+++ /dev/null
-from django import newforms as forms
-from django.newforms.util import ErrorList
-
-
-SPECIES_LIST = [#('--choose--', '--Choose--'),
- ('hg18', 'Homo sapiens (Hg18)'),
- ('Mm8', 'Mus musculus (Mm8)'),
- ('arabv6', 'Arabadopsis Thaliana v6'),
- ('other', 'Other species (Include in description)')]
-
-
-class DivErrorList(ErrorList):
- def __unicode__(self):
- return self.as_divs()
-
- def as_divs(self):
- if not self: return u''
- return u'<div class="errorlist">%s</div>' % (''.join([u'<div class="error">%s</div>' % e for e in self]))
-
-
-
-class ConfigForm(forms.Form):
-
- flow_cell_number = forms.CharField(min_length=2)
- run_date = forms.DateTimeField()
- advanced_run = forms.BooleanField(required=False)
- read_length = forms.IntegerField(min_value=1, initial=32)
- #eland_repeat = forms.BooleanField()
-
- #needs a for loop or something to allow for n configurations
- #analysis_type = forms.ChoiceField(choices=[('eland','eland')])
- lane1_species = forms.ChoiceField(choices=SPECIES_LIST)
- lane1_description = forms.CharField(widget=forms.TextInput(attrs={'size':'60'}))
-
- lane2_species = forms.ChoiceField(choices=SPECIES_LIST)
- lane2_description = forms.CharField(widget=forms.TextInput(attrs={'size':'60'}))
-
- lane3_species = forms.ChoiceField(choices=SPECIES_LIST)
- lane3_description = forms.CharField(widget=forms.TextInput(attrs={'size':'60'}))
-
- lane4_species = forms.ChoiceField(choices=SPECIES_LIST)
- lane4_description = forms.CharField(widget=forms.TextInput(attrs={'size':'60'}))
-
- lane5_species = forms.ChoiceField(choices=SPECIES_LIST)
- lane5_description = forms.CharField(widget=forms.TextInput(attrs={'size':'60'}))
-
- lane6_species = forms.ChoiceField(choices=SPECIES_LIST)
- lane6_description = forms.CharField(widget=forms.TextInput(attrs={'size':'60'}))
-
- lane7_species = forms.ChoiceField(choices=SPECIES_LIST)
- lane7_description = forms.CharField(widget=forms.TextInput(attrs={'size':'60'}))
-
- lane8_species = forms.ChoiceField(choices=SPECIES_LIST)
- lane8_description = forms.CharField(widget=forms.TextInput(attrs={'size':'60'}))
-
- notes = forms.CharField(widget=forms.Textarea(attrs={'cols':'70'}), required=False)
-
- #lane_specific_read_length = forms.IntegerField(min_value=1)
-
- #eland_genome_lanes = forms.MultipleChoiceField(choices=[('lane1','1'),
- # ('lane2','2'),
- # ('lane3','3'),
- # ('lane4','4'),
- # ('lane5','5'),
- # ('lane6','6'),
- # ('lane7','7'),
- # ('lane8','8') ])
-
- #eland_genome = forms.ChoiceField(choices=)
-
- #use_bases_lanes = forms.MultipleChoiceField(choices=[('lane1','1'),
- # ('lane2','2'),
- # ('lane3','3'),
- # ('lane4','4'),
- # ('lane5','5'),
- # ('lane6','6'),
- # ('lane7','7'),
- # ('lane8','8') ])
-
- #use_bases_mask = forms.CharField()
-
- #sequence_format = forms.ChoiceField(choices=[('scarf', 'scarf')])
-
-
-
- #subject = forms.CharField(max_length=100)
- #message = forms.CharField()
- #sender = forms.EmailField()
- #cc_myself = forms.BooleanField()
-
- def as_custom(self):
- """
- Displays customized html output
- """
- html = []
-
- fcn = self['flow_cell_number']
-
- html.append(fcn.label_tag() + ': ' + str(fcn) + str(fcn.errors) + '<br />')
-
- run_date = self['run_date']
- html.append(run_date.label_tag() + ': ' + str(run_date) + str(run_date.errors) + '<br />')
-
- arun = self['advanced_run']
- html.append(arun.label_tag() + ': ' + str(arun) + str(arun.errors) + '<br />')
-
- rl = self['read_length']
- html.append(rl.label_tag() + ': ' + str(rl) + str(rl.errors) + '<br /><br />')
-
- html.append('<table border="0">')
- html.append(' <tr><td>%s</td><td>%s</td><td>%s</td></tr>' \
- % ('Lane', 'Species', 'Description'))
-
- l1s = self['lane1_species']
- l1d = self['lane1_description']
- html.append(' <tr><td>%s</td><td>%s %s</td><td>%s %s</td></tr>' \
- % ('1', str(l1s), str(l1s.errors), str(l1d), str(l1d.errors)))
-
- l2s = self['lane2_species']
- l2d = self['lane2_description']
- html.append(' <tr><td>%s</td><td>%s %s</td><td>%s %s</td></tr>' \
- % ('2', str(l2s), str(l2s.errors), str(l2d), str(l2d.errors)))
-
- l3s = self['lane3_species']
- l3d = self['lane3_description']
- html.append(' <tr><td>%s</td><td>%s %s</td><td>%s %s</td></tr>' \
- % ('3', str(l3s), str(l3s.errors), str(l3d), str(l3d.errors)))
-
- l4s = self['lane4_species']
- l4d = self['lane4_description']
- html.append(' <tr><td>%s</td><td>%s %s</td><td>%s %s</td></tr>' \
- % ('4', str(l4s), str(l4s.errors), str(l4d), str(l4d.errors)))
-
- l5s = self['lane5_species']
- l5d = self['lane5_description']
- html.append(' <tr><td>%s</td><td>%s %s</td><td>%s %s</td></tr>' \
- % ('5', str(l5s), str(l5s.errors), str(l5d), str(l5d.errors)))
-
- l6s = self['lane6_species']
- l6d = self['lane6_description']
- html.append(' <tr><td>%s</td><td>%s %s</td><td>%s %s</td></tr>' \
- % ('6', str(l6s), str(l6s.errors), str(l6d), str(l6d.errors)))
-
- l7s = self['lane7_species']
- l7d = self['lane7_description']
- html.append(' <tr><td>%s</td><td>%s %s</td><td>%s %s</td></tr>' \
- % ('7', str(l7s), str(l7s.errors), str(l7d), str(l7d.errors)))
-
- l8s = self['lane8_species']
- l8d = self['lane8_description']
- html.append(' <tr><td>%s</td><td>%s %s</td><td>%s %s</td></tr>' \
- % ('8', str(l8s), str(l8s.errors), str(l8d), str(l8d.errors)))
-
- html.append('</table><br />')
-
- notes = self['notes']
- html.append('<p>Notes:</p>')
- html.append(' %s<br />' % (str(notes)))
-
- return '\n'.join(html)
-
-
-
\ No newline at end of file
+++ /dev/null
-from django.db import models
-
-# Create your models here.
+++ /dev/null
-from django.conf.urls.defaults import *
-
-urlpatterns = patterns('',
- # Example:
-
- (r'^(?P<flowcell>\w+)/$', 'gaworkflow.frontend.eland_config.views.config'),
- (r'^$', 'gaworkflow.frontend.eland_config.views.config'),
- #(r'^$', 'gaworkflow.frontend.eland_config.views.index')
-
-)
+++ /dev/null
-from django.http import HttpResponse
-from django.shortcuts import render_to_response
-from django.core.exceptions import ObjectDoesNotExist
-
-from gaworkflow.frontend.eland_config import forms
-from gaworkflow.frontend import settings
-from gaworkflow.frontend.fctracker import models
-
-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):
-
- file_path = os.path.join(settings.UPLOADTO_CONFIG_FILE, 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
- l1d = str(fcObj.lane_1_library.library_id) + '|' \
- + fcObj.lane_1_library.library_name.replace('\r\n', '\n').replace('\r', '\n')
- l2d = str(fcObj.lane_2_library.library_id) + '|' \
- + fcObj.lane_2_library.library_name.replace('\r\n', '\n').replace('\r', '\n')
- l3d = str(fcObj.lane_3_library.library_id) + '|' \
- + fcObj.lane_3_library.library_name.replace('\r\n', '\n').replace('\r', '\n')
- l4d = str(fcObj.lane_4_library.library_id) + '|' \
- + fcObj.lane_4_library.library_name.replace('\r\n', '\n').replace('\r', '\n')
-
- l5d = str(fcObj.lane_5_library.library_id) + '|' \
- + fcObj.lane_5_library.library_name.replace('\r\n', '\n').replace('\r', '\n')
- l6d = str(fcObj.lane_6_library.library_id) + '|' \
- + fcObj.lane_6_library.library_name.replace('\r\n', '\n').replace('\r', '\n')
- l7d = str(fcObj.lane_7_library.library_id) + '|' \
- + fcObj.lane_7_library.library_name.replace('\r\n', '\n').replace('\r', '\n')
- l8d = str(fcObj.lane_8_library.library_id) + '|' \
- + fcObj.lane_8_library.library_name.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 = fcObj.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']
- l1s = fcObj.lane_1_library.library_species.scientific_name #+ '|' + \
- #fcObj.lane_1_library.library_species.use_genome_build
- genome_dict.setdefault(l1s, []).append('1')
- l2s = fcObj.lane_2_library.library_species.scientific_name #+ '|' + \
- #fcObj.lane_2_library.library_species.use_genome_build
- genome_dict.setdefault(l2s, []).append('2')
- l3s = fcObj.lane_3_library.library_species.scientific_name #+ '|' + \
- #fcObj.lane_3_library.library_species.use_genome_build
- genome_dict.setdefault(l3s, []).append('3')
- l4s = fcObj.lane_4_library.library_species.scientific_name #+ '|' + \
- #fcObj.lane_4_library.library_species.use_genome_build
- genome_dict.setdefault(l4s, []).append('4')
- l5s = fcObj.lane_5_library.library_species.scientific_name #+ '|' + \
- #fcObj.lane_5_library.library_species.use_genome_build
- genome_dict.setdefault(l5s, []).append('5')
- l6s = fcObj.lane_6_library.library_species.scientific_name #+ '|' + \
- #fcObj.lane_6_library.library_species.use_genome_build
- genome_dict.setdefault(l6s, []).append('6')
- l7s = fcObj.lane_7_library.library_species.scientific_name #+ '|' + \
- #fcObj.lane_7_library.library_species.use_genome_build
- genome_dict.setdefault(l7s, []).append('7')
- l8s = fcObj.lane_8_library.library_species.scientific_name #+ '|' + \
- #fcObj.lane_8_library.library_species.use_genome_build
- 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, '%%(%s)s' % (genome)))
- data.append('%s:USE_BASES %s' % (lanes, 'Y'*int(read_length)))
-
- data.append('SEQUENCE_FORMAT --scarf')
-
- data = '\n'.join(data)
-
- f = open(file_path, 'w')
- f.write(data)
- f.close()
-
- 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 })
from django.db import models
from gaworkflow.frontend import settings
+class Primer(models.Model):
+ primer_name = models.CharField(max_length=100, db_index=True)
+ primer_seq = models.CharField(max_length=50, blank=True, null=True)
+ notes = models.TextField(blank=True)
+ def __str__(self):
+ return '%s' % (self.primer_name)
+ class Meta:
+ ordering = ["primer_name"]
+ class Admin:
+ list_display = ('primer_name','primer_seq','notes')
+ fields = (
+ (None, {
+ 'fields': (('primer_name'),('primer_seq'),('notes'))
+ }),
+ )
+
class Antibody(models.Model):
antigene = models.CharField(max_length=500, db_index=True)
catalog = models.CharField(max_length=50, unique=True, db_index=True)
ordering = ["cellline_name"]
class Admin:
+ list_display = ('cellline_name','notes')
fields = (
(None, {
'fields': (('cellline_name'),('notes'),)
ordering = ["condition_name"]
class Admin:
+ list_display = ('condition_name','notes')
fields = (
(None, {
'fields': (('condition_name'),('notes'),)
class Species(models.Model):
scientific_name = models.CharField(max_length=256, unique=False, db_index=True, core=True)
common_name = models.CharField(max_length=256, blank=True)
- use_genome_build = models.CharField(max_length=100, blank=True) #blank=False, null=False)
+ use_genome_build = models.CharField(max_length=100, blank=False, null=False)
def __str__(self):
return '%s (%s)|%s' % (self.scientific_name, self.common_name, self.use_genome_build)
)
experiment_type = models.CharField(max_length=50, choices=EXPERIMENT_TYPES, default='ChIP-seq')
- made_by = models.CharField(max_length=50, blank=True)
creation_date = models.DateField(blank=True, null=True)
- made_for = models.CharField(max_length=50, blank=True)
- made_by = models.CharField(max_length=50, blank=True)
+ made_for = models.CharField(max_length=50, blank=True,verbose_name = 'ChIP/DNA/RNA Made By')
+ made_by = models.CharField(max_length=50, blank=True,verbose_name = 'Library Made By')
PROTOCOL_END_POINTS = (
('Completed','Completed'),
('?', 'Unknown'),
('Sample', 'Raw sample'),
- ('Gel', 'Ran gel'),
- ('1A', 'Gel purification'),
- ('2A', '2nd PCR'),
('Progress', 'In progress'),
+ ('1A', 'Ligation, then gel'),
+ ('PCR', 'Ligation, then PCR'),
+ ('1Ab', 'Ligation, PCR, then gel'),
+ ('1Aa', 'Ligation, gel, then PCR'),
+ ('2A', 'Ligation, PCR, gel, PCR'),
)
stopping_point = models.CharField(max_length=50, choices=PROTOCOL_END_POINTS, default='Completed')
amplified_from_sample = models.ForeignKey('self', blank=True, null=True)
undiluted_concentration = models.DecimalField("Template concentr. (ng/ul)",max_digits=5, decimal_places=2, blank=True, null=True)
ten_nM_dilution = models.BooleanField()
successful_pM = models.DecimalField(max_digits=5, decimal_places=2,blank=True, null=True)
- avg_lib_size = models.IntegerField()
+ avg_lib_size = models.IntegerField(default=225, blank=True, null=True)
notes = models.TextField(blank=True)
def __str__(self):
date_hierarchy = "creation_date"
save_as = True
save_on_top = True
- search_fields = ['library_name']
- list_display = ('library_id', 'library_name', 'made_by', 'creation_date', 'ten_nM_dilution', 'stopping_point', 'successful_pM')
+ search_fields = ['library_name', 'library_id','made_by','made_for','antibody__antigene','antibody__catalog','antibody__antibodies','antibody__source','cell_line__cellline_name','library_species__scientific_name','library_species__common_name','library_species__use_genome_build']
+ list_display = ('library_id', 'library_name','experiment_type','cell_line','made_by','creation_date')
list_display_links = ('library_id', 'library_name')
- list_filter = ('stopping_point', 'ten_nM_dilution', 'library_species', 'made_for', 'made_by')
+ list_filter = ('experiment_type','library_species','made_for', 'made_by')
fields = (
(None, {
'fields': (('library_id', 'library_name'),('library_species'),('experiment_type'),('cell_line','condition','antibody'),)
'fields' : (('made_for', 'made_by', 'creation_date'), ('stopping_point', 'amplified_from_sample'), ('avg_lib_size','undiluted_concentration', 'ten_nM_dilution', 'successful_pM'), 'notes',)
}),
)
-
-class FlowCell(models.Model):
-
- flowcell_id = models.CharField(max_length=20, unique=True, db_index=True, core=True)
- run_date = models.DateTimeField(core=True)
- advanced_run = models.BooleanField(default=False)
- read_length = models.IntegerField(default=32) #Stanford is currenlty 25
-
- lane_1_library = models.ForeignKey(Library, related_name="lane_1_library")
- lane_2_library = models.ForeignKey(Library, related_name="lane_2_library")
- lane_3_library = models.ForeignKey(Library, related_name="lane_3_library")
- lane_4_library = models.ForeignKey(Library, related_name="lane_4_library")
- lane_5_library = models.ForeignKey(Library, related_name="lane_5_library")
- lane_6_library = models.ForeignKey(Library, related_name="lane_6_library")
- lane_7_library = models.ForeignKey(Library, related_name="lane_7_library")
- lane_8_library = models.ForeignKey(Library, related_name="lane_8_library")
-
- lane_1_pM = models.DecimalField(max_digits=5, decimal_places=2,blank=False, null=False,default=2.5)
- lane_2_pM = models.DecimalField(max_digits=5, decimal_places=2,blank=False, null=False,default=2.5)
- lane_3_pM = models.DecimalField(max_digits=5, decimal_places=2,blank=False, null=False,default=2.5)
- lane_4_pM = models.DecimalField(max_digits=5, decimal_places=2,blank=False, null=False,default=2.5)
- lane_5_pM = models.DecimalField(max_digits=5, decimal_places=2,blank=False, null=False,default=2.5)
- lane_6_pM = models.DecimalField(max_digits=5, decimal_places=2,blank=False, null=False,default=2.5)
- lane_7_pM = models.DecimalField(max_digits=5, decimal_places=2,blank=False, null=False,default=2.5)
- lane_8_pM = models.DecimalField(max_digits=5, decimal_places=2,blank=False, null=False,default=2.5)
-
- lane_1_cluster_estimate = models.IntegerField(blank=True, null=True)
- lane_2_cluster_estimate = models.IntegerField(blank=True, null=True)
- lane_3_cluster_estimate = models.IntegerField(blank=True, null=True)
- lane_4_cluster_estimate = models.IntegerField(blank=True, null=True)
- lane_5_cluster_estimate = models.IntegerField(blank=True, null=True)
- lane_6_cluster_estimate = models.IntegerField(blank=True, null=True)
- lane_7_cluster_estimate = models.IntegerField(blank=True, null=True)
- lane_8_cluster_estimate = models.IntegerField(blank=True, null=True)
-
- #Machine Names
- CLUSTER_MAC = (
- ('M304','M304'),
- ('R349','R349'),
- ('Tinkerbell','Tinkerbell'),
- ('BitBit','BitBit'),
- )
-
- SEQ_MAC = (
- ('EAS149','EAS149'),
- ('EAS46','EAS46'),
- ('EAS45','Paris'),
- ('Britney','Britney'),
- )
-
- cluster_mac_id = models.CharField(max_length=50, choices=CLUSTER_MAC, default='M304')
- seq_mac_id = models.CharField(max_length=50, choices=SEQ_MAC, verbose_name = 'Sequencer', default='EAS149')
-
- notes = models.TextField(blank=True)
-
- def __str__(self):
- #return '%s (%s)' % (self.flowcell_id, self.run_date)
- return '%s' % (self.flowcell_id)
-
-
- def Lanes(self):
- return '<div><span style="margin-right:10px">1)%s</span><span style="margin-right:10px">2)%s</span><span style="margin-right:10px">3)%s</span><span style="margin-right:10px">4)%s</span><span style="margin-right:10px">5)%s</span><span style="margin-right:10px">6)%s</span><span style="margin-right:10px">7)%s</span><span style="margin-right:10px">8)%s</span></div>' % (self.lane_1_library,self.lane_2_library,self.lane_3_library,self.lane_4_library,self.lane_5_library,self.lane_6_library,self.lane_7_library,self.lane_8_library)
- Lanes.allow_tags = True
-
- class Meta:
- ordering = ["-run_date"]
-
- class Admin:
- save_on_top = True
- date_hierarchy = "run_date"
- save_on_top = True
- search_fields = ['lane_1_library', 'lane_2_library', 'lane_3_library', 'lane_4_library', 'lane_5_library', 'lane_6_library', 'lane_7_library', 'lane_8_library']
- list_display = ('flowcell_id','seq_mac_id','run_date', 'Lanes')
- list_filter = ('seq_mac_id',)
- fields = (
- (None, {
- 'fields': ('run_date', ('flowcell_id','cluster_mac_id','seq_mac_id'), ('read_length'),)
- }),
- ('Lanes:', {
- 'fields' : (('lane_1_library', 'lane_1_pM', 'lane_1_cluster_estimate'), ('lane_2_library', 'lane_2_pM', 'lane_2_cluster_estimate'), ('lane_3_library', 'lane_3_pM', 'lane_3_cluster_estimate'), ('lane_4_library', 'lane_4_pM', 'lane_4_cluster_estimate'), ('lane_5_library', 'lane_5_pM', 'lane_5_cluster_estimate'), ('lane_6_library', 'lane_6_pM', 'lane_6_cluster_estimate'), ('lane_7_library', 'lane_7_pM', 'lane_7_cluster_estimate'), ('lane_8_library', 'lane_8_pM', 'lane_8_cluster_estimate'),)
- }),
- (None, {
- 'fields' : ('notes',)
- }),
- )
-
-#class ElandResult(models.Model):
-#
-# class Admin: pass
-#
-# flow_cell = models.ForeignKey(FlowCell)
-# config_file = models.FileField(upload_to=settings.UPLOADTO_CONFIG_FILE)
-# eland_result_pack = models.FileField(upload_to=settings.UPLOADTO_ELAND_RESULT_PACKS)
-# bed_file_pack = models.FileField(upload_to=settings.UPLOADTO_BED_PACKS)
-#
-# notes = models.TextField(blank=True)
# Project specific settings
ALLOWED_IPS = {"74.51.115.100":"HudsonAlpha","64.89.97.100":"HudsonAlpha","127.0.0.1":"Localhost"}
-ALLOWED_ANALYS_IPS = {"171.65.76.194":"Stanford Analysis 1"}
+ALLOWED_ANALYS_IPS = {"171.65.76.194":"Stanford Analysis 1","127.0.0.1":"Localhost"}
#UPLOADTO_HOME = os.path.abspath('../../uploads')
#UPLOADTO_CONFIG_FILE = os.path.join(UPLOADTO_HOME, 'eland_config')
#UPLOADTO_ELAND_RESULT_PACKS = os.path.join(UPLOADTO_HOME, 'eland_results')
from django.conf.urls.defaults import *
# Databrowser:
-from django.contrib import databrowse
-from fctracker.models import Library, FlowCell
-databrowse.site.register(Library)
-databrowse.site.register(FlowCell)
+#from django.contrib import databrowse
+#from fctracker.models import Library
+#databrowse.site.register(Library)
+#databrowse.site.register(FlowCell)
urlpatterns = patterns('',
- # Base:
- #(r'^eland_config/', include('gaworkflow.frontend.eland_config.urls')),
# Admin:
(r'^admin/', include('django.contrib.admin.urls')),
# ExpTrack:
(r'^exp_track/', include('gaworkflow.frontend.exp_track.et_urls')),
- # Databrowser:
- (r'^databrowse/(.*)', databrowse.site.root),
+ # AnalysTrack:
+ (r'^analys_track/', include('gaworkflow.frontend.analys_track.an_urls')),
+ # Report Views:
+ # (r'^reports/', include('gaworkflow.frontend....urls')),
)
projects / htsworkflow.git / commitdiff