Merge branch 'release/v1.1.2'

.gitignore

@@ -1,10 +1,17 @@
 ## Custom
 *.xml
 *.bin
+*.gz
 migrations/
 tmp/
 log/
 static/
+#--- updates introduced for iSkyLIMS in submodules packaging ---
+virtualenv/
+iSkyLIMS/
+documents/
+manage.py
+
 
 # Byte-compiled / optimized / DLL files
 __pycache__/

.gitmodules

@@ -1,12 +1,12 @@
-[submodule "iSkyLIMS-wetlab"]
-	path = iSkyLIMS-wetlab
-	url = https://github.com/BU-ISCIII/iSkyLIMS-wetlab
-[submodule "iSkyLIMS-drylab"]
-	path = iSkyLIMS-drylab
-	url = https://github.com/BU-ISCIII/iSkyLIMS-drylab
-[submodule "django-utils"]
-	path = django-utils
-	url = https://github.com/BU-ISCIII/django-utils
+[submodule "iSkyLIMS_drylab"]
+	path = iSkyLIMS_drylab
+	url = [email protected]:BU-ISCIII/iSkyLIMS_drylab.git
+[submodule "iSkyLIMS_wetlab"]
+	path = iSkyLIMS_wetlab
+	url = [email protected]:BU-ISCIII/iSkyLIMS_wetlab.git
 [submodule "iSkyLIMS_home"]
 	path = iSkyLIMS_home
-	url = https://github.com/BU-ISCIII/iSkyLIMS_home
+	url = [email protected]:BU-ISCIII/iSkyLIMS_home.git
+[submodule "django_utils"]
+	path = django_utils
+	url = [email protected]:BU-ISCIII/django_utils.git

conf/admin_zinnia_wymeditor.py

@@ -0,0 +1,72 @@
+"""EntryAdmin for zinnia-wymeditor"""
+from django.forms import Media
+from django.conf.urls import url
+from django.contrib import admin
+#jlgarcia 19/04/2018. Change needed for django 2.0
+from django.urls import reverse
+#from django.core.urlresolvers import reverse
+from django.utils.translation import get_language
+from django.template.response import TemplateResponse
+from django.contrib.staticfiles.storage import staticfiles_storage
+
+from zinnia.models import Entry
+from zinnia.admin.entry import EntryAdmin
+from zinnia.settings import ENTRY_BASE_MODEL
+
+
+class EntryAdminWYMEditorMixin(object):
+    """
+    Mixin adding WYMeditor for editing Entry.content field.
+    """
+
+    def wymeditor(self, request):
+        """
+        View for serving the config of WYMEditor.
+        """
+        return TemplateResponse(
+            request, 'admin/zinnia/entry/wymeditor.js',
+            {'lang': get_language().split('-')[0]},
+            content_type='application/javascript')
+
+    def get_urls(self):
+        """
+        Overload the admin's urls for WYMEditor.
+        """
+        entry_admin_urls = super(EntryAdminWYMEditorMixin, self).get_urls()
+        urls = [
+            url(r'^wymeditor/$',
+                self.admin_site.admin_view(self.wymeditor),
+                name='zinnia_entry_wymeditor'),
+        ]
+        return urls + entry_admin_urls
+
+    def _media(self):
+        """
+        The medias needed to enhance the admin page.
+        """
+        def static_url(url):
+            return staticfiles_storage.url('zinnia_wymeditor/%s' % url)
+
+        media = super(EntryAdminWYMEditorMixin, self).media
+
+        media += Media(
+            js=(static_url('js/jquery.min.js'),
+                static_url('js/wymeditor/jquery.wymeditor.pack.js'),
+                static_url('js/wymeditor/plugins/hovertools/'
+                           'jquery.wymeditor.hovertools.js'),
+                reverse('admin:zinnia_entry_wymeditor')))
+        return media
+    media = property(_media)
+
+
+class EntryAdminWYMEditor(EntryAdminWYMEditorMixin,
+                          EntryAdmin):
+    """
+    Enrich the default EntryAdmin with WYMEditor.
+    """
+    pass
+
+
+if ENTRY_BASE_MODEL == 'zinnia.models_bases.entry.AbstractEntry':
+    admin.site.unregister(Entry)
+    admin.site.register(Entry, EntryAdminWYMEditor)

conf/index_file

@@ -0,0 +1 @@
+0000-AA

conf/pythonPackagesRequired.txt

@@ -0,0 +1,21 @@
+## 30/05/2018
+## encoding (1.0.0) --deprecated
+## mod-wsgi (4.5.17): package to be installed manually if Apache needed later
+
+asn1crypto
+bcrypt
+biopython
+cryptography
+Django
+django-blog-zinnia
+django-crispy-forms
+django-crontab
+django-js-asset
+django-mptt
+django-mptt-admin
+interop
+mysqlclient
+paramiko
+pysmb
+zinnia-wysiwyg-wymeditor
+

iSkyLIMS/settings.py → conf/settings.py

@@ -31,9 +31,9 @@
 # Application definition
 
 INSTALLED_APPS = [
-    'wetlab.apps.WetlabConfig',
-    'drylab.apps.DrylabConfig',
-    'utils.apps.UtilsConfig',
+    'iSkyLIMS_wetlab',
+    'iSkyLIMS_drylab',
+    'django_utils',
     'iSkyLIMS_home',
     'mptt',
     'crispy_forms',
@@ -162,8 +162,8 @@
 
 # Crontab settings
 CRONJOBS = [
-        ('2-59/5 * * * *', 'wetlab.cron.check_recorded_folder', '>> PATH2LOG'), # run every 5 min wit an offset of 2 minutes
-        ('*/5 * * * *', 'wetlab.cron.check_not_finish_run', '>> PATH2LOG') # run every 5 min
+        ('2-59/5 * * * *', 'iSkyLIMS_wetlab.cron.check_recorded_folder', '>> PATH2LOG'), # run every 5 min wit an offset of 2 minutes
+        ('*/5 * * * *', 'iSkyLIMS_wetlab.cron.check_not_finish_run', '>> PATH2LOG') # run every 5 min
 		]
 
 CRONTAB_COMMAND_SUFFIX = '2>&1'

conf/settings_zinnia.py

@@ -0,0 +1,96 @@
+"""Settings of Zinnia"""
+from django.conf import settings
+
+from mots_vides import stop_words
+
+
+PING_DIRECTORIES = getattr(settings, 'ZINNIA_PING_DIRECTORIES',
+                           ('https://django-blog-zinnia.com/xmlrpc/',))
+SAVE_PING_DIRECTORIES = getattr(settings, 'ZINNIA_SAVE_PING_DIRECTORIES',
+                                bool(PING_DIRECTORIES))
+SAVE_PING_EXTERNAL_URLS = getattr(settings, 'ZINNIA_PING_EXTERNAL_URLS', True)
+
+TRANSLATED_URLS = getattr(settings, 'ZINNIA_TRANSLATED_URLS', False)
+
+#'Zinnia' --> 'BU-ISCIII'
+COPYRIGHT = getattr(settings, 'ZINNIA_COPYRIGHT', 'BU-ISCIII')
+
+# 10 ---> 1 entry per page
+PAGINATION = getattr(settings, 'ZINNIA_PAGINATION', 1)
+ALLOW_EMPTY = getattr(settings, 'ZINNIA_ALLOW_EMPTY', True)
+ALLOW_FUTURE = getattr(settings, 'ZINNIA_ALLOW_FUTURE', True)
+
+ENTRY_BASE_MODEL = getattr(settings, 'ZINNIA_ENTRY_BASE_MODEL',
+                           'zinnia.models_bases.entry.AbstractEntry')
+
+ENTRY_DETAIL_TEMPLATES = getattr(
+    settings, 'ZINNIA_ENTRY_DETAIL_TEMPLATES', [])
+ENTRY_CONTENT_TEMPLATES = getattr(
+    settings, 'ZINNIA_ENTRY_CONTENT_TEMPLATES', [])
+ENTRY_LOOP_TEMPLATES = getattr(
+    settings, 'ZINNIA_ENTRY_LOOP_TEMPLATES', {})
+ENTRY_LOOP_TEMPLATES.setdefault('default', {})
+
+MARKUP_LANGUAGE = getattr(settings, 'ZINNIA_MARKUP_LANGUAGE', 'html')
+
+MARKDOWN_EXTENSIONS = getattr(settings, 'ZINNIA_MARKDOWN_EXTENSIONS', [])
+
+RESTRUCTUREDTEXT_SETTINGS = getattr(
+    settings, 'ZINNIA_RESTRUCTUREDTEXT_SETTINGS', {})
+
+PREVIEW_SPLITTERS = getattr(settings, 'ZINNIA_PREVIEW_SPLITTERS',
+                            ['<!-- more -->', '<!--more-->'])
+
+PREVIEW_MAX_WORDS = getattr(settings, 'ZINNIA_PREVIEW_MAX_WORDS', 55)
+
+PREVIEW_MORE_STRING = getattr(settings, 'ZINNIA_PREVIEW_MORE_STRING', ' ...')
+
+AUTO_CLOSE_PINGBACKS_AFTER = getattr(
+    settings, 'ZINNIA_AUTO_CLOSE_PINGBACKS_AFTER', None)
+
+AUTO_CLOSE_TRACKBACKS_AFTER = getattr(
+    settings, 'ZINNIA_AUTO_CLOSE_TRACKBACKS_AFTER', None)
+
+AUTO_CLOSE_COMMENTS_AFTER = getattr(
+    settings, 'ZINNIA_AUTO_CLOSE_COMMENTS_AFTER', None)
+
+AUTO_MODERATE_COMMENTS = getattr(settings, 'ZINNIA_AUTO_MODERATE_COMMENTS',
+                                 False)
+
+MAIL_COMMENT_REPLY = getattr(settings, 'ZINNIA_MAIL_COMMENT_REPLY', False)
+
+MAIL_COMMENT_AUTHORS = getattr(settings, 'ZINNIA_MAIL_COMMENT_AUTHORS', True)
+
+MAIL_COMMENT_NOTIFICATION_RECIPIENTS = getattr(
+    settings, 'ZINNIA_MAIL_COMMENT_NOTIFICATION_RECIPIENTS',
+    [manager_tuple[1] for manager_tuple in settings.MANAGERS])
+
+COMMENT_MIN_WORDS = getattr(settings, 'ZINNIA_COMMENT_MIN_WORDS', 4)
+
+COMMENT_FLAG_USER_ID = getattr(settings, 'ZINNIA_COMMENT_FLAG_USER_ID', 1)
+
+UPLOAD_TO = getattr(settings, 'ZINNIA_UPLOAD_TO', 'uploads/zinnia')
+
+PROTOCOL = getattr(settings, 'ZINNIA_PROTOCOL', 'http')
+
+FEEDS_FORMAT = getattr(settings, 'ZINNIA_FEEDS_FORMAT', 'rss')
+FEEDS_MAX_ITEMS = getattr(settings, 'ZINNIA_FEEDS_MAX_ITEMS', 15)
+
+PINGBACK_CONTENT_LENGTH = getattr(settings,
+                                  'ZINNIA_PINGBACK_CONTENT_LENGTH', 300)
+
+SEARCH_FIELDS = getattr(settings, 'ZINNIA_SEARCH_FIELDS',
+                        ['title', 'lead', 'content',
+                         'excerpt', 'image_caption', 'tags'])
+
+COMPARISON_FIELDS = getattr(settings, 'ZINNIA_COMPARISON_FIELDS',
+                            ['title', 'lead', 'content',
+                             'excerpt', 'image_caption', 'tags'])
+
+SPAM_CHECKER_BACKENDS = getattr(settings, 'ZINNIA_SPAM_CHECKER_BACKENDS',
+                                [])
+
+URL_SHORTENER_BACKEND = getattr(settings, 'ZINNIA_URL_SHORTENER_BACKEND',
+                                'zinnia.url_shortener.backends.default')
+
+STOP_WORDS = stop_words(settings.LANGUAGE_CODE.split('-')[0])

iSkyLIMS/urls.py → conf/urls.py

@@ -44,9 +44,9 @@
     path('faqs', LoginView.as_view(template_name='iSkyLIMS_home/faqs.html'), name="faqs"),
     path('contact', LoginView.as_view(template_name='iSkyLIMS_home/contact.html'), name="contact"),
     path('admin/', admin.site.urls),
-    path('wetlab/', include('wetlab.urls')),
-    path('drylab/',include('drylab.urls')),
-    path('utils/',include('utils.urls')),
+    path('iSkyLIMS_wetlab/', include('iSkyLIMS_wetlab.urls')),
+    path('iSkyLIMS_drylab/',include('iSkyLIMS_drylab.urls')),
+    path('django_utils/',include('django_utils.urls')),
     path('accounts/', include('django.contrib.auth.urls')),
     path('tutorials/', include('zinnia.urls')),
 ]