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 _refresh_root(self):
if "/" not in self.slug:
try:
self.root = URLPath.get_by_path("/")
except:
if self.slug == "root":
self.root = self._create_root()
else:
raise ValueError("No root created. Make sure root.md is processed first")
else:
try:
root_name = "/".join(self.slug.split("/")[:-1])
self.root = URLPath.get_by_path(root_name)
except:
self.root = None
def initialize_documentation(root):
try:
URLPath.get_by_path("use")
except:
URLPath.create_urlpath(root,
slug="use",
title="Using QUOREM",
content=get_content_from_file(
"quorem/static/markdown/docs/use.md"))
try:
URLPath.get_by_path("develop")
except:
URLPath.create_urlpath(root,
slug="develop",
title="Developing QUOREM",
content=get_content_from_file(
"quorem/static/markdown/docs/develop.md"))
try:
URLPath.get_by_path("deploy")
except:
URLPath.create_urlpath(root,
slug="deploy",
title="Deploying QUOREM",
content=get_content_from_file(
"quorem/static/markdown/docs/deploy.md"))
def get_root(self):
try:
base_root = URLPath.get_by_path(path="")
except NoRootURL:
if (self.slug == "root") and (self.prefix == "/"):
root = URLPath.create_root(title="QUOREM Wiki",
content=self.content)
return root
else:
raise ValueError(
"No root created for prefix '%s'. Make sure root.md is processed first"
% (self.prefix, ))
try:
root = URLPath.get_by_path(self.prefix)
except URLPath.DoesNotExist:
if (self.slug == "root") and (self.prefix != "/"):
root = URLPath.create_urlpath(base_root,
slug=self.prefix,
title=self.title,
content=self.content)
else:
raise ValueError("No root created for prefix '%s'." %
(self.prefix, ))
return root
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 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)
