feat(pubmed): implementar GroupList/Group/GroupName/IndividualName

packtools/sps/formats/pubmed.py

@@ -270,6 +270,7 @@ def pipeline_pubmed(xml_tree, pretty_print=True):
     xml_pubmed_elocation_pipe(xml_pubmed, xml_tree)
     xml_pubmed_language_pipe(xml_pubmed, xml_tree)
     xml_pubmed_author_list(xml_pubmed, xml_tree)
+    xml_pubmed_group_list(xml_pubmed, xml_tree)
     xml_pubmed_publication_type(xml_pubmed, xml_tree)
     xml_pubmed_article_id(xml_pubmed, xml_tree)
     xml_pubmed_history(xml_pubmed, xml_tree)
@@ -290,25 +291,47 @@ def get_authors(xml_tree):
 
 
 def add_first_name(author_reg, author_tag):
-    author_first_name = author_reg.get("contrib_name", {}).get("given-names")
+    contrib_name = author_reg.get("contrib_name", {})
+    # A DTD do PubMed exige FirstName e LastName juntos (nenhum dos dois é
+    # opcional isoladamente). Quando o XML fonte só tem um dos dois campos
+    # (autores sem <surname>, por exemplo), duplicamos o valor disponível
+    # em ambos para gerar um Author válido em vez de descartar o autor.
+    author_first_name = contrib_name.get("given-names") or contrib_name.get("surname")
     if author_first_name:
         first = ET.Element("FirstName")
         first.text = author_first_name
         author_tag.append(first)
 
 
 def add_last_name(author_reg, author_tag):
-    author_last_name = author_reg.get("contrib_name", {}).get("surname")
+    contrib_name = author_reg.get("contrib_name", {})
+    author_last_name = contrib_name.get("surname") or contrib_name.get("given-names")
     if author_last_name:
         last = ET.Element("LastName")
         last.text = author_last_name
         author_tag.append(last)
 
 
+def add_suffix(author_reg, author_tag):
+    author_suffix = author_reg.get("contrib_name", {}).get("suffix")
+    if author_suffix:
+        suffix = ET.Element("Suffix")
+        suffix.text = author_suffix
+        author_tag.append(suffix)
+
+
+def add_collective_name(author_reg, author_tag):
+    collab = author_reg.get("collab")
+    if collab:
+        collective_name = ET.Element("CollectiveName")
+        collective_name.text = collab
+        author_tag.append(collective_name)
+
+
 def get_affiliations(author_reg, xml_tree):
     affiliations = aff.AffiliationExtractor(xml_tree).get_affiliation_dict(subtag=False)
     affiliation_list = []
-    for item in author_reg.get("affs"):
+    for item in author_reg.get("affs") or []:
         affiliation_list.append(
             affiliations.get(item.get("id"), {}).get("institution", {})[0].get("original")
         )
@@ -337,68 +360,112 @@ def add_orcid(author_reg, author_tag):
 
 
 def xml_pubmed_author_list(xml_pubmed, xml_tree):
-    authors = list(get_authors(xml_tree))
+    # Contribs de contrib-group[@content-type="collab-list"] são os membros
+    # nomeados de um grupo de autoria (ver xml_pubmed_group_list) e não
+    # devem aparecer soltos em AuthorList.
+    authors = [
+        author_reg
+        for author_reg in get_authors(xml_tree)
+        if author_reg.get("contrib-group-type") != "collab-list"
+    ]
     if authors:
         author_list_tag = ET.Element("AuthorList")
         for author_reg in authors:
             author_tag = ET.Element("Author")
-            add_first_name(author_reg, author_tag)
-
-            # TODO
-            # add_middle_name(author_reg, author_tag)
-            # The Author’s full middle name, or initial if the full name is not available.
-            # Multiple names are allowed in this tag.
-            # There is no example of using this value in the files.
 
-            add_last_name(author_reg, author_tag)
+            # A DTD do PubMed exige que Author tenha nome pessoal
+            # (FirstName/MiddleName/LastName/Suffix) OU CollectiveName,
+            # nunca os dois ao mesmo tempo.
+            if author_reg.get("collab"):
+                add_collective_name(author_reg, author_tag)
+            else:
+                add_first_name(author_reg, author_tag)
 
-            # TODO
-            # add_suffix(author_reg, author_tag)
-            # The Author's suffix, if any, e.g. "Jr", "Sr", "II", "IV". Do not include honorific titles,
-            # e.g. "M.D.", "Ph.D.".
-            # There is no example of using this value in the files
+                # TODO
+                # add_middle_name(author_reg, author_tag)
+                # The Author’s full middle name, or initial if the full name is not available.
+                # Multiple names are allowed in this tag.
+                # There is no example of using this value in the files.
 
-            # TODO
-            # add_collective_name(author_reg, author_tag)
-            # The name of the authoring committee or organization. The CollectiveName tag should be placed within
-            # an Author tag. Omit extraneous text like, “on behalf of.”
-            # Please see the following example:
-            #   <AuthorList>
-            #       <Author>
-            #           <CollectiveName>Plastic Surgery Educational Foundation DATA Committee</CollectiveName>
-            #       </Author>
-            #   </AuthorList>
-            # There is no example of using this value in the files
+                add_last_name(author_reg, author_tag)
+                add_suffix(author_reg, author_tag)
 
             affiliations = get_affiliations(author_reg, xml_tree)
             add_affiliations(affiliations, author_tag)
             add_orcid(author_reg, author_tag)
             author_list_tag.append(author_tag)
 
-            # TODO
-            # add_group_list(author_reg, author_tag)
-            # Group information should be enclosed in these tags. If an article has one or more Groups, this tag
-            # must be submitted. Groups should be listed in the same order as in the printed article, and Group name
-            # format should accurately reflect the article. This tag is Required if the tag Group is present.
-            # There is no example of using this value in the files
+        xml_pubmed.append(author_list_tag)
 
-            # TODO
-            # add_group(author_reg, author_tag)
-            # Information about a single Group must begin with this tag.
-            # There is no example of using this value in the files
 
-            # TODO
-            # add_group_name(author_reg, author_tag)
-            # The name of the authoring committee or organization. Omit extraneous text like, “on behalf of.”
-            # There is no example of using this value in the files
+def get_group_members(authors):
+    return [
+        author_reg
+        for author_reg in authors
+        if author_reg.get("contrib-group-type") == "collab-list"
+    ]
 
-            # TODO
-            # add_individual_name(author_reg, author_tag)
-            # The name of individual members belonging to the authoring committee or organization.
-            # The name should be tagged with the FirstName, MiddleName, LastName, Suffix, and Affiliation tags.
-            # There is no example of using this value in the files
 
-        xml_pubmed.append(author_list_tag)
+def get_group_name(authors):
+    for author_reg in authors:
+        if author_reg.get("collab") and author_reg.get("contrib-group-type") != "collab-list":
+            return author_reg.get("collab")
+
+
+def add_individual_name(member_reg, xml_tree, group_tag):
+    """
+    <IndividualName>
+        <FirstName>Felipe</FirstName>
+        <LastName>Esteves</LastName>
+        <Affiliation>Universidade Federal do Pará (UFPA)</Affiliation>
+    </IndividualName>
+    """
+    individual_name_tag = ET.Element("IndividualName")
+    add_first_name(member_reg, individual_name_tag)
+    add_last_name(member_reg, individual_name_tag)
+    add_suffix(member_reg, individual_name_tag)
+    affiliations = get_affiliations(member_reg, xml_tree)
+    add_affiliations(affiliations, individual_name_tag)
+    add_orcid(member_reg, individual_name_tag)
+    group_tag.append(individual_name_tag)
+
+
+def xml_pubmed_group_list(xml_pubmed, xml_tree):
+    """
+    <GroupList>
+        <Group>
+            <GroupName>The SciELO Group</GroupName>
+            <IndividualName>
+                <FirstName>Felipe</FirstName>
+                <LastName>Esteves</LastName>
+                <Affiliation>Universidade Federal do Pará (UFPA)</Affiliation>
+            </IndividualName>
+        </Group>
+    </GroupList>
+
+    Membros de contrib-group[@content-type="collab-list"] (ver
+    xml_pubmed_author_list), agrupados sob o nome do grupo declarado no
+    <collab> do contrib-group irmão.
+    """
+    authors = list(get_authors(xml_tree))
+    members = get_group_members(authors)
+    if not members:
+        return
+
+    group_list_tag = ET.Element("GroupList")
+    group_tag = ET.Element("Group")
+
+    group_name = get_group_name(authors)
+    if group_name:
+        group_name_tag = ET.Element("GroupName")
+        group_name_tag.text = group_name
+        group_tag.append(group_name_tag)
+
+    for member_reg in members:
+        add_individual_name(member_reg, xml_tree, group_tag)
+
+    group_list_tag.append(group_tag)
+    xml_pubmed.append(group_list_tag)
 
 
 def get_publication_type(xml_tree):