[MarkAPI-122] feat: add PubMed/PMC XML generation for XML documents

Add models, tasks, admin views and forms to upload an XML document and
convert it to PubMed/PMC XML formats independently of other workflows,
plus a "Last error" column in the XML Documents list to surface
conversion errors. Also fixes a double-serialization bug where
generate_pubmed_for_xml_document/generate_pmc_for_xml_document wrote
xml_utils.tostring(...) over strings already returned by packtools'
pipeline_pubmed/pipeline_pmc.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

Author: Rossi-Luciano

markup_doc/wagtail_hooks.py

@@ -34,6 +34,9 @@
     SPSPackageValidationSnippetViewSet,
     XMLDocumentHTMLSnippetViewSet,
     XMLDocumentPDFSnippetViewSet,
+    XMLDocumentPMCSnippetViewSet,
+    XMLDocumentPubMedSnippetViewSet,
+    XMLDocumentSnippetViewSet,
 )
 
 
@@ -226,8 +229,11 @@ class XMLSPSSnippetViewSetGroup(SnippetViewSetGroup):
         MarkupXMLViewSet,
         SPSPackageValidationSnippetViewSet,
         ProcessedDocxViewSet,
+        XMLDocumentSnippetViewSet,
         XMLDocumentPDFSnippetViewSet,
         XMLDocumentHTMLSnippetViewSet,
+        XMLDocumentPubMedSnippetViewSet,
+        XMLDocumentPMCSnippetViewSet,
     )
 
 

tracker/choices.py

@@ -35,6 +35,8 @@
 XML_DOCUMENT_CONVERSION_TO_HTML_ERROR = "CHE"
 XML_DOCUMENT_CONVERSION_TO_PDF_ERROR = "CPE"
 XML_DOCUMENT_CONVERSION_TO_TEX_ERROR = "CTE"
+XML_DOCUMENT_CONVERSION_TO_PUBMED_ERROR = "PME"
+XML_DOCUMENT_CONVERSION_TO_PMC_ERROR = "PCE"
 XML_DOCUMENT_UNKNOWN_ERROR = "UNE"
 
 XML_DOCUMENT_EVENT = [
@@ -44,5 +46,7 @@
     (XML_DOCUMENT_CONVERSION_TO_HTML_ERROR, _("XML Conversion to HTML Error")),
     (XML_DOCUMENT_CONVERSION_TO_PDF_ERROR, _("XML Conversion to PDF Error")),
     (XML_DOCUMENT_CONVERSION_TO_TEX_ERROR, _("XML Conversion to TEX Error")),
+    (XML_DOCUMENT_CONVERSION_TO_PUBMED_ERROR, _("XML Conversion to PubMed Error")),
+    (XML_DOCUMENT_CONVERSION_TO_PMC_ERROR, _("XML Conversion to PMC Error")),
     (XML_DOCUMENT_UNKNOWN_ERROR, _("Unknown Error")),
 ]

xml_manager/exceptions.py

@@ -13,5 +13,11 @@ class XML_File_PDF_Generation_Error(Exception):
 class XML_File_HTML_Generation_Error(Exception):
     pass
 
+class XML_File_PubMed_Generation_Error(Exception):
+    pass
+
+class XML_File_PMC_Generation_Error(Exception):
+    pass
+
 class SPS_Package_Validation_Error(Exception):
     pass

xml_manager/forms.py

@@ -5,7 +5,7 @@
 from django.utils.translation import gettext_lazy as _
 from wagtail.admin.forms import WagtailAdminModelForm
 
-from xml_manager.models import SPSPackageValidation
+from xml_manager.models import SPSPackageValidation, XMLDocument
 
 
 class SPSPackageValidationForm(WagtailAdminModelForm):
@@ -57,3 +57,22 @@ def save_wagtail_document_from_path(file_path, title=None):
             document = Document(title=document_title)
             document.file.save(basename, File(fp), save=True)
         return document
+
+
+class XMLConvertUploadForm(WagtailAdminModelForm):
+    xml_upload = forms.FileField(
+        label=_("XML file"),
+        help_text=_("Upload an XML file (SciELO Publishing Schema) to convert."),
+    )
+
+    class Meta:
+        model = XMLDocument
+        fields = []
+
+    def clean_xml_upload(self):
+        xml_upload = self.cleaned_data["xml_upload"]
+        if not xml_upload.name.lower().endswith(".xml"):
+            raise ValidationError(_("Only .xml files are allowed."))
+        if xml_upload.size == 0:
+            raise ValidationError(_("The file is empty."))
+        return xml_upload

xml_manager/migrations/0005_xmldocumentpmc_xmldocumentpubmed.py

@@ -0,0 +1,40 @@
+# Generated by Django 6.0.5 on 2026-06-11 14:25
+
+import django.db.models.deletion
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('xml_manager', '0004_spspackagevalidation'),
+    ]
+
+    operations = [
+        migrations.CreateModel(
+            name='XMLDocumentPMC',
+            fields=[
+                ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
+                ('pmc_file', models.FileField(upload_to='xml_manager/pmc/', verbose_name='PMC XML File')),
+                ('uploaded_at', models.DateTimeField(auto_now_add=True, verbose_name='Uploaded At')),
+                ('xml_document', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, related_name='pmcs', to='xml_manager.xmldocument', verbose_name='XML Document')),
+            ],
+            options={
+                'verbose_name': 'XML Document PMC',
+                'verbose_name_plural': 'XML Document PMCs',
+            },
+        ),
+        migrations.CreateModel(
+            name='XMLDocumentPubMed',
+            fields=[
+                ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
+                ('pubmed_file', models.FileField(upload_to='xml_manager/pubmed/', verbose_name='PubMed XML File')),
+                ('uploaded_at', models.DateTimeField(auto_now_add=True, verbose_name='Uploaded At')),
+                ('xml_document', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, related_name='pubmeds', to='xml_manager.xmldocument', verbose_name='XML Document')),
+            ],
+            options={
+                'verbose_name': 'XML Document PubMed',
+                'verbose_name_plural': 'XML Document PubMeds',
+            },
+        ),
+    ]

xml_manager/models.py

@@ -122,6 +122,58 @@ def create(cls, xml_document, html_file, language="pt"):
         return html_instance
 
 
+class XMLDocumentPubMed(models.Model):
+    xml_document = models.ForeignKey(
+        XMLDocument,
+        on_delete=models.CASCADE,
+        related_name="pubmeds",
+        verbose_name=_("XML Document"),
+    )
+    pubmed_file = models.FileField(
+        upload_to="xml_manager/pubmed/", verbose_name=_("PubMed XML File")
+    )
+    uploaded_at = models.DateTimeField(auto_now_add=True, verbose_name=_("Uploaded At"))
+
+    def __str__(self):
+        return f"PubMed XML for {self.xml_document.xml_file.name}"
+
+    class Meta:
+        verbose_name = _("XML Document PubMed")
+        verbose_name_plural = _("XML Document PubMeds")
+
+    @classmethod
+    def create(cls, xml_document, pubmed_file):
+        instance = cls(xml_document=xml_document, pubmed_file=pubmed_file)
+        instance.save()
+        return instance
+
+
+class XMLDocumentPMC(models.Model):
+    xml_document = models.ForeignKey(
+        XMLDocument,
+        on_delete=models.CASCADE,
+        related_name="pmcs",
+        verbose_name=_("XML Document"),
+    )
+    pmc_file = models.FileField(
+        upload_to="xml_manager/pmc/", verbose_name=_("PMC XML File")
+    )
+    uploaded_at = models.DateTimeField(auto_now_add=True, verbose_name=_("Uploaded At"))
+
+    def __str__(self):
+        return f"PMC XML for {self.xml_document.xml_file.name}"
+
+    class Meta:
+        verbose_name = _("XML Document PMC")
+        verbose_name_plural = _("XML Document PMCs")
+
+    @classmethod
+    def create(cls, xml_document, pmc_file):
+        instance = cls(xml_document=xml_document, pmc_file=pmc_file)
+        instance.save()
+        return instance
+
+
 class SPSPackageValidation(models.Model):
     package_document = models.OneToOneField(
         "wagtaildocs.Document",

xml_manager/tasks.py

@@ -12,6 +12,8 @@
     XML_DOCUMENT_CONVERSION_TO_DOCX_ERROR,
     XML_DOCUMENT_CONVERSION_TO_HTML_ERROR,
     XML_DOCUMENT_CONVERSION_TO_PDF_ERROR,
+    XML_DOCUMENT_CONVERSION_TO_PMC_ERROR,
+    XML_DOCUMENT_CONVERSION_TO_PUBMED_ERROR,
     XML_DOCUMENT_PARSING_ERROR,
     XML_DOCUMENT_UNKNOWN_ERROR,
     XML_DOCUMENT_VALIDATION_ERROR,
@@ -25,6 +27,8 @@
     XMLDocument,
     XMLDocumentHTML,
     XMLDocumentPDF,
+    XMLDocumentPMC,
+    XMLDocumentPubMed,
 )
 
 User = get_user_model()
@@ -33,7 +37,7 @@
 def _get_user(request, username=None, user_id=None):
     try:
         return User.objects.get(pk=request.user_id)
-    except AttributeError:
+    except (AttributeError, User.DoesNotExist):
         if user_id:
             return User.objects.get(pk=user_id)
         if username:
@@ -52,6 +56,8 @@ def task_process_xml_document(self, xml_id, user_id=None, username=None):
     task_validate_xml_file.delay(xml_id, user_id=user_id, username=username)
     task_generate_pdf_file.delay(xml_id, user_id=user_id, username=username)
     task_generate_html_file.delay(xml_id, user_id=user_id, username=username)
+    task_generate_pubmed_file.delay(xml_id, user_id=user_id, username=username)
+    task_generate_pmc_file.delay(xml_id, user_id=user_id, username=username)
 
     return True
 
@@ -235,6 +241,128 @@ def task_generate_html_file(self, xml_id, user_id=None, username=None):
         return False
 
 
+@celery_app.task(bind=True, timelimit=-1)
+def task_generate_pubmed_file(self, xml_id, user_id=None, username=None):
+    try:
+        xml_document = XMLDocument.objects.get(id=xml_id)
+    except XMLDocument.DoesNotExist:
+        logging.error(f"XML file with ID {xml_id} does not exist.")
+        return False
+
+    user = _get_user(self.request, username=username, user_id=user_id)
+
+    logging.info(
+        f"Starting PubMed XML generation for XML file {xml_document.xml_file.name}."
+    )
+    try:
+        path_pubmed = utils.generate_pubmed_for_xml_document(
+            xml_document.xml_file.path,
+            output_root_dir=os.path.join(settings.MEDIA_ROOT, "xml_manager", "pubmed"),
+            params={},
+        )
+
+        pubmed_instance = XMLDocumentPubMed(xml_document=xml_document)
+        pubmed_instance.pubmed_file.name = os.path.relpath(
+            path_pubmed, settings.MEDIA_ROOT
+        )
+        pubmed_instance.save()
+
+    except exceptions.XML_File_Parsing_Error as e:
+        logging.error(f"Error during XML parsing: {e}")
+        XMLDocumentEvent.create(
+            xml_document=xml_document,
+            error_type=XML_DOCUMENT_PARSING_ERROR,
+            data={},
+            message=str(e),
+            save=True,
+        )
+        return False
+
+    except exceptions.XML_File_PubMed_Generation_Error as e:
+        logging.error(f"Error during PubMed XML generation: {e}")
+        XMLDocumentEvent.create(
+            xml_document=xml_document,
+            error_type=XML_DOCUMENT_CONVERSION_TO_PUBMED_ERROR,
+            data={},
+            message=str(e),
+            save=True,
+        )
+        return False
+
+    except Exception as e:
+        logging.error(f"Unexpected error during PubMed XML generation: {e}")
+        XMLDocumentEvent.create(
+            xml_document=xml_document,
+            error_type=XML_DOCUMENT_UNKNOWN_ERROR,
+            data={},
+            message=str(e),
+            save=True,
+        )
+        return False
+
+    return True
+
+
+@celery_app.task(bind=True, timelimit=-1)
+def task_generate_pmc_file(self, xml_id, user_id=None, username=None):
+    try:
+        xml_document = XMLDocument.objects.get(id=xml_id)
+    except XMLDocument.DoesNotExist:
+        logging.error(f"XML file with ID {xml_id} does not exist.")
+        return False
+
+    user = _get_user(self.request, username=username, user_id=user_id)
+
+    logging.info(
+        f"Starting PMC XML generation for XML file {xml_document.xml_file.name}."
+    )
+    try:
+        path_pmc = utils.generate_pmc_for_xml_document(
+            xml_document.xml_file.path,
+            output_root_dir=os.path.join(settings.MEDIA_ROOT, "xml_manager", "pmc"),
+            params={},
+        )
+
+        pmc_instance = XMLDocumentPMC(xml_document=xml_document)
+        pmc_instance.pmc_file.name = os.path.relpath(path_pmc, settings.MEDIA_ROOT)
+        pmc_instance.save()
+
+    except exceptions.XML_File_Parsing_Error as e:
+        logging.error(f"Error during XML parsing: {e}")
+        XMLDocumentEvent.create(
+            xml_document=xml_document,
+            error_type=XML_DOCUMENT_PARSING_ERROR,
+            data={},
+            message=str(e),
+            save=True,
+        )
+        return False
+
+    except exceptions.XML_File_PMC_Generation_Error as e:
+        logging.error(f"Error during PMC XML generation: {e}")
+        XMLDocumentEvent.create(
+            xml_document=xml_document,
+            error_type=XML_DOCUMENT_CONVERSION_TO_PMC_ERROR,
+            data={},
+            message=str(e),
+            save=True,
+        )
+        return False
+
+    except Exception as e:
+        logging.error(f"Unexpected error during PMC XML generation: {e}")
+        XMLDocumentEvent.create(
+            xml_document=xml_document,
+            error_type=XML_DOCUMENT_UNKNOWN_ERROR,
+            data={},
+            message=str(e),
+            save=True,
+        )
+        return False
+
+    return True
+
+
 @celery_app.task(bind=True)
 def task_validate_sps_package(self, validation_pk):
     try: