Add file unpacking form to editor tools.

Author: tompollard

physionet-django/console/templates/console/submission_info_card.html

@@ -22,6 +22,9 @@
       <li class="nav-item">
         <a class="nav-link {% if passphrase %} active {% endif %}" id="embargo-tab" data-toggle="tab" href="#embargo" role="tab" aria-controls="reassign" aria-selected="false">Embargo</a>
       </li>
+      <li class="nav-item">
+        <a class="nav-link" id="manage-files-tab" data-toggle="tab" href="#manage-files" role="tab" aria-controls="manage-files" aria-selected="false">Manage Files</a>
+      </li>
       {% endif %}
       {% if project.submission_status >= SubmissionStatus.NEEDS_COPYEDIT %}
       <li class="nav-item">
@@ -230,6 +233,90 @@ <h5 class="modal-title" id="exampleModalLongTitle">Embargo files</h5>
       </div>
       {% endif %}
 
+      {# Manage Files #}
+      {% if project.editor == user %}
+      <div class="tab-pane fade" id="manage-files" role="tabpanel" aria-labelledby="manage-files-tab">
+        <h5 class="card-title">File Management</h5>
+        <p class="card-text">
+          This tool allows you to unpack compressed files (tar.gz, zip, gz, bz2, xz) within the project directory.
+          This is useful for extracting archives that authors have uploaded.
+        </p>
+
+        <div class="alert alert-info">
+          <strong>Project files are located at:</strong> {{ project.file_root }}
+        </div>
+
+        <div class="alert alert-info">
+          <strong>Supported formats:</strong> .tar.gz, .tgz, .tar.bz2, .tar.xz, .zip, .gz, .bz2, .xz
+        </div>
+
+        <form action="{% url 'submission_info' project.slug %}" method="POST" id="file_unpack_form">
+          {% csrf_token %}
+                  <div class="form-group">
+          <label for="{{ file_unpack_form.file_path.id_for_label }}">{{ file_unpack_form.file_path.label }}</label>
+          {{ file_unpack_form.file_path }}
+          {% if file_unpack_form.file_path.help_text %}
+            <small class="form-text text-muted">{{ file_unpack_form.file_path.help_text }}</small>
+          {% endif %}
+          <small class="form-text text-muted">
+            <strong>Tip:</strong> Use relative paths from the project root. For example, if your file is in a subdirectory called "data", enter "data/CFPFlyer.zip"
+          </small>
+          {% if file_unpack_form.file_path.errors %}
+            <div class="invalid-feedback d-block">
+              {% for error in file_unpack_form.file_path.errors %}
+                {{ error }}
+              {% endfor %}
+            </div>
+          {% endif %}
+        </div>
+
+          <div class="form-group">
+            <label for="{{ file_unpack_form.target_directory.id_for_label }}">{{ file_unpack_form.target_directory.label }}</label>
+            {{ file_unpack_form.target_directory }}
+            {% if file_unpack_form.target_directory.help_text %}
+              <small class="form-text text-muted">{{ file_unpack_form.target_directory.help_text }}</small>
+            {% endif %}
+            {% if file_unpack_form.target_directory.errors %}
+              <div class="invalid-feedback d-block">
+                {% for error in file_unpack_form.target_directory.errors %}
+                  {{ error }}
+                {% endfor %}
+              </div>
+            {% endif %}
+          </div>
+
+          <div class="form-group">
+            <div class="form-check">
+              {{ file_unpack_form.overwrite_existing }}
+              <label class="form-check-label" for="{{ file_unpack_form.overwrite_existing.id_for_label }}">
+                {{ file_unpack_form.overwrite_existing.label }}
+              </label>
+              {% if file_unpack_form.overwrite_existing.help_text %}
+                <small class="form-text text-muted">{{ file_unpack_form.overwrite_existing.help_text }}</small>
+              {% endif %}
+            </div>
+            {% if file_unpack_form.overwrite_existing.errors %}
+              <div class="invalid-feedback d-block">
+                {% for error in file_unpack_form.overwrite_existing.errors %}
+                  {{ error }}
+                {% endfor %}
+              </div>
+            {% endif %}
+          </div>
+
+          <button type="submit" class="btn btn-primary" name="unpack_file">
+            <i class="fas fa-archive"></i> Unpack File
+          </button>
+        </form>
+
+        <hr>
+
+        <div class="alert alert-warning">
+          <strong>Note:</strong> This operation will modify the project files. Make sure you have the necessary permissions and that the file paths are correct.
+        </div>
+      </div>
+      {% endif %}
+
       {# Draft DOI #}
       <div class="tab-pane fade" id="doi" role="tabpanel" aria-labelledby="doi-tab">
         <p>The following DOIs have been registered for the project. These may be useful 

physionet-django/console/views.py

@@ -77,6 +77,7 @@
 from physionet.enums import LogCategory
 from console import forms, utility, services
 from console.forms import ProjectFilterForm, UserFilterForm
+from console.file_utils import FileUnpacker
 from project.cloud.s3 import (
     create_s3_bucket,
     upload_project_to_S3,
@@ -282,7 +283,8 @@ def submission_info_card_params(request,
                                 embargo_form,
                                 internal_note_form,
                                 bulk_download,
-                                force_calculate):
+                                force_calculate,
+                                file_unpack_form=None):
     """
     Parameters used across submission_info_card.html pages, including:
 
@@ -311,6 +313,7 @@ def submission_info_card_params(request,
         'embargo_form': embargo_form,
         'notes': notes,
         'internal_note_form': internal_note_form,
+        'file_unpack_form': file_unpack_form,
     }
 
 
@@ -328,6 +331,7 @@ def submission_info(request, project_slug):
     reassign_editor_form = forms.ReassignEditorForm(project=project, data=data)
     internal_note_form = forms.InternalNoteForm(data)
     embargo_form = forms.EmbargoFilesDaysForm()
+    file_unpack_form = forms.FileUnpackForm(data)
     passphrase = ''
     anonymous_url = project.get_anonymous_url()
 
@@ -376,6 +380,40 @@ def submission_info(request, project_slug):
         else:
             messages.error(request, "You are not authorized to delete this note.")
         return redirect(f'{request.path}?tab=notes')
+    elif 'unpack_file' in request.POST and user == project.editor:
+        if file_unpack_form.is_valid():
+            try:
+                project_root = project.file_root()
+
+                LOGGER.info(f"Project root: {project_root}")
+                LOGGER.info(f"File path: {file_unpack_form.cleaned_data['file_path']}")
+                LOGGER.info(f"Full file path: {os.path.join(project_root, file_unpack_form.cleaned_data['file_path'])}")
+
+                result = FileUnpacker.unpack_file(
+                    project_root=project_root,
+                    file_path=file_unpack_form.cleaned_data['file_path'],
+                    target_directory=file_unpack_form.cleaned_data['target_directory'] or None,
+                    overwrite_existing=file_unpack_form.cleaned_data['overwrite_existing']
+                )
+
+                if result['success']:
+                    messages.success(
+                        request,
+                        f"Successfully unpacked {len(result['extracted_files'])} files to {result['extract_directory']}"
+                    )
+                    # Reset form after successful unpacking
+                    file_unpack_form = forms.FileUnpackForm()
+                else:
+                    messages.error(request, "File unpacking failed")
+
+            except Exception as e:
+                error_msg = f"Error unpacking file: {str(e)}"
+                if "File not found" in str(e):
+                    error_msg += f" (searched in: {project_root})"
+                messages.error(request, error_msg)
+                LOGGER.error(f"File unpacking error for project {project.slug}: {str(e)}")
+        else:
+            messages.error(request, 'Invalid file unpacking submission. See errors below.')
 
     return render(request, 'console/submission_info.html',
                   {**submission_info_card_params(
@@ -385,11 +423,13 @@ def submission_info(request, project_slug):
                    embargo_form,
                    internal_note_form,
                    bulk_download=True,
-                   force_calculate=False
+                   force_calculate=False,
+                   file_unpack_form=file_unpack_form
                    ),
                    'copyedit_logs': copyedit_logs,
                    'passphrase': passphrase,
                    'anonymous_url': anonymous_url,
+                   'file_unpack_form': file_unpack_form,
                    }
                   )
 
@@ -449,7 +489,8 @@ def edit_submission(request, project_slug, *args, **kwargs):
                    embargo_form,
                    internal_note_form,
                    bulk_download=True,
-                   force_calculate=False
+                   force_calculate=False,
+                   file_unpack_form=None
                    ),
                    'edit_submission_form': edit_submission_form,
                    'editor_home': True,
@@ -590,15 +631,16 @@ def copyedit_submission(request, project_slug, *args, **kwargs):
     response = render(
         request,
         'console/copyedit_submission.html',
-        {**submission_info_card_params(
-         request,
-         project,
-         reassign_editor_form,
-         embargo_form,
-         internal_note_form,
-         bulk_download=False,
-         force_calculate=True,
-         ),
+            {**submission_info_card_params(
+                   request,
+                   project,
+                   reassign_editor_form,
+                   embargo_form,
+                   internal_note_form,
+                   bulk_download=False,
+                   force_calculate=True,
+                   file_unpack_form=None
+                   ),
          'description_form': description_form,
          'ethics_form': ethics_form,
          'individual_size_limit': readable_size(ActiveProject.INDIVIDUAL_FILE_SIZE_LIMIT),
@@ -674,6 +716,7 @@ def awaiting_authors(request, project_slug, *args, **kwargs):
                    internal_note_form,
                    bulk_download=True,
                    force_calculate=False,
+                   file_unpack_form=None
                    ),
                    'copyedit_logs': copyedit_logs,
                    'outstanding_emails': outstanding_emails,
@@ -790,7 +833,8 @@ def publish_submission(request, project_slug, *args, **kwargs):
                    embargo_form,
                    internal_note_form,
                    bulk_download=True,
-                   force_calculate=True
+                   force_calculate=True,
+                   file_unpack_form=None
                    ),
                    'publishable': publishable,
                    'copyedit_logs': copyedit_logs,