autopopulate fields / #214

jdhapi/admin.py

@@ -112,6 +112,8 @@ class ArticleAdmin(admin.ModelAdmin):
     list_display = ['abstract_pid', 'issue_name', 'issue', 'abstract_title', 'status', 'clickable_dataverse_url']
     list_filter = ('issue__name', 'status', 'copyright_type', EmptyDataverseURLFilter)
     actions = [save_notebook_fingerprint, save_notebook_specific_cell, save_article_citation, save_article_package, save_article_references]
+    #readonly_fields = ("notebook_url", "notebook_path", "binder_url", "notebook_ipython_url")
+
     fieldsets = (
         (
             "Information related to the article", {
@@ -126,7 +128,12 @@ class ArticleAdmin(admin.ModelAdmin):
                 # Section Description
                 # "description" : "Enter the vehicle information",
                 # Group Make and Model
-                "fields": (("repository_type", "repository_url"), "notebook_url", "notebook_path", "binder_url", "notebook_ipython_url", "dataverse_url")
+                "fields": (("repository_type", "full_url_article_path"), ("repository_url", "notebook_url", "notebook_path", "binder_url", "notebook_ipython_url"))
+            }
+        ),
+ (
+            "Information related to the dataverse repository", {
+                "fields": ("dataverse_url",)
             }
         ),
         (

jdhapi/forms/articleForm.py

@@ -17,9 +17,10 @@ class Meta:
         model = Article
         fields = '__all__'
 
-    def clean(self):
+    """ def clean(self):
         # Get the article data
         article = self.instance
+        full_url_article_path = self.cleaned_data['full_url_article_path']
         doi = self.cleaned_data['doi']
         status = self.cleaned_data['status']
         repository_url = self.cleaned_data['repository_url']
@@ -29,6 +30,7 @@ def clean(self):
         notebook_ipython_url = self.cleaned_data['notebook_ipython_url']
         if self.has_changed():
             logger.info("The following fields changed: %s" % ", ".join(self.changed_data))
+
             if 'status' in self.changed_data:
                 # IF PUBLISHED
                 if status == Article.Status.PUBLISHED:
@@ -60,3 +62,4 @@ def clean(self):
             logger.info("no changed fields")
 
 
+ """

jdhapi/migrations/0039_article_full_url_article_path.py

@@ -0,0 +1,18 @@
+# Generated by Django 3.2.14 on 2024-01-11 14:51
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('jdhapi', '0038_article_dataverse_url'),
+    ]
+
+    operations = [
+        migrations.AddField(
+            model_name='article',
+            name='full_url_article_path',
+            field=models.CharField(blank=True, help_text='Full URL of the article', max_length=254, null=True),
+        ),
+    ]

jdhapi/models/article.py

@@ -11,6 +11,7 @@
 from django.db.models.signals import post_save
 from django.dispatch import receiver
 from lxml import html
+from django.dispatch import receiver
 from model_utils import FieldTracker
 
 logger = logging.getLogger(__name__)
@@ -43,8 +44,9 @@ class RepositoryType(models.TextChoices):
         choices=Status.choices,
         default=Status.DRAFT,
     )
-    tracker = FieldTracker(fields=['status'])
+
     issue = models.ForeignKey('jdhapi.Issue', on_delete=models.CASCADE)
+    full_url_article_path = models.CharField(max_length=254, null=True, blank=True, help_text="Full URL of the article")
     repository_url = models.URLField(max_length=254, null=True, blank=True, help_text="GitHub's repository URL ")
     repository_type = models.CharField(
         max_length=15,
@@ -79,6 +81,8 @@ class RepositoryType(models.TextChoices):
     tags = models.ManyToManyField('jdhapi.Tag', blank=True)
     authors = models.ManyToManyField('jdhapi.Author', through='Role')
 
+    tracker = FieldTracker(fields=['status','full_url_article_path'])
+
     def get_kernel_language(self):
         tool_tags = self.tags.filter(category='tool')
         if tool_tags.exists():
@@ -119,4 +123,6 @@ def send_email_if_peer_review(self):
                     email.send()
                     logger.info("Email sent")
                 except Exception as e:
-                    print(f'Error sending email: {str(e)}')
+                    print(f'Error sending email: {str(e)}')
+
+

jdhapi/serializers/article.py

@@ -25,7 +25,7 @@ class Meta:
         model = Article
         fields = [
             "abstract", "repository_url", "status", "publication_date", "repository_type",
-            "copyright_type", "notebook_url", "notebook_commit_hash", "notebook_path",
+            "copyright_type", "notebook_url", "full_url_article_path" , "notebook_commit_hash", "notebook_path",
             "binder_url", "doi", "dataverse_url", "data", "citation", "kernel_language",
             "tags", "issue", "authors", "fingerprint"
         ]

jdhapi/signals.py

@@ -1,10 +1,31 @@
-from django.db.models.signals import post_save
-from django.dispatch import receiver
+from django.db.models.signals import pre_save, post_save
 from django.core.mail import send_mail
 from jdhapi.models import Article
+from django.dispatch import receiver
+from jdhapi.utils.articleUtils import get_notebook_from_github
+import logging
+
+logger = logging.getLogger(__name__)
 
 
 @receiver(post_save, sender=Article)
 def send_email_for_peer_review_article(sender, instance, created, **kwargs):
     if not created and instance.tracker.has_changed('status') and instance.status == Article.Status.PEER_REVIEW:
         instance.send_email_if_peer_review()
+
+@receiver(pre_save, sender=Article)
+def pre_save_article(sender, instance, **kwargs):
+    logger.debug("Inside pre_save_article")
+
+    # Check if full_url_article_path has changed
+    if instance.tracker.has_changed('full_url_article_path'):
+        # Update other fields if necessary
+        repository_url, notebook_path, notebook_ipython_url = get_notebook_from_github(instance.full_url_article_path)
+
+        # Set the values directly without calling save
+        instance.notebook_ipython_url = notebook_ipython_url
+        instance.repository_url = repository_url
+        instance.notebook_path = notebook_path
+
+    logger.debug("Fields populated: notebook_ipython_url=%s, repository_url=%s, notebook_path=%s" % (
+        instance.notebook_ipython_url, instance.repository_url, instance.notebook_path))

jdhapi/utils/articleUtils.py

@@ -33,27 +33,34 @@ def get_notebook_from_raw_github(raw_url):
     except Exception as e:
         logger.error(f"An unexpected error occurred: {e}")
 
-
 def get_notebook_from_github(
     repository_url, host='https://raw.githubusercontent.com'
 ):
-    logger.info(
-        f'get_notebook_from_github - parsing repository_url: {repository_url}')
-    result = re.search(
-        r'github\.com\/([^\/]+)\/([^\/]+)\/(blob\/)?(.*\.ipynb$)',
-        repository_url
-    )
-    github_user = result.group(1)
-    github_repo = result.group(2)
-    github_filepath = result.group(4)
-    raw_url = f'{host}/{github_user}/{github_repo}/{github_filepath}'
-    # https://raw.githubusercontent.com/jdh-observer/jdh001-WBqfZzfi7nHK/blob/8315a108416f4a5e9e6da0c5e9f18b5e583ed825/scripts/Digital_epigraphy_cite2c_biblio.ipynb
-    # Match github.com/<github_user abc>/<github_filepath XXX/yyy/zzz.ipynb>
-    # and exclude the `/blob/` part of the url if any.
-    # then extract the gighub username nd the filepath to download
-    # conveniently from githubusercontent server.
-    logger.info(f'get_notebook_from_github - requesting raw_url: {raw_url}...')
-    return get_notebook_from_raw_github(raw_url)
+    try:
+        logger.info(
+            f'get_notebook_from_github - parsing repository_url: {repository_url}')
+        result = re.search(
+            r'github\.com\/([^\/]+)\/([^\/]+)\/(blob\/)?(.*\.ipynb$)',
+            repository_url
+        )
+        github_user = result.group(1)
+        github_repo = result.group(2)
+        github_filepath = result.group(4)
+        github_full_url = f'https://github.com/{github_user}/{github_repo}'
+        raw_url = f'{host}/{github_user}/{github_repo}/{github_filepath}'
+
+        logger.info(f'get_notebook_from_github - requesting github_filepath: {github_filepath}...')
+        logger.info(f'get_notebook_from_github - requesting github_repo: {github_full_url}...')
+        logger.info(f'get_notebook_from_github - requesting raw_url: {raw_url}...')
+
+        return github_full_url, github_filepath, raw_url
+
+    except requests.exceptions.RequestException as e:
+        logger.error(f'Error accessing GitHub URL: {e}')
+        return None
+    except Exception as e:
+        logger.error(f'An unexpected error occurred: {e}')
+        return None
 
 
 # Method to use to generate the fingerprint datas
@@ -417,7 +424,6 @@ def convert_notebook(notebook_file, output_format='pdf'):
     try:
         # Run the nbconvert command to generate the output file
         command = f'jupyter nbconvert --to {output_format} {notebook_file}'
-        #subprocess.run(command, shell=True, check=True, capture_output=True, text=True)
         subprocess.check_output(command, shell=True, stderr=subprocess.STDOUT, text=True)
 
         logger.info("Conversion successful!")

subprocess_article.py

@@ -0,0 +1,13 @@
+import subprocess
+
+notebook_file = 'notebook_with_ref.ipynb'
+output_format = 'pdf'
+command = f'jupyter nbconvert --to {output_format} {notebook_file}'
+
+try:
+    result = subprocess.check_output(command, shell=True, stderr=subprocess.STDOUT, text=True)
+    print("Conversion successful!")
+    print(result)  # Print the entire output
+except subprocess.CalledProcessError as e:
+    print(f"Error during conversion: {e}")
+    print("Command output:\n", e.output)