Add elocation and other article identifiers

portality/crosswalks/article_crossref_xml.py

@@ -171,6 +171,7 @@ def crosswalk_article(self, record, journal):
         self.extract_issue(journal, bibjson)
         self.extract_pages(record, journal, bibjson)
         self.extract_doi(record, journal, bibjson)
+        self.extract_identifiers(record, journal, bibjson)
         self.extract_fulltext(record, journal, bibjson)
         self.extract_article_title(record, journal, bibjson)
         self.extract_authors(record, journal, bibjson)
@@ -284,6 +285,39 @@ def extract_doi(self, record, journal, bibjson):
             if doi is not None:
                 bibjson.add_identifier(bibjson.DOI, doi)
 
+    def extract_identifiers(self, record, journal, bibjson):
+        # This is used to extract item_number such as article number, eLocator, or e-location
+        # and capture other identifiers such as handle, ark, doi, urn, dor and purl
+        # Both item_number and identifier have a type attribute which is free text.
+        # ToDO - Do we need to differentiate between item_number and other identifiers?
+        publisher_item = record.find("x:publisher_item", self.NS)
+        if publisher_item is not None:
+            ans = []
+            ans1 = publisher_item.findall("x:item_number", self.NS)
+            ans2 = publisher_item.findall("x:identifier", self.NS)
+            if ans1 is not None:
+                ans = ans + ans1
+            if ans2 is not None:
+                ans = ans + ans2
+            for an in ans:
+                typ = None
+                typ1 = an.attrib["item_number_type"]
+                typ2 = an.attrib["id_type"]
+                if typ1:
+                    typ = typ1
+                elif typ2:
+                    typ = typ2
+                if typ and typ.lower() in ["eLocator", "e-location"]:
+                    bibjson.add_identifier(bibjson.ELOCATION, an[0].text.upper())
+                elif typ and typ.lower() in bibjson.IDENTIFIER_TYPES:
+                    bibjson.add_identifier(typ.lower(), an[0].text.upper())
+                elif typ:
+                    # TODO - Do we capture identifiers of other types?
+                    bibjson.add_identifier(typ.lower(), an[0].text.upper())
+                else:
+                    # TODO - Do we capture identifiers of unknown type?
+                    bibjson.add_identifier('other', an[0].text.upper())
+
     def extract_fulltext(self, record, journal, bibjson):
         d = record.find("x:doi_data", self.NS)
         ftel = _element(d, "x:resource", self.NS)

portality/crosswalks/article_form.py

@@ -91,6 +91,15 @@ def form2obj(cls, form, add_journal_info=True):
         end = form.end.data
         if end is not None and end != "":
             bibjson.end_page = end
+        elocation = form.elocation.data
+        if elocation is not None and elocation != "":
+            bibjson.add_identifier(bibjson.ELOCATION, elocation)
+        for subfield in form.other_identifiers:
+            if (subfield.form.type.data is not None and subfield.form.type.data != "" and
+                subfield.form.id.data is not None and subfield.form.id.data != ""):
+                id_typ = subfield.form.type.data
+                id_val = subfield.form.id.data
+                bibjson.add_identifier(id_typ, id_val)
 
         # add the journal info if requested
         if add_journal_info:
@@ -153,4 +162,25 @@ def obj2form(cls, form, article):
             form.end.data = bibjson.end_page
         if bibjson.abstract:
             form.abstract.data = bibjson.abstract
+        elocation = bibjson.get_one_identifier(bibjson.ELOCATION)
+        if elocation:
+            form.elocation.data = elocation
+        other_identifiers = []
+        for each_id in bibjson.get_identifiers():
+            if not each_id['type'] in bibjson.NAMED_IDENTIFIERS:
+                other_identifiers.append(each_id)
+        if other_identifiers:
+            for i in range(len(form.other_identifiers)):
+                form.other_identifiers.pop_entry()
+            for i in other_identifiers:
+                id_form = OtherIdentifierForm()
+                if "type" in i:
+                    id_form.type = i["type"]
+                else:
+                    id_form.type = ""
+                if "id" in i:
+                    id_form.id = i["id"]
+                else:
+                    id_form.id = ""
+                form.other_identifiers.append_entry(id_form)
 

portality/forms/article_forms.py

@@ -14,6 +14,7 @@
 from portality.forms.fields import DOAJSelectField, TagListField
 from portality.forms.validate import OptionalIf, ThisOrThat, NoScriptTag, DifferentTo
 from portality.lib import dates
+from portality.models.v1 import bibjson
 from portality.ui.messages import Messages
 from portality.ui import templates
 
@@ -561,6 +562,20 @@ class AuthorForm(Form):
     orcid_id = StringField("ORCID iD", [validators.Optional(), validators.Regexp(regex=regex.ORCID_COMPILED, message=ORCID_ERROR)])
 
 
+class OtherIdentifierForm(Form):
+    """
+    ~~->$ OtherIdentifiers:Form~~
+    """
+    # WTForms choices are (value, label) - value is what actually gets submitted, so it
+    # must stay lower-case to match bibjson.GenericBibJSON.IDENTIFIER_TYPES / add_identifier
+    choices = [('', 'Select type')]
+    choices += [(i, i.upper()) for i in bibjson.GenericBibJSON.IDENTIFIER_TYPES]
+    choices += [('other', 'Other')]
+    id_types = DOAJSelectField("Type of identifier", [validators.Optional()], choices=choices, default="" )
+    type = StringField("Type", [validators.Optional(), NoScriptTag()])
+    id = StringField("ID", [validators.Optional(), NoScriptTag()])
+
+
 class ArticleForm(Form):
     title = StringField("Article title <em>(required)</em>", [validators.DataRequired(), NoScriptTag()])
     doi = StringField("DOI", [OptionalIf("fulltext", "You must provide the DOI or the Full-Text URL"), validators.Regexp(regex=regex.DOI_COMPILED, message=DOI_ERROR)], description="(You must provide a DOI and/or a Full-Text URL)")
@@ -583,6 +598,8 @@ class ArticleForm(Form):
     number = StringField("Issue", [validators.Optional(), NoScriptTag()])
     start = StringField("Start", [validators.Optional(), NoScriptTag()])
     end = StringField("End", [validators.Optional(), NoScriptTag()])
+    elocation = StringField("eLocation ID", [validators.Optional(), NoScriptTag()])
+    other_identifiers = FieldList(FormField(OtherIdentifierForm), min_entries=1)
 
     def __init__(self, *args, **kwargs):
         super(ArticleForm, self).__init__(*args, **kwargs)
@@ -599,7 +616,6 @@ def set_choices(self, user=None, article_id=None):
             app.logger.exception(str(e))
 
 
-
 #########################################
 # Formcontexts and factory
 
@@ -626,6 +642,7 @@ class MetadataForm(FormContext):
     def __init__(self, source, form_data, user):
         self.user = user
         self.author_error = False
+        self.other_identifier_error = False
         super(MetadataForm, self).__init__(source=source, form_data=form_data)
 
     def _set_choices(self):
@@ -671,6 +688,48 @@ def _validate_authors(self):
                 counted += 1
         return counted >= 1
 
+    def modify_other_identifiers_if_required(self, request_data):
+
+        more_ids = request_data.get("more_other_identifiers")
+        remove_id = None
+        for v in list(request.values.keys()):
+            if v.startswith("remove_other_identifiers"):
+                remove_id = v.split("-")[1]
+
+        # if the user wants more ids, add an extra entry
+        if more_ids:
+            return self.render_template(more_other_identifiers=True)
+
+        # if the user wants to remove an author, do the various back-flips required
+        if remove_id is not None:
+            return self.render_template(remove_other_identifiers=remove_id)
+
+    def _check_for_other_identifier_errors(self, **kwargs):
+
+        if "more_other_identifiers" in kwargs and kwargs["more_other_identifiers"] == True:
+            self.form.other_identifiers.append_entry()
+        if "remove_other_identifiers" in kwargs:
+            keep = []
+            while len(self.form.other_identifiers.entries) > 0:
+                entry = self.form.other_identifiers.pop_entry()
+                if entry.short_name == "other_identifiers-" + kwargs["remove_other_identifier"]:
+                    break
+                else:
+                    keep.append(entry)
+            while len(keep) > 0:
+                self.form.other_identifiers.append_entry(keep.pop().data)
+
+    def _validate_other_identifiers(self):
+        errors = 0
+        for entry in self.form.other_identifiers.entries:
+            typ = entry.data.get("type")
+            id = entry.data.get("id")
+            if typ is not None and typ != "" and (id is None or id == "") :
+                errors += 1
+            elif id is not None and id != "" and (typ is None or typ == ""):
+                errors += 1
+        return errors == 0
+
     def blank_form(self):
         self.form = ArticleForm()
         self._set_choices()
@@ -690,6 +749,8 @@ def form2target(self):
     def validate(self):
         if not self._validate_authors():
             self.author_error = True
+        if not self._validate_other_identifiers():
+            self.other_identifier_error = True
         if not self.form.validate():
             return False
         return True
@@ -720,9 +781,11 @@ def set_template(self):
 
     def render_template(self, **kwargs):
         self._check_for_author_errors(**kwargs)
+        self._check_for_other_identifier_errors(**kwargs)
         if "validated" in kwargs and kwargs["validated"] == True:
             self.blank_form()
-        return render_template(self.template, form=self.form, form_context=self, author_error=self.author_error)
+        return render_template(self.template, form=self.form, form_context=self, author_error=self.author_error,
+                               other_identifier_error=self.other_identifier_error)
 
 
 class AdminMetadataArticleForm(MetadataForm):
@@ -737,4 +800,6 @@ def set_template(self):
 
     def render_template(self, **kwargs):
         self._check_for_author_errors(**kwargs)
-        return render_template(self.template, form=self.form, form_context=self, author_error=self.author_error)
+        self._check_for_other_identifier_errors(**kwargs)
+        return render_template(self.template, form=self.form, form_context=self, author_error=self.author_error,
+                               other_identifier_error=self.other_identifier_error)

portality/models/article.py

@@ -749,6 +749,22 @@ def end_page(self):
     def end_page(self, val):
         self._set_with_struct("end_page", val)
 
+    @property
+    def elocation(self):
+        self.elocation += self.get_identifiers(self.ELOCATION)
+
+    @elocation.setter
+    def elocation(self, val):
+        self.add_identifier(self.ELOCATION, val)
+
+    @property
+    def other_identifiers(self):
+        identifiers = []
+        for each_id in self.get_identifiers():
+            if not each_id['type'] in self.NAMED_IDENTIFIERS:
+                identifiers.append(each_id)
+        return identifiers
+
     @property
     def abstract(self):
         return self._get_single("abstract")

portality/models/v1/bibjson.py

@@ -6,6 +6,9 @@ class GenericBibJSON(dataobj.DataObj):
     P_ISSN = "pissn"
     E_ISSN = "eissn"
     DOI = "doi"
+    IDENTIFIER_TYPES = ['handle', 'ark', 'doi', 'urn', 'dor', 'purl']
+    ELOCATION = 'e-location'
+    NAMED_IDENTIFIERS = [P_ISSN, E_ISSN, DOI, ELOCATION]
 
     # allowable values for the url types
     HOMEPAGE = "homepage"