only keep blast seq api

blast/api.py

@@ -1,4 +1,11 @@
 from rest_framework import renderers
+from rest_framework.renderers import JSONRenderer, BrowsableAPIRenderer
+from rest_framework import viewsets
+from django.contrib.auth.models import User
+from app.models import Organism
+from blast.models import SequenceType, BlastDb, Sequence
+from blast.serializers import OrganismSerializer, BlastDbSerializer, SequenceSerializer, SequenceTypeSerializer
+
 
 class FASTARenderer(renderers.BaseRenderer):
     media_type = 'text/plain'
@@ -12,11 +19,6 @@ def render(self, data, media_type=None, renderer_context=None):
         else:
             return ''
 
-from rest_framework.renderers import JSONRenderer, BrowsableAPIRenderer
-from rest_framework import viewsets
-from django.contrib.auth.models import User
-from .models import *
-from .serializers import *
 
 class OrganismViewSet(viewsets.ReadOnlyModelViewSet):
     """
@@ -26,6 +28,7 @@ class OrganismViewSet(viewsets.ReadOnlyModelViewSet):
     serializer_class = OrganismSerializer
     lookup_field = 'short_name'
 
+
 class SequenceTypeViewSet(viewsets.ReadOnlyModelViewSet):
     """
     Retrieve sequence types.
@@ -34,6 +37,7 @@ class SequenceTypeViewSet(viewsets.ReadOnlyModelViewSet):
     serializer_class = SequenceTypeSerializer
     lookup_field = 'dataset_type'
 
+
 class BlastDbViewSet(viewsets.ReadOnlyModelViewSet):
     """
     Retrieve BLAST databases.
@@ -43,58 +47,13 @@ class BlastDbViewSet(viewsets.ReadOnlyModelViewSet):
     lookup_field = 'title'
     lookup_value_regex = '[^/]+'
 
-    #@link()
-    #def sequence_set(self, request, title=None):
-    #    empty_error = "Empty list and '%(class_name)s.allow_empty' is False."
-    #    blastdb = self.get_object()
-    #    object_list = self.filter_queryset(blastdb.sequence_set.all())
-
-    #    # Default is to allow empty querysets.  This can be altered by setting
-    #    # `.allow_empty = False`, to raise 404 errors on empty querysets.
-    #    if not self.allow_empty and not object_list:
-    #        warnings.warn(
-    #            'The `allow_empty` parameter is deprecated. '
-    #            'To use `allow_empty=False` style behavior, You should override '
-    #            '`get_queryset()` and explicitly raise a 404 on empty querysets.',
-    #            DeprecationWarning
-    #        )
-    #        class_name = self.__class__.__name__
-    #        error_msg = self.empty_error % {'class_name': class_name}
-    #        raise Http404(error_msg)
-
-    #    # Switch between paginated or standard style responses
-    #    page = self.paginate_queryset(object_list)
-    #    if page is not None:
-    #        serializer = PaginatedSequenceSerializer(instance=page, context={'request': request})
-    #    else:
-    #        serializer = SequenceSerializer(object_list, many=True, context={'request': request})
-
-    #    return Response(serializer.data)
-
 class SequenceViewSet(viewsets.ReadOnlyModelViewSet):
     """
     Retrieve fasta sequences.
     """
     queryset = Sequence.objects.all()
     serializer_class = SequenceSerializer
-    renderer_classes = (JSONRenderer, BrowsableAPIRenderer, FASTARenderer)
+    renderer_classes = [FASTARenderer]
     lookup_field = 'id'
     lookup_value_regex = '[^/]+'
 
-class BlastQueryRecordViewSet(viewsets.ReadOnlyModelViewSet):
-    """
-    Retrieve tasks.
-    """
-    queryset = BlastQueryRecord.objects.all()
-    serializer_class = BlastQueryRecordSerializer
-    lookup_field = 'task_id'
-
-class UserViewSet(viewsets.ReadOnlyModelViewSet):
-    """
-    Retrieve users.
-    """
-    queryset = User.objects.all()
-    serializer_class = UserSerializer
-    lookup_field = 'pk'
-
-

blast/models.py

@@ -59,12 +59,10 @@ class BlastDb(models.Model):
     objects = BlastDbManager()
     organism = models.ForeignKey(app.models.Organism)
     type = models.ForeignKey(SequenceType)
-    # fasta_file = models.FileField(upload_to='blastdb') # upload file
     fasta_file = FileBrowseField('FASTA file path', max_length=200, directory='blast/db/', extensions='FASTA', format='FASTA')
     title = models.CharField(max_length=200, unique=True, help_text='This is passed into makeblast -title') # makeblastdb -title
     description = models.TextField(blank=True)  # shown in blast db selection ui
     is_shown = models.BooleanField(default=None, help_text='Display this database in the BLAST submit form') # to temporarily remove from blast db selection ui
-    # sequence_count = models.PositiveIntegerField(null=True, blank=True)  # number of sequences in this fasta
 
     # properties
     def fasta_file_exists(self):

blast/serializers.py

@@ -1,62 +1,55 @@
-from rest_framework import serializers
+from rest_framework.serializers import ModelSerializer, HyperlinkedModelSerializer, HyperlinkedIdentityField, ReadOnlyField, HyperlinkedRelatedField
 from django.contrib.auth.models import User
 from app.models import Organism
 from blast.models import SequenceType, BlastDb, Sequence, BlastQueryRecord
 
-class OrganismSerializer(serializers.HyperlinkedModelSerializer):
-    url = serializers.HyperlinkedIdentityField(view_name='blast:organism-detail', lookup_field='short_name')
 
+class OrganismSerializer(HyperlinkedModelSerializer):
     class Meta:
         model = Organism
+        fields = ('display_name', 'short_name', 'description', 'tax_id')
 
 
-class SequenceTypeSerializer(serializers.HyperlinkedModelSerializer):
-    url = serializers.HyperlinkedIdentityField(view_name='blast:sequencetype-detail', lookup_field='dataset_type')
-
+class SequenceTypeSerializer(HyperlinkedModelSerializer):
     class Meta:
         model = SequenceType
-
-
-class BlastDbSerializer(serializers.HyperlinkedModelSerializer):
-    url = serializers.HyperlinkedIdentityField(view_name='blast:blastdb-detail', lookup_field='title')
-    organism = serializers.HyperlinkedRelatedField(view_name='blast:organism-detail', lookup_field='short_name', read_only=True)
-    type = serializers.HyperlinkedRelatedField(view_name='blast:sequencetype-detail', lookup_field='dataset_type', read_only=True)
-    sequence_set = serializers.HyperlinkedRelatedField(view_name='blast:blastdb-sequence-set', lookup_field='title', read_only=True)
-    fasta_file_exists = serializers.Field()
-    blast_db_files_exists = serializers.Field()
-    sequence_set_exists = serializers.Field()
-    db_ready = serializers.Field()
+        fields = ('molecule_type', 'dataset_type')
+
+
+class BlastDbSerializer(HyperlinkedModelSerializer):
+    organism = HyperlinkedRelatedField(
+        view_name='blast:organism-detail',
+        lookup_field='short_name',
+        read_only=True)
+    type = HyperlinkedRelatedField(
+        view_name='blast:sequencetype-detail',
+        lookup_field='dataset_type',
+        read_only=True)
+    fasta_file_exists = ReadOnlyField()
+    blast_db_files_exists = ReadOnlyField()
+    sequence_set_exists = ReadOnlyField()
+    db_ready = ReadOnlyField()
 
     class Meta:
         model = BlastDb
-        fields = ('url', 'organism', 'type', 'fasta_file', 'title', 'description', 'is_shown', 'fasta_file_exists', 'blast_db_files_exists', 'sequence_set_exists', 'db_ready', 'sequence_set', )
+        fields = ('organism', 'type', 'fasta_file', 'title', 'description',
+                  'is_shown', 'fasta_file_exists', 'blast_db_files_exists',
+                  'sequence_set_exists', 'db_ready')
 
 
-class SequenceSerializer(serializers.HyperlinkedModelSerializer):
-    blast_db = serializers.HyperlinkedRelatedField(view_name='blast:blastdb-detail', lookup_field='title', read_only=True)
-    fasta_seq = serializers.ReadOnlyField()
+class SequenceSerializer(HyperlinkedModelSerializer):
+    blast_db = HyperlinkedRelatedField(
+        view_name='blast:blastdb-detail', lookup_field='title', read_only=True)
+    fasta_seq = ReadOnlyField()
 
     class Meta:
         model = Sequence
-        fields = ('blast_db', 'id', 'length', 'seq_start_pos', 'seq_end_pos', 'modified_date', 'fasta_seq', )
-
-
-class BlastQueryRecordSerializer(serializers.HyperlinkedModelSerializer):
-    url = serializers.HyperlinkedIdentityField(view_name='blast:blastqueryrecord-detail', lookup_field='task_id')
-
-    class Meta:
-        model = BlastQueryRecord
-
-
-class UserSerializer(serializers.ModelSerializer):
-    url = serializers.HyperlinkedIdentityField(view_name='blast:user-detail', lookup_field='pk')
-
-    class Meta:
-        model = User
-        fields = ('id', 'url',)
-
-
-class UserBlastQueryRecordSerializer(serializers.ModelSerializer):
-    class Meta:
-        model = BlastQueryRecord
-        fields = ('task_id', 'enqueue_date', 'result_status')
+        fields = (
+            'blast_db',
+            'id',
+            'length',
+            'seq_start_pos',
+            'seq_end_pos',
+            'modified_date',
+            'fasta_seq',
+        )

blast/static/blast/scripts/blast-results.js

@@ -155,7 +155,7 @@ $(function () { // document ready
     var url_root = /(https?:\/\/.*(?:blast)*)\/task\//g.exec(document.URL)[1];
     function get_fasta(sseqid) {
         // Returns a jqXHR or true if already in cache, for use with $.when
-        //http://localhost:8000/api/seq/gnl%7CLoxosceles_reclusa_transcript_v0.5.3%7CLREC000002-RA/?format=fasta
+        // base_url/blast/api/seq/gnl%7CLoxosceles_reclusa_transcript_v0.5.3%7CLREC000002-RA/?format=fasta
         if (sseqid in fasta_cache)
             return true;
         else if (sseqid in fasta_loading)

blast/urls.py

@@ -1,32 +1,20 @@
 from django.conf.urls import url, include
 from django.conf import settings
 from blast import views
-from blast.api import OrganismViewSet, SequenceTypeViewSet, BlastDbViewSet, SequenceViewSet, BlastQueryRecordViewSet, UserViewSet
-from rest_framework import routers
-
-router = routers.DefaultRouter()
-router.register(r'organism', OrganismViewSet)
-router.register(r'seqtype', SequenceTypeViewSet)
-router.register(r'blastdb', BlastDbViewSet)
-router.register(r'seq', SequenceViewSet)
-router.register(r'task', BlastQueryRecordViewSet)
-router.register(r'user', UserViewSet)
 
 urlpatterns = [
     # ex: /blast/
     url(r'^$', views.create, name='create'),
     # url(r'^iframe$', views.create, {'iframe': True}, name='iframe'),
     # ex: /blast/5/
     url(r'^task/(?P<task_id>[0-9a-zA-Z]+)$', views.retrieve, name='retrieve'),
-    url(r'^task/(?P<task_id>[0-9a-zA-Z]+)/status$', views.status, name='status'),
+    url(r'^task/(?P<task_id>[0-9a-zA-Z]+)/status$',
+        views.status,
+        name='status'),
     # url(r'^read_gff3/(?P<task_id>[0-9a-fA-F]*)/*(?P<dbname>[\w\-\|.]*)/*$', views.read_gff3, name='read_gff3'),
-    url(r'^api/', include(router.urls)),
-    # url(r'^api-auth/', include('rest_framework.urls', namespace='rest_framework')),
-    url(r'^user-tasks/(?P<user_id>[0-9]+)$', views.user_tasks),
+    url(r'^api/seq/(?P<seq_id>[a-zA-Z0-9_-]+)/', views.get_seq, name='seq'),
 ]
 
 if settings.DEBUG:
     from blast import test_views
-    urlpatterns += [
-        url(r'^test/$', test_views.test_main)
-    ]
+    urlpatterns += [url(r'^test/$', test_views.test_main)]

blast/views.py

@@ -1,13 +1,13 @@
 from __future__ import absolute_import
 from django.shortcuts import render
-from django.shortcuts import redirect
+from django.shortcuts import redirect, get_object_or_404
 from django.http import Http404
 from django.http import HttpResponse
 from django.conf import settings
 from django.core.cache import cache
 from uuid import uuid4
 from os import path, makedirs, chmod, remove
-from blast.models import BlastQueryRecord, BlastDb
+from blast.models import BlastQueryRecord, BlastDb, Sequence
 from blast.tasks import run_blast_task
 from datetime import datetime, timedelta
 from django.utils.timezone import localtime, now
@@ -18,6 +18,7 @@
 from itertools import groupby
 from multiprocessing import cpu_count
 from util.get_bin_name import get_bin_name
+from rest_framework.renderers import JSONRenderer
 
 blast_customized_options = {'blastn': ['max_target_seqs', 'evalue', 'word_size', 'reward', 'penalty', 'gapopen', 'gapextend', 'strand', 'low_complexity', 'soft_masking'],
                             'tblastn': ['max_target_seqs', 'evalue', 'word_size', 'matrix', 'threshold', 'gapopen', 'gapextend', 'low_complexity', 'soft_masking'],
@@ -248,25 +249,6 @@ def status(request, task_id):
     else:
         return HttpResponse('Invalid Post')
 
-
-# to-do: integrate with existing router of restframework
-from rest_framework.renderers import JSONRenderer
-from .serializers import UserBlastQueryRecordSerializer
-class JSONResponse(HttpResponse):
-    """
-    An HttpResponse that renders its content into JSON.
-    """
-    def __init__(self, data, **kwargs):
-        content = JSONRenderer().render(data)
-        kwargs['content_type'] = 'application/json'
-        super(JSONResponse, self).__init__(content, **kwargs)
-
-def user_tasks(request, user_id):
-    """
-    Return tasks performed by the user.
-    """
-    if request.method == 'GET':
-        records = BlastQueryRecord.objects.filter(user__id=user_id, is_shown=True, result_date__gt=(localtime(now())+ timedelta(days=-7)))
-        serializer = UserBlastQueryRecordSerializer(records, many=True)
-        return JSONResponse(serializer.data)
-
+def get_seq(request, seq_id):
+    seq = get_object_or_404(Sequence, id=seq_id)
+    return HttpResponse(seq.fasta_seq(), content_type='text/plain')

clustal/urls.py

@@ -1,15 +1,13 @@
 from django.conf.urls import url
 from clustal import views
-# from .api import *
 
 urlpatterns = [
     # ex: /clustal/
     url(r'^$', views.create, name='create'),
     # ex: /clustal/5/
     url(r'^task/(?P<task_id>[0-9a-zA-Z]+)$', views.retrieve, name='retrieve'),
-    url(r'^task/(?P<task_id>[0-9a-zA-Z]+)/status$', views.status, name='status'),
-    # url(r'^api/', include(router.urls)),
-    # url(r'^api-auth/', include('rest_framework.urls', namespace='rest_framework')),
-    url('^user-tasks/(?P<user_id>[0-9]+)$', views.user_tasks),
+    url(r'^task/(?P<task_id>[0-9a-zA-Z]+)/status$',
+        views.status,
+        name='status'),
     url(r'^manual/$', views.manual, name='manual'),
 ]