def get(self, request, rid, rtype_src, rtype_dst):
resource_class = {
Resource.RESOURCE_TYPES.STRUCTURE: Structure,
Resource.RESOURCE_TYPES.ASSEMBLY: Assembly,
Resource.RESOURCE_TYPES.SAMPLE: Sample,
Resource.RESOURCE_TYPES.EXPRESSION: Expression,
Resource.RESOURCE_TYPES.PUBLICATION: Publication,
Resource.RESOURCE_TYPES.TOOL: Tool,
Resource.RESOURCE_TYPES.READS: ReadsArchive,
Resource.RESOURCE_TYPES.ORGANIZATION: Organization,
Resource.RESOURCE_TYPES.PERSON: Person,
}
level = int(self.request.GET.get("level", "1"))
neighborhood_ids = GraphRepo.get_neighborhood_ids(rid,
rtype_src,
rtype_dst,
level=1)
if level > 1:
neighborhood_ids += GraphRepo.get_neighborhood_ids(rid,
rtype_src,
rtype_dst,
level=level)
obj = resource_class[Resource.name2code[
rtype_src.upper()]].objects.get(id=rid)
repo = resource_class[Resource.name2code[rtype_dst.upper()]]
return render(
request, self.template_name, {
"rtype_dst": rtype_dst,
"obj": obj,
"results": repo.objects.filter(id__in=neighborhood_ids)
})
def publication(request, pk):
publication = Publication.objects.prefetch_related(
"targets__target", "affiliations__author",
"affiliations__organizations").get(id=pk)
orgs = publication.affiliation_names()
org_map = {}
authors = []
for aff in publication.affiliations.all():
author = aff.author
author.affs = " ".join([
"(" + str(orgs.index(org.name) + 1) + ")"
for org in aff.organizations.all()
])
if author not in authors:
authors.append(author)
for org in aff.organizations.all():
org_map[org.name] = org
graph, related_resources = GraphRepo.get_neighborhood(pk,
"Publication",
level=1)
return render(
request, 'resources/publication.html', {
"graph": graph,
"related_resources": related_resources,
"pk": pk,
"rtype_src": "Publication",
"level": 1,
"publication": publication,
"authors": authors,
"org_map": org_map,
"sidebarleft": 1
})
def reads(request, pk):
sra = ReadsArchive.objects.prefetch_related("external_ids").get(id=pk)
graph, related_resources = GraphRepo.get_neighborhood(pk, "Reads", level=1)
external_ids = [
x.identifier for x in sra.external_ids.all() if x.type == "accession"
]
external_url = ""
if external_ids:
external_url = ("https://www.ncbi.nlm.nih.gov/" +
NCBISearch.rtype2ncbb[ReadsArchive.TYPE] + "/" +
external_ids[0] + "[accn]")
collaboration = request.user.get_collaboration(
sra) if request.user.is_authenticated else None
params = {
"readsarchive": sra,
"sidebarleft": 1,
"level": 1,
"external_url": external_url,
"graph": graph,
"related_resources": related_resources,
"pk": pk,
"rtype_src": "Reads",
"collaboration": collaboration
}
return render(request, 'resources/readsarchive.html', params)
def bioproject(request, pk):
bioproject = BioProject.objects.get(id=pk)
graph, related_resources = GraphRepo.get_neighborhood(
bioproject.id, "BioProject", 1)
external_ids = [
x.identifier for x in bioproject.external_ids.all()
if x.type == "accession"
]
external_url = ""
if external_ids:
external_url = ("https://www.ncbi.nlm.nih.gov/" +
NCBISearch.rtype2ncbb[BioProject.TYPE] + "/" +
external_ids[0])
collaboration = request.user.get_collaboration(
bioproject) if request.user.is_authenticated else None
params = {
"external_url": external_url,
"bioproject": bioproject,
"graph": graph,
"related_resources": related_resources,
"sidebarleft": 1,
"collaboration": collaboration
}
return render(request, 'resources/bioproject.html', params)
def organization(request, pk):
org = Organization.objects.get(id=pk)
graph, related_resources = GraphRepo.get_neighborhood(pk, "Organization",level=2)
return render(request, 'resources/organization.html',
{"graph": graph, "related_resources": related_resources, "pk": pk,
"rtype_src":"Organization","organization": org, "sidebarleft": 1, })
def expression(request, pk):
expression = Expression.objects.get(id=pk)
graph, related_resources = GraphRepo.get_neighborhood(pk,
"Expression",
level=2)
external_ids = [
x.identifier for x in expression.external_ids.all()
if x.type == "accession"
]
external_url = ""
if external_ids:
external_url = ("https://www.ncbi.nlm.nih.gov/" +
NCBISearch.rtype2ncbb[Expression.TYPE] + "/" +
external_ids[0])
collaboration = request.user.get_collaboration(
expression) if request.user.is_authenticated else None
params = {
"expression": expression,
"sidebarleft": 1,
"external_url": external_url,
"collaboration": collaboration,
"graph": graph,
"related_resources": related_resources,
"pk": pk,
"rtype_src": "Expression"
}
return render(request, 'resources/expression.html', params)
def structure(request, pk):
pdb = Structure.objects.get(id=pk)
graph, related_resources = GraphRepo.get_neighborhood(pk,
"Structure",
level=1)
external_url = "https://www.rcsb.org/structure/" + pdb.name
loaded = True
job = LoadPDBJob.objects.filter(pdb=pdb.name)
if job.exists():
job = job.order_by("-id")[0]
if job.status != Job.STATUS.FINISHED:
loaded = False
collaboration = request.user.get_collaboration(
pdb) if request.user.is_authenticated else None
params = {
"external_url": external_url,
"loaded": loaded,
"collaboration": collaboration,
"graph": graph,
"related_resources": related_resources,
"pk": pk,
"rtype_src": "Structure",
"pdb": pdb,
"sidebarleft": 1,
"level": 1
}
return render(request, 'resources/structure.html', params)
def barcode(request, pk):
barcode = Barcode.objects.get(id=pk)
graph, related_resources = GraphRepo.get_neighborhood(pk, "Barcode",level=1)
external_url ="http://www.boldsystems.org/index.php/Public_RecordView?processid=" + barcode.name
return render(request, 'resources/barcode.html', { "external_url":external_url,
"graph": graph, "related_resources": related_resources, "pk": pk, "rtype_src": "Barcode",
"barcode": barcode, "sidebarleft": 1, })
def person(request, pk):
person = Person.objects.get(id=pk)
graph, related_resources = GraphRepo.get_neighborhood(pk, "Person")
return render(
request, 'resources/person.html', {
"pk": person.id,
"related_resources": related_resources,
"person": person,
"graph": graph,
"sidebarleft": 1,
})
def tool(request, pk):
relate_with = None
if "relate_with" in request.session:
relate_with = Resource.objects.get(id=int(request.session["relate_with"]))
tool = Tool.objects.get(id=pk)
graph, related_resources = GraphRepo.get_neighborhood(pk, "Tool", level=1)
collaboration = request.user.get_collaboration(tool) if request.user.is_authenticated else None
params = {"external_url": tool.url, "collaboration": collaboration,
"graph": graph, "related_resources": related_resources, "pk": pk,
"rtype_src": "Tool",
"tool": tool, "sidebarleft": 1, "relate_with": relate_with}
return render(request, 'resources/tool.html', params)
def sample_view(request, pk):
sample = Sample.objects.get(id=pk)
graph, related_resources = GraphRepo.get_neighborhood(pk,
"Sample",
level=2)
return render(
request, 'resources/sample.html', {
"graph": graph,
"related_resources": related_resources,
"pk": pk,
"rtype_src": "Sample",
"sample": sample,
"sidebarleft": 1,
"level": 1
})
def UserResourcesView(request, username=""):
person = request.user.person
collaborations = None
graph = None
if person:
collaborations = set(
Collaboration.objects.prefetch_related("resource").filter(
person=person))
for c in collaborations:
c.resource.tname = Resource.RESOURCE_TYPES[c.resource.type]
if person:
graph, _ = GraphRepo.get_neighborhood(person.id, "Person", 1)
else:
graph = {}
return render(
request, 'user/user_resources.html', {
"user": request.user,
"person": person,
"collaborations": collaborations,
"graph": graph
})
def assembly_view(request, pk):
assembly = Assembly.objects.get(id=pk)
graph, related_resources = GraphRepo.get_neighborhood(pk,
"Assembly",
level=1)
job = LoadGenomeJob.objects.filter(assembly=assembly)
contigs = None
lengths = None
qsbdb = Biodatabase.objects.filter(name=assembly.name)
loaded = bool(qsbdb.count())
processing = False
if job.exists():
processing = True
job = job.order_by("-id")[0]
if job.status != Job.STATUS.FINISHED:
loaded = False
external_ids = [
x.identifier for x in assembly.external_ids.all()
if x.type == "accession"
]
external_url = ""
if external_ids:
external_url = ("https://www.ncbi.nlm.nih.gov/" +
NCBISearch.rtype2ncbb[Assembly.TYPE] + "/" +
external_ids[0])
page = None
if qsbdb.count():
bdb = qsbdb.get()
beqs = bdb.entries.all()
lengths = {}
# for x in be.entries.all():
# SELECT s.bioentry_id, s.version , s.length , s.alphabet
seqs = Biosequence.objects.prefetch_related("bioentry").raw("""
SELECT s.bioentry_id, s.length
FROM biosequence s,bioentry b WHERE b.biodatabase_id = %i AND b.bioentry_id = s.bioentry_id ;
""" % (bdb.biodatabase_id))
for seq in seqs:
lengths[seq.bioentry.accession] = seq.length
# assembly.assembly_type = str(Assembly.ASSEMBLY_TYPES[assembly.assembly_type])
# assembly.level = str(Assembly.ASSEMBLY_LEVEL[assembly.level])
page = Page.from_request(request, count=beqs.count())
contigs = beqs[page.offset():page.end()]
collaboration = request.user.get_collaboration(
assembly) if request.user.is_authenticated else None
can_upload = not loaded and collaboration and not external_ids and not bool(
qsbdb.count())
params = {
"query": "",
"page_obj": page,
"collaboration": collaboration,
"can_upload": can_upload,
"lengths": lengths,
"external_url": external_url,
"loaded": loaded,
"level": {k: str(v)
for k, v in Assembly.ASSEMBLY_LEVEL},
"object": assembly,
"graph": graph,
"atypes": {k: str(v)
for k, v in Assembly.ASSEMBLY_TYPES},
"related_resources": related_resources,
"contigs": contigs,
"sidebarleft": {},
"processing": processing
}
return render(request, 'resources/assembly_detail.html', params)