+from __future__ import absolute_import, print_function
+
from django.conf import settings
from django.http import HttpResponse
-from django.shortcuts import render_to_response
from django.core.exceptions import ObjectDoesNotExist
-from htsworkflow.frontend.eland_config import forms
from htsworkflow.frontend.experiments import models
import os
-import glob
def _validate_input(data):
- return data.replace('..', '').replace('/', '_').replace('\\', '_')
+ return data.replace('..', '').replace('/', '_').replace('\\', '_')
def getElandConfig(flowcell, regenerate=False):
- if hasattr(settings, 'UPLOADTO_CONFIG_FILE'):
- dest = settings.UPLOADTO_CONFIG_FILE
- 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.
- if not regenerate and os.path.isfile(file_path):
- f = open(file_path, 'r')
- 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])
- if fcObj.paired_end:
- data.append('%s:ANALYSIS eland_pair' % (lanes))
+ if hasattr(settings, 'UPLOADTO_CONFIG_FILE'):
+ dest = settings.UPLOADTO_CONFIG_FILE
else:
- data.append('%s:ANALYSIS eland_extended' % (lanes))
- 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()
+ 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.
+ if not regenerate and os.path.isfile(file_path):
+ f = open(file_path, 'r')
+ 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
+
+ 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('%', '%%')))
+
+ 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])
+ if fcObj.paired_end:
+ data.append('%s:ANALYSIS eland_pair' % (lanes))
+ else:
+ data.append('%s:ANALYSIS eland_extended' % (lanes))
+ 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.
- """
+ """
+ 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() ]
+ # Provide INDEX of available Flowcell config files.
+ if flowcell is None:
+ 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 ]
+ #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))
+ return HttpResponse('<br />'.join(fc_html))
- #FIXME: Should validate flowcell input before using.
- flowcell = _validate_input(flowcell)
- cfg = getElandConfig(flowcell, regenerate=True)
+ #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))
+ if not cfg:
+ return HttpResponse(
+ "Hmm, config file for %s does not seem to exist." % (flowcell))
- return HttpResponse(cfg, mimetype="text/plain")
+ return HttpResponse(cfg, mimetype="text/plain")
projects / htsworkflow.git / commitdiff