def create_root(cls, site=None, title="Root", request=None, **kwargs):
if not site: site = Site.objects.get_current()
root_nodes = cls.objects.root_nodes().filter(site=site)
if not root_nodes:
# (get_or_create does not work for MPTT models??)
article = Article()
revision = ArticleRevision(title=title, **kwargs)
if request: revision.set_from_request(request)
article.add_revision(revision, save=True)
article.save()
root = cls.objects.create(site=site, article=article)
article.add_object_relation(root)
else:
root = root_nodes[0]
return root
def create_root(cls, site=None, title="Root", request=None, **kwargs):
if not site: site = Site.objects.get_current()
root_nodes = cls.objects.root_nodes().filter(site=site)
if not root_nodes:
# (get_or_create does not work for MPTT models??)
article = Article()
revision = ArticleRevision(title=title, **kwargs)
if request: revision.set_from_request(request)
article.add_revision(revision, save=True)
article.save()
root = cls.objects.create(site=site, article=article)
article.add_object_relation(root)
else:
root = root_nodes[0]
return root
def get_context_data(self, **kwargs):
context = super(GroupDescriptionDetailView,
self).get_context_data(**kwargs)
workgroup = context['workgroup']
# First be sure that the home Wiki article already exists
try:
home_article = Article.get_for_object(workgroup)
except ArticleForObject.DoesNotExist:
return redirect('workgroup-detail', slug=workgroup.slug)
# now check that the description article exists
try:
desc_article = Article.get_for_object(home_article)
except ArticleForObject.DoesNotExist:
desc_article = Article.objects.create()
desc_article.add_object_relation(home_article)
revision = ArticleRevision(title="description of %s" %
workgroup.name,
content='')
desc_article.add_revision(revision)
context.update({
'wiki_article': desc_article,
})
return context
def get_context_data(self, **kwargs):
"""
Adds the member of the associated ML if there's one
"""
context = super(GroupDetailView, self).get_context_data(**kwargs)
workgroup = context['workgroup']
# Look up mailing list members
context.update(lookup_ml_membership(workgroup))
# Wiki
try:
article = Article.get_for_object(workgroup)
except ArticleForObject.DoesNotExist:
article = Article.objects.create()
article.add_object_relation(workgroup)
revision = ArticleRevision(title=workgroup.name, content='')
article.add_revision(revision)
context['wiki_article'] = article
context['group_projects'] = workgroup.projects.prefetch_related(
'locations').all().order_by('?')
return context
def create_urlpath(
cls,
parent,
slug,
site=None,
title="Root",
article_kwargs={},
request=None,
article_w_permissions=None,
**revision_kwargs):
"""
Utility function:
Creates a new urlpath with an article and a new revision for the
article
:returns: A new URLPath instance
"""
if not site:
site = Site.objects.get_current()
article = Article(**article_kwargs)
article.add_revision(ArticleRevision(title=title, **revision_kwargs),
save=True)
article.save()
newpath = cls.objects.create(
site=site,
parent=parent,
slug=slug,
article=article)
article.add_object_relation(newpath)
return newpath
def get_lost_and_found():
if ns.lost_and_found:
return ns.lost_and_found
try:
ns.lost_and_found = URLPath.objects.get(
slug=settings.LOST_AND_FOUND_SLUG,
parent=URLPath.root(),
site=site)
except URLPath.DoesNotExist:
article = Article(group_read=True,
group_write=False,
other_read=False,
other_write=False)
article.add_revision(
ArticleRevision(
content=_(
'Articles who lost their parents\n'
'===============================\n\n'
'The children of this article have had their parents deleted. You should probably find a new home for them.'),
title=_("Lost and found")))
ns.lost_and_found = URLPath.objects.create(
slug=settings.LOST_AND_FOUND_SLUG,
parent=URLPath.root(),
site=site,
article=article)
article.add_object_relation(ns.lost_and_found)
return ns.lost_and_found
def on_article_delete(instance, *args, **kwargs):
# If an article is deleted, then throw out its URLPaths
# But move all descendants to a lost-and-found node.
site = get_current_site(get_current_request())
# Get the Lost-and-found path or create a new one
try:
lost_and_found = URLPath.objects.get(slug=settings.LOST_AND_FOUND_SLUG,
parent=URLPath.root(),
site=site)
except URLPath.DoesNotExist:
article = Article(group_read = True,
group_write = False,
other_read = False,
other_write = False)
article.add_revision(ArticleRevision(
content=_(u'Articles who lost their parents\n'
'===============================\n\n'
'The children of this article have had their parents deleted. You should probably find a new home for them.'),
title=_(u"Lost and found")))
lost_and_found = URLPath.objects.create(slug=settings.LOST_AND_FOUND_SLUG,
parent=URLPath.root(),
site=site,
article=article)
article.add_object_relation(lost_and_found)
for urlpath in URLPath.objects.filter(articles__article=instance, site=site):
# Delete the children
for child in urlpath.get_children():
child.move_to(lost_and_found)
# ...and finally delete the path itself
# TODO: This should be unnecessary because of URLPath.article(...ondelete=models.CASCADE)
urlpath.delete()
def initialize_wiki():
try:
root = URLPath.root()
except NoRootURL:
print("Root URL not found, creating...")
root = URLPath.create_root(title="QUOREM Wiki",
content=get_content_from_file(
"quorem/static/markdown/docs/root.md"))
article_revision = ArticleRevision(
title=root.article.current_revision.title,
content=get_content_from_file("quorem/static/markdown/docs/root.md"))
root.article.add_revision(article_revision)
try:
investigation = URLPath.get_by_path("investigation")
except URLPath.DoesNotExist:
print("Investigation page not found, creating...")
URLPath.create_urlpath(root,
slug="investigation",
title="List of Investigations",
content="""This page lists the
investigations that are present in your QUOREM database. You may
edit anything on this page, except the Automated Report
section.\r\n\r\n""")
try:
protocol = URLPath.get_by_path("protocol")
except URLPath.DoesNotExist:
print("Protocol page not found, creating...")
URLPath.create_urlpath(root,
slug="protocol",
title="List of Protocols",
content="""This page lists the
protocols that are present in your QUOREM database. You may
edit anything on this page, except the Automated Report
section.\r\n\r\n""")
try:
pipeline = URLPath.get_by_path("pipeline")
except URLPath.DoesNotExist:
print("Pipeline page not found, creating...")
URLPath.create_urlpath(root,
slug="pipeline",
title="List of Pipelines",
content="""This page lists the
pipelines that are present in your QUOREM database. You may
edit anything on this page, except the Automated Report
section.\r\n\r\n""")
try:
sample = URLPath.get_by_path("sample")
except URLPath.DoesNotExist:
print("Sample page not found, creating...")
URLPath.create_urlpath(
root,
slug="sample",
title="List of Samples",
content=
"This page lists the samples that are present in your QUOREM database. You may edit anything on this page, except the Automated Report section.\r\n\r\n"
)
initialize_documentation(root)
def refresh_automated_report(slug, pk=None):
Investigation = apps.get_model('db.Investigation')
Sample = apps.get_model('db.Sample')
BiologicalReplicate = apps.get_model('db.BiologicalReplicate')
BiologicalReplicateProtocol = apps.get_model(
'db.BiologicalReplicateProtocol')
ComputationalPipeline = apps.get_model('db.ComputationalPipeline')
slug_to_model = {'investigation': Investigation, 'sample': Sample}
if pk is None:
article = URLPath.get_by_path(slug).article
else:
try:
article = URLPath.get_by_path("%s/%d" % (slug, pk)).article
except URLPath.DoesNotExist:
try:
obj = slug_to_model[slug].objects.get(pk=pk)
except slug_to_model[slug].DoesNotExist:
raise ValueError("No such pk found, no wiki entry to update")
try:
root = URLPath.get_by_path(slug)
except URLPath.DoesNotExist:
raise ValueError(
"No such slug found, is your wiki initialized?")
print("Creating new article")
try:
slug_to_model[slug]._meta.get_field("name")
title = obj.name
except:
title = "%s %d" % (slug, pk)
article = URLPath.create_urlpath(root,
slug="%d" % (pk,),
title=title,
content="This page has been automatically" \
"generated. You may edit at will").article
current_content = article.current_revision.content
md = markdown.Markdown()
inv_html = md.convert(current_content)
new_content = ""
skip_until_h1 = False
added = False
for line in md.lines:
if skip_until_h1 & (not line.startswith("# ")):
continue
elif skip_until_h1 & line.startswith("# "):
skip_until_h1 = False
if line == '# Automated Report':
new_content += get_wiki_report(slug, pk=pk)
skip_until_h1 = True
added = True
else:
new_content += line + "\r\n"
if not added:
new_content += get_wiki_report(slug, pk=pk)
article_revision = ArticleRevision(title=article.current_revision.title,
content=new_content)
article.add_revision(article_revision)
def create_article(cls, parent, slug, site=None, title="Root", article_kwargs={}, **kwargs):
"""Utility function:
Create a new urlpath with an article and a new revision for the article"""
if not site: site = get_current_site(get_current_request())
article = Article(**article_kwargs)
article.add_revision(ArticleRevision(title=title, **kwargs),
save=True)
article.save()
newpath = cls.objects.create(site=site, parent=parent, slug=slug, article=article)
article.add_object_relation(newpath)
return newpath
def update_wiki(self):
if (self.slug == "root"):
return #Already made in get_root() if not made
try:
wiki_page = URLPath.get_by_path(self.prefix + "/" + self.slug)
#Create a new revision and update with the template content
article = wiki_page.article
article_revision = ArticleRevision(
title=article.current_revision.title, content=self.content)
article.add_revision(article_revision)
except URLPath.DoesNotExist:
print("Creating wiki page for slug %s prefix %s" %
(self.slug, self.prefix))
wiki_page = URLPath.create_urlpath(self.root,
slug=self.slug,
title=self.title,
content=self.content)
def create_article(bustopic,title="Root", article_kwargs={}, content="",user_message="",request=None):
"""Utility function:
Create a new urlpath with an article and a new revision for the article"""
article = Article(**article_kwargs)
ar = ArticleRevision()
ar.content = content
ar.user_message = user_message
ar.deleted = False
if request:
ar.set_from_request(request)
else:
ar.ip_address = None
ar.user = get_default_user()
article.add_revision(ar, save=True)
article.save()
bustopic.article=article
bustopic.save()
return ar
def update_wiki(self):
try:
print("Retrieving slug %s" % (self.slug,))
wiki_page = URLPath.get_by_path(self.slug)
#Create a new revision and update with the template content
article = wiki_page.article
article_revision = ArticleRevision(title=article.current_revision.title,
content=self.content)
article.add_revision(article_revision)
except URLPath.DoesNotExist:
print("Creating a new article")
if self.root is None:
self._refresh_root()
print("Using root %s" % (self.root,))
print("Pushing to slug %s"% (self.slug,))
base_slug = self.slug.split("/")[-1]
wiki_page = URLPath.create_urlpath(self.root, slug=base_slug,
title=self.title,
content=self.content)
def import_page(self, api, site, page, current_site, url_root,
user_matching, replace_existing):
import pypandoc
# Filter titles, to avoid stranges charaters.
title = only_printable(page.title)
urltitle = slugify(only_printable(urllib.unquote(page.urltitle))[:50])
added = 1
while urltitle in self.articles_worked_on:
title = only_printable(page.title) + " " + str(added)
urltitle = only_printable(
slugify((urllib.unquote(page.urltitle))[:47] + " " +
str(added)))
added += 1
self.articles_worked_on.append(urltitle)
print("Working on %s (%s)" % (title, urltitle))
# Check if the URL path already exists
try:
urlp = URLPath.objects.get(slug=urltitle)
self.matching_old_link_new_link[
page.title] = urlp.article.get_absolute_url()
if not replace_existing:
print("\tAlready existing, skipping...")
return
print("\tDestorying old version of the article")
urlp.article.delete()
except URLPath.DoesNotExist:
pass
# Create article
article = Article()
for history_page in page.getHistory()[-2:][::-1]:
try:
if history_page['user'] in user_matching:
user = get_user_model().objects.get(
pk=user_matching[history_page['user']])
else:
user = get_user_model().objects.get(
username=history_page['user'])
except get_user_model().DoesNotExist:
print(
"\tCannot found user with username=%s. Use --user-matching \"%s:<user_pk>\" to manualy set it"
% (
history_page['user'],
history_page['user'],
))
user = None
article_revision = ArticleRevision()
article_revision.content = pypandoc.convert(
history_page['*'], 'md', 'mediawiki')
article_revision.title = title
article_revision.user = user
article_revision.owner = user
article.add_revision(article_revision, save=True)
article_revision.created = history_page['timestamp']
article_revision.save()
# Updated lastest content WITH expended templates
# TODO ? Do that for history as well ?
article_revision.content = pypandoc.convert(
striptags(page.getWikiText(True, True).decode('utf-8')).replace(
'__NOEDITSECTION__', '').replace('__NOTOC__', ''), 'md',
'mediawiki')
article_revision.save()
article.save()
upath = URLPath.objects.create(site=current_site,
parent=url_root,
slug=urltitle,
article=article)
article.add_object_relation(upath)
self.matching_old_link_new_link[
page.title] = upath.article.get_absolute_url()
self.articles_imported.append((article, article_revision))
def create_revision(bustopic, title, content, summary,request):
revision = ArticleRevision()
revision.inherit_predecessor(bustopic.article)
if not title:
revision.title=bustopic.article.current_revision.title
else:
revision.title = title
revision.content = content
revision.user_message = summary
revision.deleted = False
revision.set_from_request(request)
revision.save()
return revision
def import_page(self, api, site, page, current_site, url_root, user_matching, replace_existing):
import pypandoc
# Filter titles, to avoid stranges charaters.
title = only_printable(page.title)
urltitle = slugify(only_printable(urllib.unquote(page.urltitle))[:50])
added = 1
while urltitle in self.articles_worked_on:
title = only_printable(page.title) + " " + str(added)
urltitle = only_printable(slugify((urllib.unquote(page.urltitle))[:47] + " " + str(added)))
added += 1
self.articles_worked_on.append(urltitle)
print "Working on %s (%s)" % (title, urltitle)
# Check if the URL path already exists
try:
urlp = URLPath.objects.get(slug=urltitle)
self.matching_old_link_new_link[page.title] = urlp.article.get_absolute_url()
if not replace_existing:
print "\tAlready existing, skipping..."
return
print "\tDestorying old version of the article"
urlp.article.delete()
except URLPath.DoesNotExist:
pass
# Create article
article = Article()
for history_page in page.getHistory()[-2:][::-1]:
try:
if history_page['user'] in user_matching:
user = get_user_model().objects.get(pk=user_matching[history_page['user']])
else:
user = get_user_model().objects.get(username=history_page['user'])
except get_user_model().DoesNotExist:
print "\tCannot found user with username=%s. Use --user-matching \"%s:<user_pk>\" to manualy set it" % (history_page['user'], history_page['user'], )
user = None
article_revision = ArticleRevision()
article_revision.content = pypandoc.convert(history_page['*'], 'md', 'mediawiki')
article_revision.title = title
article_revision.user = user
article_revision.owner = user
article.add_revision(article_revision, save=True)
article_revision.created = history_page['timestamp']
article_revision.save()
# Updated lastest content WITH expended templates
# TODO ? Do that for history as well ?
article_revision.content = pypandoc.convert(striptags(page.getWikiText(True, True).decode('utf-8')).replace('__NOEDITSECTION__', '').replace('__NOTOC__', ''), 'md', 'mediawiki')
article_revision.save()
article.save()
upath = URLPath.objects.create(site=current_site, parent=url_root, slug=urltitle, article=article)
article.add_object_relation(upath)
self.matching_old_link_new_link[page.title] = upath.article.get_absolute_url()
self.articles_imported.append((article, article_revision))
def import_page(
self,
api,
site,
page,
current_site,
url_root,
user_matching,
replace_existing,
):
from wikitools.pagelist import listFromQuery
# Filter titles, to avoid stranges charaters.
title = page.title
urltitle = title
urltitle = urltitle.replace("ø", "o")
urltitle = urltitle.replace("æ", "ae")
urltitle = urltitle.replace("å", "a")
urltitle = urltitle.replace("Ø", "O")
urltitle = urltitle.replace("Æ", "AE")
urltitle = urltitle.replace("Å", "A")
urltitle = only_printable(urltitle)
urltitle = slugify(only_printable(urllib.parse.unquote(urltitle))[:50])
added = 1
while urltitle in self.articles_worked_on:
title = only_printable("{} {}".format(page.title, added))
urltitle = slugify(
"{} {}".format(only_printable(urllib.parse.unquote(page.urltitle))[:47], added)
)
added += 1
self.articles_worked_on.append(urltitle)
print("Working on {} ({})".format(title, urltitle))
print(url_root)
print(urltitle)
print()
# Check if the URL path already exists
try:
urlp = URLPath.objects.get(slug=urltitle)
self.matching_old_link_new_link[
page.title] = urlp.article.get_absolute_url()
if not replace_existing:
print("\tAlready existing, skipping...")
return
print("\tDestorying old version of the article")
urlp.article.delete()
except URLPath.DoesNotExist:
pass
# Create article
article = Article()
history_page = page.getHistory()[0]
try:
if history_page['user'] in user_matching:
user = get_user_model().objects.get(
pk=user_matching[
history_page['user']])
else:
user = get_user_model().objects.get(
username=history_page['user'])
except get_user_model().DoesNotExist:
user = None
except Exception:
print("Couldn't find user. Something is weird.")
article_revision = ArticleRevision()
article_revision.content = refactor(page.getWikiText())
article_revision.title = title
article_revision.user = user
article_revision.owner = user
article_revision.content = re.sub("\[\[.*(Category|Kategori).*\]\]\n", "", article_revision.content)
article.add_revision(article_revision, save=True)
article_revision.created = history_page['timestamp']
article_revision.save()
# Updated lastest content WITH expended templates
# TODO ? Do that for history as well ?
article_revision.save()
article.save()
upath = URLPath.objects.create(
site=current_site,
parent=url_root,
slug=urltitle,
article=article)
article.add_object_relation(upath)
self.matching_old_link_new_link[
page.title] = upath.article.get_absolute_url()
self.articles_imported.append((article, article_revision))
def import_page(
self,
api,
site,
page,
current_site,
url_root,
user_matching,
replace_existing,
):
from wikitools.pagelist import listFromQuery
# Filter titles, to avoid stranges charaters.
title = page.title
urltitle = title
urltitle = urltitle.replace("ø", "o")
urltitle = urltitle.replace("æ", "ae")
urltitle = urltitle.replace("å", "a")
urltitle = urltitle.replace("Ø", "O")
urltitle = urltitle.replace("Æ", "AE")
urltitle = urltitle.replace("Å", "A")
urltitle = only_printable(urltitle)
urltitle = slugify(only_printable(urllib.parse.unquote(urltitle))[:50])
added = 1
while urltitle in self.articles_worked_on:
title = only_printable("{} {}".format(page.title, added))
urltitle = slugify("{} {}".format(
only_printable(urllib.parse.unquote(page.urltitle))[:47],
added))
added += 1
self.articles_worked_on.append(urltitle)
print("Working on {} ({})".format(title, urltitle))
print(url_root)
print(urltitle)
print()
# Check if the URL path already exists
try:
urlp = URLPath.objects.get(slug=urltitle)
self.matching_old_link_new_link[
page.title] = urlp.article.get_absolute_url()
if not replace_existing:
print("\tAlready existing, skipping...")
return
print("\tDestorying old version of the article")
urlp.article.delete()
except URLPath.DoesNotExist:
pass
# Create article
article = Article()
history_page = page.getHistory()[0]
try:
if history_page['user'] in user_matching:
user = get_user_model().objects.get(
pk=user_matching[history_page['user']])
else:
user = get_user_model().objects.get(
username=history_page['user'])
except get_user_model().DoesNotExist:
user = None
except Exception:
print("Couldn't find user. Something is weird.")
article_revision = ArticleRevision()
article_revision.content = refactor(page.getWikiText())
article_revision.title = title
article_revision.user = user
article_revision.owner = user
article_revision.content = re.sub("\[\[.*(Category|Kategori).*\]\]\n",
"", article_revision.content)
article.add_revision(article_revision, save=True)
article_revision.created = history_page['timestamp']
article_revision.save()
# Updated lastest content WITH expended templates
# TODO ? Do that for history as well ?
article_revision.save()
article.save()
upath = URLPath.objects.create(site=current_site,
parent=url_root,
slug=urltitle,
article=article)
article.add_object_relation(upath)
self.matching_old_link_new_link[
page.title] = upath.article.get_absolute_url()
self.articles_imported.append((article, article_revision))