-details" suffix=". "/>
+      <text macro="access"/>
+    </layout>
+  </bibliography>
+</style>

commonmeta/schema_utils.py

@@ -0,0 +1,27 @@
+"""Schema utils for commonmeta-py"""
+from os import path
+import orjson as json
+from jsonschema import Draft202012Validator, ValidationError
+
+
+def json_schema_errors(instance, schema: str = "commonmeta"):
+    """validate against JSON schema"""
+    schema_map = {
+        "commonmeta": "commonmeta_v0.14",
+        "datacite": "datacite-v4.5",
+        "crossref": "crossref-v0.2",
+        "csl": "csl-data",
+        "cff": "cff_v1.2.0",
+    }
+    try:
+        if schema not in schema_map.keys():
+            raise ValueError("No schema found")
+        file_path = path.join(
+            path.dirname(__file__), f"resources/{schema_map[schema]}.json"
+        )
+        with open(file_path, encoding="utf-8") as file:
+            string = file.read()
+            schema = json.loads(string)
+        return Draft202012Validator(schema).validate(instance)
+    except ValidationError as error:
+        return error.message

commonmeta/translators.py

@@ -0,0 +1,47 @@
+"""Web translators for commonmeta. Using BeautifulSoup to extract metadata from web pages."""
+
+from furl import furl
+import re
+
+from .doi_utils import doi_as_url
+
+
+def web_translator(soup, url: str):
+    """Extract metadata from web pages"""
+    f = furl(url)
+    if f.host == "arxiv.org":
+        return arxiv_translator(soup)
+    elif f.host == "datacite.org":
+        return datacite_translator(soup)
+    elif f.host == "app.pan.pl":
+        return pan_translator(soup)
+    return {}
+
+
+def arxiv_translator(soup):
+    """Extract metadata from arXiv. Find the DOI and return it."""
+    arxiv_id = soup.select_one("meta[name='citation_arxiv_id']")
+    if arxiv_id is None:
+        return {}
+    return {"@id": f"https://doi.org/10.48550/arXiv.{arxiv_id['content']}"}
+
+
+def datacite_translator(soup):
+    """Extract metadata from DataCite blog posts. Find the DOI and return it."""
+    doi = soup.select_one("div#citation")
+    if doi is None:
+        return {}
+    return {"@id": doi.get("data-doi", None)}
+
+
+def pan_translator(soup):
+    """Extract metadata from Acta Palaeontologica Polonica. Find the DOI and return it."""
+    caption = soup.select_one("p.caption div.vol").text
+    match = re.search(
+        r"doi:(10\.4202/.+)\Z",
+        caption,
+    )
+    if match is None:
+        return {}
+    doi = doi_as_url(match.group(1))
+    return {"@id": doi}