add template create view (#1961)

isatemplates/forms.py

@@ -1,4 +1,180 @@
 """Forms for the isatemplates app"""
 
-# TODO: Add template create/update form
-# TODO: Copy file uploading from samplesheets
+import json
+import logging
+
+from cubi_isa_templates import _TEMPLATES as CUBI_TEMPLATES
+
+from django import forms
+from django.conf import settings
+from django.db import transaction
+
+# Projectroles dependency
+from projectroles.forms import MultipleFileField
+
+# Samplesheets dependency
+# NOTE: Importing for generic Zip file helpers, move elsewhere?
+from samplesheets.io import SampleSheetIO, ARCHIVE_TYPES
+
+from isatemplates.models import (
+    CookiecutterISATemplate,
+    CookiecutterISAFile,
+    FILE_PREFIXES,
+)
+
+
+logger = logging.getLogger(__name__)
+
+
+# Local constants
+FILE_SKIP_MSG = 'Skipping unrecognized file in template archive: {file_name}'
+
+
+class ISATemplateForm(forms.ModelForm):
+    """Form for importing and updating a custom ISA-Tab template."""
+
+    @classmethod
+    def _get_files_from_zip(cls, zip_file):
+        """
+        Return template files from Zip archive.
+
+        :param zip_file: ZipFile object
+        :return: Dict
+        """
+        ret = {'json': None, 'files': {}}
+        for path in [n for n in zip_file.namelist() if not n.endswith('/')]:
+            file_name = path.split('/')[-1]
+            if file_name == 'cookiecutter.json':
+                with zip_file.open(str(path), 'r') as f:
+                    ret['json'] = json.load(f)
+            elif file_name[:2] in FILE_PREFIXES:
+                with zip_file.open(str(path), 'r') as f:
+                    ret['files'][file_name] = f.read().decode('utf-8')
+            else:
+                logger.warning(FILE_SKIP_MSG.format(file_name=file_name))
+        return ret
+
+    @classmethod
+    def _get_files_from_multi(cls, files):
+        """
+        Return template files from multi-file upload.
+
+        :param files: List
+        :return: Dict
+        """
+        ret = {'json': None, 'files': {}}
+        for file in files:
+            if file.name == 'cookiecutter.json':
+                ret['json'] = json.load(file)
+            elif file.name[:2] in FILE_PREFIXES:
+                ret['files'][file.name] = file.read().decode('utf-8')
+            else:
+                logger.warning(FILE_SKIP_MSG.format(file_name=file.name))
+        return ret
+
+    file_upload = MultipleFileField(
+        allow_empty_file=False,
+        help_text='Zip archive or JSON/text files for an ISA-Tab template',
+    )
+
+    class Meta:
+        model = CookiecutterISATemplate
+        fields = ['file_upload', 'description', 'name', 'active']
+
+    def __init__(self, current_user=None, *args, **kwargs):
+        super().__init__(*args, **kwargs)
+        self.current_user = current_user
+        self.isa_zip = None
+        self.fields['name'].required = False  # Will be auto-generated if empty
+
+    def clean(self):
+        self.cleaned_data = super().clean()
+        sheet_io = SampleSheetIO()
+
+        # Check file_upload
+        files = self.files.getlist('file_upload')
+        # Zip archive upload
+        if len(files) == 1:
+            file = self.cleaned_data.get('file_upload')[0]
+            try:
+                self.isa_zip = sheet_io.get_zip_file(file)
+            except OSError as ex:
+                self.add_error('file_upload', str(ex))
+                return self.cleaned_data
+        # Multi-file checks
+        else:
+            json_found = False
+            inv_found = False
+            study_found = False
+            for file in files:
+                if file.content_type in ARCHIVE_TYPES:
+                    self.add_error(
+                        'file_upload',
+                        'You can only upload one Zip archive at a time',
+                    )
+                    return self.cleaned_data
+                if not file.name.endswith('.json') and not file.name.endswith(
+                    '.txt'
+                ):
+                    self.add_error(
+                        'file_upload',
+                        'Only a Zip archive or template JSON/txt files allowed',
+                    )
+                    return self.cleaned_data
+                if file.name == 'cookiecutter.json':
+                    json_found = True
+                elif file.name.startswith('i_'):
+                    inv_found = True
+                elif file.name.startswith('s_'):
+                    study_found = True
+            if not json_found:
+                self.add_error(
+                    'file_upload', 'File cookiecutter.json not found'
+                )
+            if not inv_found:
+                self.add_error('file_upload', 'Investigation file not found')
+            if not study_found:
+                self.add_error('file_upload', 'Study file not found')
+
+        # Check description
+        # NOTE: Uniqueness within custom templates checked on model level
+        if settings.ISATEMPLATES_ENABLE_CUBI_TEMPLATES:
+            cubi_descs = [t.description.lower() for t in CUBI_TEMPLATES]
+            if self.cleaned_data['description'].lower() in cubi_descs:
+                self.add_error(
+                    'description',
+                    'Template with identical description found in CUBI '
+                    'templates',
+                )
+        return self.cleaned_data
+
+    @transaction.atomic
+    def save(self, *args, **kwargs):
+        # TODO: Add support for updating
+        if self.isa_zip:  # Zip archive
+            file_data = self._get_files_from_zip(self.isa_zip)
+        else:  # Multi-file
+            file_data = self._get_files_from_multi(
+                self.files.getlist('file_upload')
+            )
+        logger.debug('Saving ISA template..')
+        template = CookiecutterISATemplate.objects.create(
+            name=self.cleaned_data['name'],
+            description=self.cleaned_data['description'],
+            json_data=file_data['json'],
+            user=self.current_user,
+        )
+        logger.debug(
+            'Saved ISA template: {} ({})'.format(
+                template.name, template.sodar_uuid
+            )
+        )
+        for k, v in file_data['files'].items():
+            file = CookiecutterISAFile.objects.create(
+                template=template, file_name=k, content=v
+            )
+            logger.debug(
+                'Saved ISA template file: {} ({})'.format(k, file.sodar_uuid)
+            )
+        logger.debug('Template save OK')
+        return template

isatemplates/templates/isatemplates/list.html

@@ -54,7 +54,7 @@
 <div class="row sodar-subtitle-container bg-white sticky-top">
   <h2><i class="iconify" data-icon="mdi:file-table"></i> ISA-Tab Templates</h2>
   <a role="button" class="btn btn-primary ml-auto"
-     href="#"> {# TODO: Set URL #}
+     href="{% url 'isatemplates:create' %}">
     <i class="iconify" data-icon="mdi:upload"></i> Import Template
   </a>
 </div>
@@ -110,10 +110,6 @@ <h4>
                       <i class="iconify" data-icon="mdi:lead-pencil"></i>
                       Update Template
                     </a>
-                    <a class="dropdown-item" href="#"> {# TODO #}
-                      <i class="iconify" data-icon="mdi:refresh"></i>
-                      Replace Template
-                    </a>
                     <a class="dropdown-item" href="#"> {# TODO #}
                       <i class="iconify" data-icon="mdi:download"></i>
                       Export Template

isatemplates/templates/isatemplates/template_form.html

@@ -0,0 +1,38 @@
+{% extends 'projectroles/base.html' %}
+
+{% load rules %}
+{% load crispy_forms_filters %}
+
+{% block title %}
+  {% if object.pk %}Update{% else %}Import{% endif %} ISA-Tab Template
+{% endblock title %}
+
+{% block projectroles %}
+
+<div class="row sodar-subtitle-container">
+  <h2>{% if object.pk %}Update{% else %}Import{% endif %} ISA-Tab Template</h2>
+</div>
+
+<div class="container-fluid sodar-page-container">
+  <form method="post" enctype="multipart/form-data">
+    {% csrf_token %}
+    {{ form | crispy }}
+    <div class="row">
+      <div class="btn-group ml-auto" role="group">
+        <a role="button" class="btn btn-secondary"
+           href="{% url 'isatemplates:list' %}">
+          <i class="iconify" data-icon="mdi:arrow-left-circle"></i> Cancel
+        </a>
+        <button type="submit" class="btn btn-primary sodar-btn-submit-once">
+          {% if object.pk %}
+            <i class="iconify" data-icon="mdi:check-bold"></i> Update
+          {% else %}
+            <i class="iconify" data-icon="mdi:upload"></i> Import
+          {% endif %}
+        </button>
+      </div>
+    </div>
+  </form>
+</div>
+
+{% endblock projectroles %}