import os
import glob
-# Create your views here.
def _validate_input(data):
- #if data.find('..') == -1 or data.find('/') == -1 or data.find('\\') == -1:
return data.replace('..', '').replace('/', '_').replace('\\', '_')
-#def contact(request):
-# if request.method == 'POST':
-# form = ContactForm(request.POST)
-# if form.is_valid():
-# # Do form processing here...
-# return HttpResponseRedirect('/url/on_success/')
-# else:
-# form = ContactForm()
-# return
-
-
-
-#def _saveConfigFile(form):
-# """
-# Given a valid form, save eland config to file based on flowcell number.
-# """
-# assert form.is_valid()
-#
-# clean_data = form.cleaned_data
-# flowcell = clean_data['flow_cell_number'].replace('/','_').replace('..', '__')
-#
-# file_path = os.path.join(settings.UPLOADTO_CONFIG_FILE, flowcell)
-#
-# f = open(file_path, 'w')
-# cfg = generateElandConfig(form)
-# f.write(cfg)
-# f.close()
-#
-#
-#def _saveToDb(form):
-# """
-# Save info to the database.
-# """
-# clean_data = form.cleaned_data
-#
-# fc_id = clean_data['flow_cell_number']
-#
-# try:
-# fc = models.FlowCell.objects.get(flowcell_id=fc_id)
-# except models.FlowCell.DoesNotExist:
-# fc = models.FlowCell()
-#
-# fc.flowcell_id = fc_id
-# fc.run_date = clean_data['run_date']
-#
-# #LANE 1
-# fc.lane1_sample = clean_data['lane1_description']
-# species_name = clean_data['lane1_species']
-# try:
-# specie = models.Specie.objects.get(scientific_name=species_name)
-# except models.Specie.DoesNotExist:
-# specie = models.Specie(scientific_name=species_name)
-# specie.save()
-# fc.lane1_species = specie
-#
-# #LANE 2
-# fc.lane2_sample = clean_data['lane2_description']
-# species_name = clean_data['lane2_species']
-# try:
-# specie = models.Specie.objects.get(scientific_name=species_name)
-# except models.Specie.DoesNotExist:
-# specie = models.Specie(scientific_name=species_name)
-# specie.save()
-# fc.lane2_species = specie
-#
-# #LANE 3
-# fc.lane3_sample = clean_data['lane3_description']
-# species_name = clean_data['lane3_species']
-# try:
-# specie = models.Specie.objects.get(scientific_name=species_name)
-# except models.Specie.DoesNotExist:
-# specie = models.Specie(scientific_name=species_name)
-# specie.save()
-# fc.lane3_species = specie
-#
-# #LANE 4
-# fc.lane4_sample = clean_data['lane4_description']
-# species_name = clean_data['lane4_species']
-# try:
-# specie = models.Specie.objects.get(scientific_name=species_name)
-# except models.Specie.DoesNotExist:
-# specie = models.Specie(scientific_name=species_name)
-# specie.save()
-# fc.lane4_species = specie
-#
-# #LANE 5
-# fc.lane5_sample = clean_data['lane5_description']
-# species_name = clean_data['lane5_species']
-# try:
-# specie = models.Specie.objects.get(scientific_name=species_name)
-# except models.Specie.DoesNotExist:
-# specie = models.Specie(scientific_name=species_name)
-# specie.save()
-# fc.lane5_species = specie
-#
-# #LANE 6
-# fc.lane6_sample = clean_data['lane6_description']
-# species_name = clean_data['lane6_species']
-# try:
-# specie = models.Specie.objects.get(scientific_name=species_name)
-# except models.Specie.DoesNotExist:
-# specie = models.Specie(scientific_name=species_name)
-# specie.save()
-# fc.lane6_species = specie
-#
-# #LANE 7
-# fc.lane7_sample = clean_data['lane7_description']
-# species_name = clean_data['lane7_species']
-# try:
-# specie = models.Specie.objects.get(scientific_name=species_name)
-# except models.Specie.DoesNotExist:
-# specie = models.Specie(scientific_name=species_name)
-# specie.save()
-# fc.lane7_species = specie
-#
-# #LANE 8
-# fc.lane8_sample = clean_data['lane8_description']
-# species_name = clean_data['lane8_species']
-# try:
-# specie = models.Specie.objects.get(scientific_name=species_name)
-# except models.Specie.DoesNotExist:
-# specie = models.Specie(scientific_name=species_name)
-# specie.save()
-# fc.lane8_species = specie
-#
-# fc.notes = clean_data['notes']
-#
-# fc.save()
-#
-# return fc
-#
-#
-#def generateElandConfig(form):
-# data = []
-#
-# form = form.cleaned_data
-#
-# BASE_DIR = '/data-store01/compbio/genomes'
-#
-# data.append("# FLOWCELL: %s" % (form['flow_cell_number']))
-# data.append("#")
-#
-# notes = form['notes'].replace('\r\n', '\n').replace('\r', '\n')
-# notes = notes.replace('\n', '\n# ')
-# data.append("# NOTES:")
-# data.append("# %s\n#" % (notes))
-#
-# #Convert all newline conventions to unix style
-# l1d = form['lane1_description'].replace('\r\n', '\n').replace('\r', '\n')
-# l2d = form['lane2_description'].replace('\r\n', '\n').replace('\r', '\n')
-# l3d = form['lane3_description'].replace('\r\n', '\n').replace('\r', '\n')
-# l4d = form['lane4_description'].replace('\r\n', '\n').replace('\r', '\n')
-# l5d = form['lane5_description'].replace('\r\n', '\n').replace('\r', '\n')
-# l6d = form['lane6_description'].replace('\r\n', '\n').replace('\r', '\n')
-# l7d = form['lane7_description'].replace('\r\n', '\n').replace('\r', '\n')
-# l8d = form['lane8_description'].replace('\r\n', '\n').replace('\r', '\n')
-#
-# # Turn new lines into indented commented newlines
-# l1d = l1d.replace('\n', '\n# ')
-# l2d = l2d.replace('\n', '\n# ')
-# l3d = l3d.replace('\n', '\n# ')
-# l4d = l4d.replace('\n', '\n# ')
-# l5d = l5d.replace('\n', '\n# ')
-# l6d = l6d.replace('\n', '\n# ')
-# l7d = l7d.replace('\n', '\n# ')
-# l8d = l8d.replace('\n', '\n# ')
-#
-# data.append("# Lane1: %s" % (l1d))
-# data.append("# Lane2: %s" % (l2d))
-# data.append("# Lane3: %s" % (l3d))
-# data.append("# Lane4: %s" % (l4d))
-# data.append("# Lane5: %s" % (l5d))
-# data.append("# Lane6: %s" % (l6d))
-# data.append("# Lane7: %s" % (l7d))
-# data.append("# Lane8: %s" % (l8d))
-#
-# #data.append("GENOME_DIR %s" % (BASE_DIR))
-# #data.append("CONTAM_DIR %s" % (BASE_DIR))
-# read_length = form['read_length']
-# data.append("READ_LENGTH %d" % (read_length))
-# #data.append("ELAND_REPEAT")
-# data.append("ELAND_MULTIPLE_INSTANCES 8")
-#
-# #Construct genome dictionary to figure out what lanes to put
-# # in the config file.
-# genome_dict = {}
-# l1s = form['lane1_species']
-# genome_dict.setdefault(l1s, []).append('1')
-# l2s = form['lane2_species']
-# genome_dict.setdefault(l2s, []).append('2')
-# l3s = form['lane3_species']
-# genome_dict.setdefault(l3s, []).append('3')
-# l4s = form['lane4_species']
-# genome_dict.setdefault(l4s, []).append('4')
-# l5s = form['lane5_species']
-# genome_dict.setdefault(l5s, []).append('5')
-# l6s = form['lane6_species']
-# genome_dict.setdefault(l6s, []).append('6')
-# l7s = form['lane7_species']
-# genome_dict.setdefault(l7s, []).append('7')
-# l8s = form['lane8_species']
-# genome_dict.setdefault(l8s, []).append('8')
-#
-# genome_list = genome_dict.keys()
-# genome_list.sort()
-#
-# #Loop through and create entries for each species.
-# for genome in genome_list:
-# lanes = ''.join(genome_dict[genome])
-# data.append('%s:ANALYSIS eland' % (lanes))
-# data.append('%s:READ_LENGTH %s' % (lanes, read_length))
-# data.append('%s:ELAND_GENOME %s' % (lanes, os.path.join(BASE_DIR, genome)))
-# data.append('%s:USE_BASES %s' % (lanes, 'Y'*int(read_length)))
-#
-# data.append('SEQUENCE_FORMAT --scarf')
-#
-# return '\n'.join(data)
-
def getElandConfig(flowcell, regenerate=False):
else:
dest = '/tmp'
file_path = os.path.join(dest, flowcell)
-
+
#If we are regenerating the config file, skip
# reading of existing file. If the file doesn't
# exist, try to generate it form the DB.
data = f.read()
f.close()
return data
-
+
try:
fcObj = models.FlowCell.objects.get(flowcell_id__iexact=flowcell)
except ObjectDoesNotExist:
return None
-
+
data = []
-
+
#form = form.cleaned_data
-
+
BASE_DIR = '/data-store01/compbio/genomes'
-
+
data.append("# FLOWCELL: %s" % (fcObj.flowcell_id))
data.append("#")
-
+
notes = fcObj.notes.replace('\r\n', '\n').replace('\r', '\n')
notes = notes.replace('\n', '\n# ')
data.append("# NOTES:")
data.append("# %s\n#" % (notes))
-
+
#Convert all newline conventions to unix style
for lane in fcObj.lane_set.all():
data.append("# Lane%d: %s | %s" % \
(lane.lane_number, unicode(lane.library.id), lane.library.library_name.replace('%', '%%')))
-
+
#data.append("GENOME_DIR %s" % (BASE_DIR))
#data.append("CONTAM_DIR %s" % (BASE_DIR))
read_length = fcObj.read_length
#data.append("ELAND_REPEAT")
data.append("ELAND_MULTIPLE_INSTANCES 8")
-
+
#Construct genome dictionary to figure out what lanes to put
# in the config file.
genome_dict = {}
-
+
#l1s = form['lane1_species']
for lane in fcObj.lane_set.all():
species = lane.library.library_species.scientific_name
genome_dict.setdefault(species, []).append(unicode(lane.lane_number))
-
+
genome_list = genome_dict.keys()
genome_list.sort()
-
+
#Loop through and create entries for each species.
for genome in genome_list:
lanes = ''.join(genome_dict[genome])
data.append('%s:READ_LENGTH %s' % (lanes, read_length))
data.append('%s:ELAND_GENOME %s' % (lanes, '%%(%s)s' % (genome)))
data.append('%s:USE_BASES %s' % (lanes, 'Y'*int(read_length)))
-
+
data.append('SEQUENCE_FORMAT --fastq')
data.append('') # want a trailing newline
-
+
data = '\n'.join(data)
-
+
f = open(file_path, 'w')
f.write(data)
f.close()
-
- return data
+ return data
def config(request, flowcell=None):
Returns eland config file for a given flowcell number,
or returns a list of available flowcell numbers.
"""
-
+
# Provide INDEX of available Flowcell config files.
if flowcell is None:
#Find all FC* config files and report an index html file
#fc_list = [ os.path.split(file_path)[1] for file_path in glob.glob(os.path.join(settings.UPLOADTO_CONFIG_FILE, 'FC*')) ]
fc_list = [ fc.flowcell_id for fc in models.FlowCell.objects.all() ]
-
+
#Convert FC* list to html links
fc_html = [ '<a href="/eland_config/%s/">%s</a>' % (fc_name, fc_name) for fc_name in fc_list ]
-
+
return HttpResponse('<br />'.join(fc_html))
-
+
#FIXME: Should validate flowcell input before using.
flowcell = _validate_input(flowcell)
cfg = getElandConfig(flowcell, regenerate=True)
-
+
if not cfg:
return HttpResponse("Hmm, config file for %s does not seem to exist." % (flowcell))
-
-
- return HttpResponse(cfg, mimetype="text/plain")
-
-
-
-#def index(request):
-# """
-# Return a form for filling out information about the flowcell
-# """
-# if request.method == 'POST':
-# form = forms.ConfigForm(request.POST, error_class=forms.DivErrorList)
-# if form.is_valid():
-# #cfg = generateElandConfig(form)
-# _saveConfigFile(form)
-# _saveToDb(form)
-# return HttpResponse("Eland Config Saved!", mimetype="text/plain")
-# else:
-# return render_to_response('config_form.html', {'form': form })
-#
-# else:
-# fm = forms.ConfigForm(error_class=forms.DivErrorList)
-# return render_to_response('config_form.html', {'form': fm })
+ return HttpResponse(cfg, mimetype="text/plain")
projects / htsworkflow.git / commitdiff