--- /dev/null
+Conversion SQLs for Caltech DB (schema of 2008Aug08 @ 5:06 PM)
+______________________________________________________________
+
+
+Step by step do the following:
+
+''' Note: Instead of '?' you can put one of your machine names.
+sqlite> ALTER TABLE fctracker_flowcell ADD cluster_mac_id varchar(50) NOT NULL DEFAULT '?';
+sqlite> ALTER TABLE fctracker_flowcell ADD seq_mac_id varchar(50) NOT NULL DEFAULT '?';
+sqlite> ALTER TABLE fctracker_library RENAME TO PREV_fctracker_library;
+
+Now, do a syncdb. The output should look like this (assuming you have migrated to the new models.py):
+sh-3.2# pym syncdb
+Creating table fctracker_cellline
+Creating table fctracker_library
+Creating table fctracker_primer
+Creating table fctracker_antibody
+Creating table fctracker_condition
+Creating table exp_track_datarun
+Creating table exp_track_flowcell
+Creating table analys_track_project
+Creating table analys_track_task
+Creating table htsw_reports_progressreport
+Installing index for fctracker.Library model
+Failed to install index for fctracker.Library model: index fctracker_library_library_species_id already existsInstalling index for fctracker.Primer model
+Installing index for fctracker.Antibody model
+Installing index for exp_track.DataRun model
+Installing index for exp_track.FlowCell model
+Installing index for analys_track.Task model
+Installing index for htsw_reports.ProgressReport model
+sh-3.2#
+
+''' Copy all records from "fctracker_flowcell" to "exp_track_flowcell" table. (Why? Because, Flowcell table moves now from the "fctracker" to the "exp_track" component).
+sqlite> insert into experiments_flowcell select * from fctracker_flowcell;
+
+''' Now to fctracker_library, a bit more complex case
+
+'''Back to the sqlite prompt..
+sqlite> insert into samples_cellline (cellline_name,notes) values('Unknown','Unknown');
+sqlite> insert into samples_condition (condition_name,notes) values('Unknown','Unknown');
+''' Now we can put 1 in these fields for the Library insert.
+''' Note: avg_lib_size field is missing in Caltech DB (although it's in the models.py Trac), so I put default value 225.
+
+''' Now the actual migration to the new fctracker_library table
+''' (This version looses data, the current Nov 11, 2008 schema, has made_for as a one to many
+''' relationship to the auth_user table, instead of being a text field. Here I just assigned
+''' the made for to a (semi)-random user.
+sqlite> INSERT INTO samples_library (library_id,library_name,library_species_id,experiment_type,cell_line_id,condition_id,replicate,made_by,creation_date,made_for_id,stopping_point,amplified_from_sample_id,undiluted_concentration,ten_nM_dilution,successful_pM,avg_lib_size,notes) select library_id,library_name,library_species_id,'unknown',1,1,1,made_by,creation_date,12,stopping_point,amplified_from_sample_id,undiluted_concentration,ten_nM_dilution,successful_pM,0,notes from PREV_fctracker_library;
+
+''' Set the right values for "experiment_type"
+sqlite> update samples_library set experiment_type = "RNA-seq" where library_idin (select library_id from prev_fctracker_library where RNASeq = 1);
+''' YOU CAN ADD SIMILAR SQL CMD TO SET THE VALUE FOR "avg_lib_size" FIELD (WHICH IS NOW SET TO 0) ...
+
+----------------------------------------------------------------------------------------
+THAT SHOULD BE IT --- NOW YOUR WEB SITE SHOULD SUCESSFULY LOAD THE NEW DB WITH YOUR DATA.
+
+2009 Jan 13
+
+I had a working database and then merged in a few more changes from
+stanford. I ended up needing to do the following:
+
+alter table analysis_task add task_params varchar(200) null;
+alter table samples_cellline add nickname varchar(20) null;
+alter table samples_condition add nickname varchar(20) null;
+
+Those changes might happen automatically when reconverting from our
+original database, or they might not.
+
+CREATE TABLE "samples_library_tags" (
+ "id" integer NOT NULL PRIMARY KEY,
+ "library_id" varchar(30) NOT NULL REFERENCES "samples_library" ("library_id"),
+ "tag_id" integer NOT NULL REFERENCES "samples_tag" ("id"),
+ UNIQUE ("library_id", "tag_id")
+)
+;
+
--- /dev/null
+from htsworkflow.frontend.analysis.models import Task, Project
+from django.contrib import admin
+from django.utils.translation import ugettext_lazy as _
+
+class ProjectOptions(admin.ModelAdmin):
+ list_display = ('ProjTitle','ProjectTasks')
+ list_filter = ()
+ search_fieldsets = ['project_name','=tasks__subject1__library_id','=tasks__subject2__library_id','tasks__subject1__library_name','tasks__subject2__library_name','project_notes']
+ fieldsets = (
+ (None, {
+ 'fields': (('project_name'),('tasks'),('project_notes'))}),
+ )
+ filter_horizontal = ('tasks',)
+
+class TaskOptions(admin.ModelAdmin):
+ list_display = ('task_name','apply_calc','subject1','subject2','task_params','InProjects','submitted_on','task_status')
+ list_filter = ('apply_calc',)
+ search_fieldsets = ['task_name','id','=subject1__library_id','=subject2__library_id']
+ fieldsets = (
+ (None, {
+ 'fields': (('task_name'),('apply_calc'),('subject1'),('subject2'),('task_params'))
+ }),
+ ('system fields', {
+ 'classes': ('collapse',),
+ 'fields': (('submitted_on'),('task_status','run_note'))
+ }),
+ )
+
+admin.site.register(Project, ProjectOptions)
+admin.site.register(Task, TaskOptions)
+
)
apply_calc = models.CharField(max_length=50,choices=CALCS,verbose_name='Applied Calculation')
## userid = # logged in user
+ task_params = models.CharField(max_length=200,blank=True,null=True,default="")
task_status = models.CharField(max_length=500,blank=True,null=True,default='defined')
results_location = models.CharField(max_length=2000,blank=True,null=True)
submitted_on = models.DateTimeField(default=datetime.now())
pstr += '%s, ' % (p.project_name)
return pstr
- class Admin:
- list_display = ('task_name','apply_calc','subject1','subject2','InProjects','submitted_on','task_status')
- list_filter = ('apply_calc',)
- search_fields = ['task_name','id','=subject1__library_id','=subject2__library_id']
- fields = (
- (None, {
- 'fields': (('task_name'),('apply_calc'),('subject1'),('subject2'))
- }),
- ('system fields', {
- 'classes': 'collapse',
- 'fields': (('submitted_on'),('task_status','run_note'))
- }),
- )
-
class Project(models.Model):
project_name = models.CharField(max_length=50,unique=True, db_index=True)
- tasks = models.ManyToManyField(Task,related_name='project_tasks',null=True,filter_interface=models.HORIZONTAL)
+ tasks = models.ManyToManyField(Task,related_name='project_tasks',null=True)
project_notes = models.CharField(max_length=500,blank=True,null=True)
def __str__(self):
def ProjectTasks(self):
ptasks = self.tasks.all().order_by('id')
- surl = 'http://m304-apple-server.stanford.edu/projects/'
+ surl = settings.ANALYSIS_SERVER+'/projects/'
tstr = '<script>'
tstr += 'function togView(eid){'
tstr += 'f=document.getElementById(eid);'
tstr += '<table><tr><th>Tasks</th><th>Job Status</th>'
isregistered = False
for t in ptasks:
- tstr += '<tr><td width=250>%s</td><td>%s</td></tr>' % (t.task_name,replace(t.task_status,'Complete','<span style="color:green;font-weight:bolder">Complete</span>'))
+ taskdesc = t.task_name+'<div style="font-size:80%">Details: '+t.apply_calc+' on '+t.subject1.library_id
+ if t.subject2 is not None:
+ taskdesc += ' and '+t.subject2.library_id
+ taskdesc += ' (TaskId:'+t.id.__str__()+')'
+ tstr += '<tr><td width=250>%s</td><td>%s</td></tr>' % (taskdesc,replace(t.task_status,'Complete','<span style="color:green;font-weight:bolder">Complete</span>'))
+
if t.task_status != 'defined': isregistered = True
tstr += '</table>'
ProjTitle.allow_tags = True
- class Admin:
- list_display = ('ProjTitle','ProjectTasks')
- list_filter = ()
- search_fields = ['project_name','=tasks__subject1__library_id','=tasks__subject2__library_id','tasks__subject1__library_name','tasks__subject2__library_name','project_notes']
- fields = (
- (None, {
- 'fields': (('project_name'),('tasks'),('project_notes'))}),
- )
-from django import newforms as forms
-from django.newforms.util import ErrorList
+from django import forms
+from django.forms.util import ErrorList
SPECIES_LIST = [#('--choose--', '--Choose--'),
return '\n'.join(html)
-
\ No newline at end of file
+
--- /dev/null
+from htsworkflow.frontend.experiments.models import FlowCell, DataRun
+from django.contrib import admin
+from django.utils.translation import ugettext_lazy as _
+
+class DataRunOptions(admin.ModelAdmin):
+ search_fieldsets = ['run_folder','run_note','config_params','=fcid__lane_1_library__library_id','=fcid__lane_2_library__library_id','=fcid__lane_3_library__library_id','=fcid__lane_4_library__library_id','=fcid__lane_5_library__library_id','=fcid__lane_6_library__library_id','=fcid__lane_7_library__library_id','=fcid__lane_8_library__library_id']
+
+class FlowCellOptions(admin.ModelAdmin):
+ date_hierarchy = "run_date"
+ save_on_top = True
+ search_fieldsets = ('flowcell_id',
+ 'seq_mac_id',
+ 'cluster_mac_id',
+ '=lane_1_library__library_id',
+ '=lane_2_library__library_id',
+ '=lane_3_library__library_id',
+ '=lane_4_library__library_id',
+ '=lane_5_library__library_id',
+ '=lane_6_library__library_id',
+ '=lane_7_library__library_id',
+ '=lane_8_library__library_id')
+ list_display = ('flowcell_id','seq_mac_id','run_date', 'Create_LOG','Lanes')
+ list_filter = ('seq_mac_id','cluster_mac_id')
+ fieldsets = (
+ (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'),)
+ }),
+ )
+
+admin.site.register(DataRun, DataRunOptions)
+admin.site.register(FlowCell, FlowCellOptions)
+
class FlowCell(models.Model):
flowcell_id = models.CharField(max_length=20, unique=True, db_index=True)
- run_date = models.DateTimeField(core=True)
+ run_date = models.DateTimeField()
advanced_run = models.BooleanField(default=False)
read_length = models.IntegerField(default=32) #Stanford is currenlty 25
notes = models.TextField(blank=True)
- def __str__(self):
- #return '%s (%s)' % (self.flowcell_id, self.run_date)
- return '%s' % (self.flowcell_id)
+ def __unicode__(self):
+ return unicode(self.flowcell_id)
def Create_LOG(self):
str = '' #<span style="color:red;font-size:80%;margin-right:3px">New!</span>'
- str +='<a target=_balnk href="/exp_track/'+self.flowcell_id+'" title="Create XLS like sheet for this Flowcell ..." ">Create LOG</a>'
+ str +='<a target=_balnk href="/experiments/'+self.flowcell_id+'" title="Create XLS like sheet for this Flowcell ..." ">Create LOG</a>'
return str
Create_LOG.allow_tags = True
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 = ['flowcell_id','seq_mac_id','cluster_mac_id','=lane_1_library__library_id','=lane_2_library__library_id','=lane_3_library__library_id','=lane_4_library__library_id','=lane_5_library__library_id','=lane_6_library__library_id','=lane_7_library__library_id','=lane_8_library__library_id']
- list_display = ('flowcell_id','seq_mac_id','run_date', 'Create_LOG','Lanes')
- list_filter = ('seq_mac_id','cluster_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_1_primer'), ('lane_2_library', 'lane_2_pM', 'lane_2_cluster_estimate', 'lane_2_primer'), ('lane_3_library', 'lane_3_pM', 'lane_3_cluster_estimate', 'lane_3_primer'), ('lane_4_library', 'lane_4_pM', 'lane_4_cluster_estimate', 'lane_4_primer'), ('lane_5_library', 'lane_5_pM', 'lane_5_cluster_estimate', 'lane_5_primer'), ('lane_6_library', 'lane_6_pM', 'lane_6_cluster_estimate', 'lane_6_primer'), ('lane_7_library', 'lane_7_pM', 'lane_7_cluster_estimate', 'lane_7_primer'), ('lane_8_library', 'lane_8_pM', 'lane_8_cluster_estimate', 'lane_8_primer'),)
- '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',)
- }),
- )
### -----------------------
run_folder = models.CharField(max_length=50,unique=True, db_index=True)
fcid = models.ForeignKey(FlowCell,verbose_name="Flowcell Id")
config_params = models.TextField(default=ConfTemplate)
- run_start_time = models.DateTimeField(core=True)
+ run_start_time = models.DateTimeField()
RUN_STATUS_CHOICES = (
(0, 'Sequencer running'), ##Solexa Data Pipeline Not Yet Started'),
(1, 'Data Pipeline Started'),
return str
Flowcell_Info.allow_tags = True
- class Admin:
- search_fields = ['run_folder','run_note','config_params','=fcid__lane_1_library__library_id','=fcid__lane_2_library__library_id','=fcid__lane_3_library__library_id','=fcid__lane_4_library__library_id','=fcid__lane_5_library__library_id','=fcid__lane_6_library__library_id','=fcid__lane_7_library__library_id','=fcid__lane_8_library__library_id']
-
- list_display = ('run_folder','Flowcell_Info','run_start_time','main_status','run_note')
- list_filter = ('run_status','run_start_time')
def index(request):
all_runs = DataRun.objects.all().order_by('-run_start_time')
- #t = loader.get_template('exptrack/index.html')
+ #t = loader.get_template('experiments/index.html')
#c = Context({
# 'data_run_list': all_runs,
#})
#return HttpResponse(t.render(c))
# shortcut to the above module usage
- return render_to_response('exptrack/index.html',{'data_run_list': all_runs})
+ return render_to_response('experiments/index.html',{'data_run_list': all_runs})
def detail(request, run_folder):
html_str = '<h2>Exp Track Details Page</h2>'
html_str += 'Run Folder: '+run_folder
r = get_object_or_404(DataRun,run_folder=run_folder)
- return render_to_response('exptrack/detail.html',{'run_f': r})
+ return render_to_response('experiments/detail.html',{'run_f': r})
def makeFCSheet(request,fcid):
# get Flowcell by input fcid
except ObjectDoesNotExist:
pass
lanes = ['1','2','3','4','5','6','7','8']
- return render_to_response('exptrack/flowcellSheet.html',{'fc': rec})
+ return render_to_response('experiments/flowcellSheet.html',{'fc': rec})
def test_Libs(request):
str = ''
--- /dev/null
+from htsworkflow.frontend.reports.models import ProgressReport
+from django.contrib import admin
+from django.utils.translation import ugettext_lazy as _
+
+class ProgressReportOptions(admin.ModelAdmin):
+ list_display = ('Study','ab_batch','cell_line','library','sequencing','aligned_reads','QPCR','submit_to_DCC','submit_to_NCBI','interactome_complete')
+ ## list_filter = ('interactome_complete')
+
+admin.site.register(ProgressReport, ProgressReportOptions)
+
+from htsworkflow.frontend import settings
from django.http import HttpResponse
from datetime import datetime
from string import *
self.searchTerm= searchTerm
self.currlibid = ''
self.LanesCount, self.ReadsCount = 0, 0
- self.Msg = ''
+ self.Msg = 'OK'
def startElement(self, name, attrs):
- if name == 'Library':
- self.currlibid = attrs.get('Name',"")
- elif name == 'Track' and self.searchTerm == self.currlibid:
- self.LanesCount += len(attrs.get('Lane',""))
- self.ReadsCount += int(attrs.get('Count',""))
- else:
- self.Msg += ' | name = '+name+', currlibid = '+ self.currlibid
+ try:
+ if name == 'Library':
+ self.currlibid = attrs.get('Name',"")
+ elif name == 'Track' and self.searchTerm == self.currlibid:
+ self.LanesCount += len(attrs.get('Lane',""))
+ self.ReadsCount += int(attrs.get('Count',""))
+ #else:
+ # self.Msg += ' | name = '+name+', currlibid = '+ self.currlibid
+ except:
+ self.Msg = 'failed parsing xml file'
return
#def characters (self, ch):
parser = make_parser()
curHandler = LibInfoHandler(searchTerm)
parser.setContentHandler(curHandler)
- parser.parse(open('/htsworkflow/htswfrontend/htswfrontend/htsw_reports/LibInfo/LibraryInfo.xml'))
+ reports_dir = os.path.split(__file__)[0]
+ library_info = os.path.join(reports_dir, 'LibraryInfo.xml')
+ parser.parse(open(library_info))
arRes = []
arRes.append(curHandler.LanesCount)
arRes.append(curHandler.ReadsCount)
+ arRes.append(curHandler.Msg)
+
return arRes
def getWebPage(url,params):
def refreshLibInfoFile(request):
varStatus = 'getting conf file from exp trac server'
- url = 'http://m304-apple-server.stanford.edu/ENCODE/LibraryInfo.xml'
+ url = settings.TASKS_PROJS_SERVER+'/LibraryInfo.xml'
params = {}
readw = getWebPage(url,params)
# make sure file content starts as xml
if day < 10: day = "0"+day.__str__()
else: day = day.__str__()
mydate = year+month+day
- folder = '/htsworkflow/htswfrontend/htswfrontend/htsw_reports/LibInfo/'
+ folder_loc = '/htsworkflow/htswfrontend/htswfrontend' # DEV
+ #folder_loc = '/Library/WebServer/gaworkflow/gaworkflow/frontend' # PROD
+ folder = folder_loc+'/htsw_reports/LibInfo/'
os.rename(folder+'LibraryInfo.xml',folder+mydate+'_LibraryInfo.xml')
# create file in curret folder
file_path = os.path.join(folder,'LibraryInfo.xml')
--- /dev/null
+from htsworkflow.frontend.experiments.models import *
+from django.http import HttpResponse
+from django.core.exceptions import ObjectDoesNotExist
+from django.shortcuts import render_to_response, get_object_or_404
+
+def getBgColor(reads_cnt,exp_type):
+ # Color Scheme: green is more than 12M, blue is more than 5M, orange is more than 3M and red is less. For RNAseq, all those thresholds are ~ double
+ bgcolor = '#ff3300' # Red is the color for minimum read counts
+ rc_thr = [12000000,5000000,3000000] # Default for ChIP-Seq and Methyl-Seq
+ if exp_type == 'RNA-seq':
+ rc_thr = [20000000,10000000,6000000]
+
+ if reads_cnt > rc_thr[0]:
+ bgcolor = '#66ff66' # Green
+ else:
+ if reads_cnt > rc_thr[1]:
+ bgcolor ='#00ccff' # Blue
+ else:
+ if reads_cnt > rc_thr[2]:
+ bgcolor ='#ffcc33' # Orange
+ #tstr = '<div style="background-color:'+bgcolor+';color:black">'
+ #tstr += res[0].__str__()+' Lanes, '+rc+' M Reads'
+ #tstr += '</div>'
+
+ return bgcolor
+
+def report1(request):
+ EXP = 'ChIP-seq'
+
+ if request.has_key('aflid'):
+ AFL_Id = request['aflid']
+ try:
+ AFL = Affiliation.objects.get(id=AFL_Id).name
+ AFL_CNT = Affiliation.objects.get(id=AFL_Id).contact
+ except ObjectDoesNotExist:
+ return HttpResponse("ERROR: Affiliation Record Not Found for: '"+AFL_ID+"'")
+ else:
+ AFL = 'ENCODE_Tier1'
+ AFL_CNT = ''
+ try:
+ AFL_Id = Affiliation.objects.get(name=AFL,contact=AFL_CNT).id.__str__()
+ except ObjectDoesNotExist:
+ return HttpResponse("ERROR: Affiliation Record Not Found for: '"+AFL+"'")
+
+ TFall = Library.objects.values('antibody').order_by('antibody').distinct()
+ CLLall = Library.objects.values('cell_line').order_by('cell_line').distinct()
+
+ TFs = TFall.filter(experiment_type=EXP,affiliations__name=AFL,affiliations__contact=AFL_CNT)
+ CLLs = CLLall.filter(experiment_type=EXP,affiliations__name=AFL,affiliations__contact=AFL_CNT)
+
+ # Check Replicate numbers
+ Reps = 1
+ RepRecs = Library.objects.filter(experiment_type=EXP,affiliations__name=AFL,affiliations__contact=AFL_CNT).order_by('-replicate')
+ if len(RepRecs) > 0: Reps = RepRecs[0].replicate
+
+ ########
+ str = ''
+ str += '<span style="margin-right:20px"><a target=_self href="/admin" target=_self">Main Page</a></span>'
+ ##str += '<span style="margin-right:20px">Max Replicates: '+MaxRep.replicate.__str__()+'</span>'
+ str += '<span>Select another <b>'+EXP+'</b> Report:</span> <select>'
+ for af in Affiliation.objects.distinct():
+ str += '<option value='+af.id.__str__()
+ if AFL_Id == af.id.__str__():
+ str += ' selected'
+ str += ' onclick="window.location=\'/htsw_reports/report?aflid='+af.id.__str__()+'\'; return false;">'+af.name+' '+af.contact+'</option>'
+ str += '</select>'
+
+ str += '<span style="margin-left:20px;padding:1px;border:solid #cccccc 1px">color scheme: <span style="margin-left:5px;background-color:#66ff66"> > 12 M</span><span style="margin-left:5px;background-color:#00ccff"> > 5 M</span><span style="margin-left:5px;background-color:#ffcc33"> > 3 M</span><span style="margin-left:5px;background-color:#ff3300"> < 3 M</span></span>'
+
+ str += '<span style="margin-left:20px">'
+ str += '<u>Switch to:</u> '+AFL+' '+AFL_CNT+' <a target=_self href="/htsw_reports/report_RM?exp=RNA-seq&aflid='+AFL_Id+'"><b>RNA-Seq</b> Report</a>'
+ str += ' | '
+ str += '<a target=_self href="/htsw_reports/report_RM?exp=Methyl-seq&aflid='+AFL_Id+'"><b>Methyl-Seq</b> Report</a>'
+
+ bgc = '#ffffff'
+ pbgc = '#f7f7f7'
+ str += '<br/><br/><table border=1 cellspacing="2">'
+ str += '<tr><th style="text-align:right">PROJECT</th><th colspan='+(Reps*len(CLLs)).__str__()+' style="text-align:center">'+AFL+' '+AFL_CNT+' <span style="font-size:140%">'+EXP+'</span></th></tr>'
+ str += '<tr><th style="text-align:right">CELL LINE</th>'
+ for H in CLLs:
+ str += '<th colspan='+Reps.__str__()+' style="text-align:center;background-color:'+bgc+'">'+Cellline.objects.get(id=H['cell_line']).cellline_name+'</th>'
+ tbgc = bgc
+ bgc = pbgc
+ pbgc = tbgc
+ str += '</tr><tr><th style="text-align:left">TF</th>'
+ bgc = '#ffffff'
+ pbgc = '#f7f7f7'
+ for H in CLLs:
+ for r in range(1,Reps+1):
+ str += '<th style="text-align:center;background-color:'+bgc+'">Rep. '+r.__str__()+'</th>'
+ tbgc = bgc
+ bgc = pbgc
+ pbgc = tbgc
+ str += '</tr>'
+ str += '<tr><td align=right><a title="View Libraries Records" target=_self href=/admin/fctracker/library/?affiliations__id__exact='+AFL_Id+'&experiment_type__exact=INPUT_RXLCh>Total Chromatin</a></td>'
+ bgc = '#ffffff'
+ pbgc = '#f7f7f7'
+ for H in CLLs:
+ for r in range(1,Reps+1):
+ repReads = Library.objects.filter(experiment_type='INPUT_RXLCh',affiliations__name=AFL,affiliations__contact=AFL_CNT,cell_line=H['cell_line'].__str__(),replicate=r)
+ str += "<td align=center style='background-color:"+bgc+"'>"
+ if len(repReads) == 0:
+ str += 'No Libraries'
+ else:
+ cnt = 0
+ for R1 in repReads:
+ rres = R1.aligned_m_reads()
+ # Check data sanlty
+ if rres[2] != 'OK':
+ str += '<div style="border:solid red 2px">'+rres[2]
+ else:
+ cnt = rres[1]
+ if cnt > 0:
+ str += "<div style='background-color:"+getBgColor(cnt,EXP)+";font-size:140%'>"
+ str += "%1.2f" % (cnt/1000000.0)+" M"
+ else: str += "<div style='background-color:#ff3300;width:100%;font-size:140%'>0 Reads"
+ str += "<div style='font-size:70%'>"+R1.library_id+", "+R1.condition.nickname+"</div>"
+ str += "</div>"
+ str += '</td>'
+ tbgc = bgc
+ bgc = pbgc
+ pbgc = tbgc
+ str += '</tr>'
+
+ for T in TFs:
+ str += '<tr>'
+ try:
+ if T['antibody']:
+ str += '<td><a title="View Libraries Records" target=_self href=/admin/fctracker/library/?affiliations__id__exact='+AFL_Id+'&antibody__id__exact='+T['antibody'].__str__()+'>'+Antibody.objects.get(id=T['antibody']).nickname+'</a></td>'
+ except Antibody.DoesNotExist:
+ str += '<td>n/a</td>'
+
+ bgc = '#ffffff'
+ pbgc = '#f7f7f7'
+ for H in CLLs:
+ for r in range(1,Reps+1):
+ repReads = Library.objects.filter(experiment_type=EXP,affiliations__name=AFL,affiliations__contact=AFL_CNT,cell_line=H['cell_line'].__str__(),antibody=T['antibody'].__str__(),replicate=r)
+ str += "<td align=center style='background-color:"+bgc+"'>"
+ if len(repReads) == 0:
+ str += 'No Libraries'
+ else:
+ cnt = 0
+ for R1 in repReads:
+ rres = R1.aligned_m_reads()
+ # Check data sanlty
+ if rres[2] != 'OK':
+ str += '<div style="border:solid red 2px">'+rres[2]
+ else:
+ cnt = rres[1]
+ if cnt > 0:
+ str += "<div style='background-color:"+getBgColor(cnt,EXP)+";font-size:140%'>"
+ str += "%1.2f" % (cnt/1000000.0)+" M"
+ else: str += "<div style='background-color:#ff3300;width:100%;font-size:140%'>0 Reads"
+ str += "<div style='font-size:70%'>"+R1.library_id+", "+R1.condition.nickname+"</div>"
+ str += "</div>"
+ str += '</td>'
+ tbgc = bgc
+ bgc = pbgc
+ pbgc = tbgc
+ str += '</tr>'
+ str += '</table>'
+
+ return render_to_response('htsw_reports/report.html',{'main': str})
+
+
+def report_RM(request): #for RNA-Seq and Methyl-Seq
+ EXP = 'RNA-seq'
+
+ if request.has_key('exp'):
+ EXP = request['exp'] # Methyl-seq
+
+ if request.has_key('aflid'):
+ AFL_Id = request['aflid']
+ try:
+ AFL = Affiliation.objects.get(id=AFL_Id).name
+ AFL_CNT = Affiliation.objects.get(id=AFL_Id).contact
+ except ObjectDoesNotExist:
+ return HttpResponse("ERROR: Affiliation Record Not Found for: '"+AFL_ID+"'")
+ else:
+ AFL = 'ENCODE_Tier1'
+ AFL_CNT = ''
+ try:
+ AFL_Id = Affiliation.objects.get(name=AFL,contact=AFL_CNT).id.__str__()
+ except ObjectDoesNotExist:
+ return HttpResponse("ERROR: Affiliation Record Not Found for: '"+AFL+"'")
+
+ CLLall = Library.objects.values('cell_line').order_by('cell_line').distinct()
+ CLLs = CLLall.filter(experiment_type=EXP,affiliations__name=AFL,affiliations__contact=AFL_CNT)
+
+ ########
+ # Check Replicate numbers
+ Reps = 1
+ RepRecs = Library.objects.filter(experiment_type=EXP,affiliations__name=AFL,affiliations__contact=AFL_CNT).order_by('-replicate')
+ if len(RepRecs) > 0: Reps = RepRecs[0].replicate
+
+ str = ''
+ str += '<span style="margin-right:20px"><a target=_self href="/admin" target=_self">Main Page</a></span>'
+ str += '<span>Select another <b>'+EXP+'</b> Report:</span> <select>'
+ for af in Affiliation.objects.distinct():
+ str += '<option value='+af.id.__str__()
+ if AFL_Id == af.id.__str__():
+ str += ' selected'
+ str += ' onclick="window.location=\'/htsw_reports/report_RM?exp='+EXP+'&aflid='+af.id.__str__()+'\'; return false;">'+af.name+' '+af.contact+'</option>'
+ str += '</select>'
+
+ if EXP == 'RNA-seq':
+ str += '<span style="margin-left:20px;padding:1px;border:solid #cccccc 1px">color scheme: <span style="margin-left:5px;background-color:#66ff66"> > 20 M</span><span style="margin-left:5px;background-color:#00ccff"> > 10 M</span><span style="margin-left:5px;background-color:#ffcc33"> > 6 M</span><span style="margin-left:5px;background-color:#ff3300"> < 6 M</span></span>'
+ str += '<span style="margin-left:20px">'
+ str += '<u>Switch to:</u> '+AFL+' '+AFL_CNT+' <a target=_self href="/htsw_reports/report?exp=RNA-seq&aflid='+AFL_Id+'"><b>ChIP-Seq</b> Report</a>'
+ str += ' | '
+ str += '<a target=_self href="/htsw_reports/report_RM?exp=Methyl-seq&aflid='+AFL_Id+'"><b>Methyl-Seq</b> Report</a>'
+ else:
+ str += '<span style="margin-left:20px;padding:1px;border:solid #cccccc 1px">color scheme: <span style="margin-left:5px;background-color:#66ff66"> > 12 M</span><span style="margin-left:5px;background-color:#00ccff"> > 5 M</span><span style="margin-left:5px;background-color:#ffcc33"> > 3 M</span><span style="margin-left:5px;background-color:#ff3300"> < 3 M</span></span>'
+ str += '<span style="margin-left:20px">'
+ str += '<u>Switch to:</u> '+AFL+' '+AFL_CNT+' <a target=_self href="/htsw_reports/report?exp=RNA-seq&aflid='+AFL_Id+'"><b>ChIP-Seq</b> Report</a>'
+ str += ' | '
+ str += '<a target=_self href="/htsw_reports/report_RM?exp=RNA-seq&aflid='+AFL_Id+'"><b>RNA-Seq</b> Report</a>'
+
+ str += '<br/><br/><table border=1 cellspacing="2">'
+ str += '<tr><th colspan='+(Reps*len(CLLs)).__str__()+' style="text-align:center">'+AFL+' '+AFL_CNT+' <span style="font-size:140%">'+EXP+'</span></th></tr>'
+ str += '<tr>'
+ bgc = '#ffffff'
+ pbgc = '#f7f7f7'
+ for H in CLLs:
+ str += '<th colspan='+Reps.__str__()+' style="text-align:center;background-color:'+bgc+'">'+Cellline.objects.get(id=H['cell_line']).cellline_name+'</th>'
+ tbgc = bgc
+ bgc = pbgc
+ pbgc = tbgc
+ str += '</tr><tr>'
+ bgc = '#ffffff'
+ pbgc = '#f7f7f7'
+ for H in CLLs:
+ for r in range(1,Reps+1):
+ str += '<th style="text-align:center;background-color:'+bgc+'">Rep. '+r.__str__()+'</th>'
+ tbgc = bgc
+ bgc = pbgc
+ pbgc = tbgc
+ str += '</tr>'
+
+ str += '<tr>'
+ bgc = '#ffffff'
+ pbgc = '#f7f7f7'
+ for H in CLLs:
+ for r in range(1,Reps+1):
+ repReads = Library.objects.filter(experiment_type=EXP,affiliations__name=AFL,affiliations__contact=AFL_CNT,cell_line=H['cell_line'],replicate=r)
+ str += "<td align=center valign=top style='background-color:"+bgc+"'>"
+ if len(repReads) == 0:
+ str += 'No Libraries'
+ else:
+ cnt = 0
+ for R1 in repReads:
+ rres = R1.aligned_m_reads()
+ # Check data sanlty
+ if rres[2] != 'OK':
+ str += '<div style="border:solid red 2px">'+rres[2]
+ else:
+ cnt = rres[1]
+ if cnt > 0:
+ str += "<div style='background-color:"+getBgColor(cnt,EXP)+";border:solid #cccccc 1px;font-size:140%'>"
+ str += "%1.2f" % (cnt/1000000.0)+" M"
+ else: str += "<div style='background-color:#ff3300;border:solid #cccccc 1px;width:100%;font-size:140%'>0 Reads"
+ str += "<div style='font-size:80%'><a title='View Record' target=_self href=/admin/fctracker/library/?q="+R1.library_id+">"+R1.library_id+"</a>, "+R1.condition.nickname+", "+R1.library_species.common_name+"</div>"
+ str += "<div style='font-size:70%'>\""+R1.library_name+"\"</div"
+ str += "</div>"
+ str += '</td>'
+ tbgc = bgc
+ bgc = pbgc
+ pbgc = tbgc
+ str += '</tr>'
+ str += '</table>'
+
+ return render_to_response('htsw_reports/report.html',{'main': str})
+
+def getNotRanFCs(request):
+ FCall = FlowCell.objects.order_by('-run_date').distinct()
+ str = '<table><tr><th>FlowCell</th><th>Lanes</th><th>Creation Date</th></tr>'
+ for f in FCall:
+ try:
+ t = DataRun.objects.get(fcid=f.id)
+ except ObjectDoesNotExist:
+ str += '<tr><td>'+f.flowcell_id+'</td><td>'+f.Lanes()+'</td><td>'+f.run_date.__str__()+'</td></tr>'
+ str += "</table>"
+ return render_to_response('htsw_reports/report.html',{'main':str})
+
+def test_Libs(request):
+ str = ''
+ str += '<table border=1><tr><th>Lib ID</th><th>Current Libaray Name (Free Text)</th><th>Auto-composed Libaray Name (antibody + celline + libid + species + [replicate])</th></tr>'
+ allLibs = Library.objects.all()
+ #allLibs = Library.objects.filter(antibody__isnull=False)
+ for L in allLibs:
+ str += '<tr>'
+ str += '<td>'+L.library_id+'</td><td>'+L.library_name+'</td>'
+ str += '<td>'
+ str += L.experiment_type+'_'
+ if L.cell_line.cellline_name != 'Unknown':
+ str += L.cell_line.cellline_name+'_'
+
+ try:
+ if L.antibody is not None:
+ str += L.antibody.nickname + '_'
+ except Antibody.DoesNotExist:
+ pass
+
+ str += 'Rep'+L.replicate.__str__()
+ str += '</td></tr>'
+
+ str += '</table>'
+ return HttpResponse(str)
urlpatterns = patterns('',
(r'^updLibInfo$', 'htsworkflow.reports.libinfopar.refreshLibInfoFile'),
+ (r'^report$', 'htsworkflow.reports.reports.report1'),
+ (r'^report_RM$', 'htsworkflow.reports.reports.report_RM'),
+ (r'^report_FCs$', 'htsworkflow.reports.reports.getNotRanFCs'),
+ (r'^liblist$', 'htsworkflow.reports.reports.test_Libs')
)
--- /dev/null
+from htsworkflow.frontend.samples.models import Antibody, Cellline, Condition, Species, Affiliation, Library, Tag
+from django.contrib import admin
+from django.utils.translation import ugettext_lazy as _
+
+class Library_Inline(admin.TabularInline):
+ model = Library
+
+class CelllineOptions(admin.ModelAdmin):
+ fieldsets = (
+ (None, {
+ 'fields': (('cellline_name'),('notes'),)
+ }),
+ )
+
+class LibraryOptions(admin.ModelAdmin):
+ date_hierarchy = "creation_date"
+ save_as = True
+ save_on_top = True
+ search_fieldsets = (
+ 'library_id',
+ 'library_name',
+ 'cell_line__cellline_name',
+ 'library_species__scientific_name',
+ 'library_species__common_name',
+ )
+ list_display = (
+ 'library_id',
+ 'aligned_reads',
+ 'DataRun',
+ 'library_name',
+ 'experiment_type',
+ 'organism',
+ 'antibody_name',
+ 'cell_line',
+ 'libtags',
+ 'made_for',
+ 'made_by',
+ 'stopping_point',
+ 'creation_date',
+ 'condition',
+ )
+ list_filter = (
+ 'experiment_type',
+ 'library_species',
+ 'tags',
+ 'made_for',
+ 'made_by',
+ 'antibody',
+ 'cell_line',
+ 'condition',
+ 'stopping_point')
+ list_display_links = ('library_id', 'library_name',)
+ fieldsets = (
+ (None, {
+ 'fields': (
+ ('replicate','library_id','library_name'),
+ ('library_species'),
+ ('experiment_type'),
+ ('cell_line','condition','antibody'),)
+ }),
+ ('Creation Information:', {
+ 'fields' : (('made_for', 'made_by', 'creation_date'), ('stopping_point', 'amplified_from_sample'), ('avg_lib_size','undiluted_concentration', 'ten_nM_dilution', 'successful_pM'), 'notes',)
+ }),
+ ('Library/Project Affiliation:', {
+ 'fields' : (('affiliations'), ('tags'),)
+ }),
+ )
+
+class AffiliationOptions(admin.ModelAdmin):
+ list_display = ('name','contact','email')
+ fieldsets = (
+ (None, {
+ 'fields': (('name','contact','email'))
+ }),
+ )
+
+# class UserOptions(admin.ModelAdmin):
+# inlines = [Library_Inline]
+
+class AntibodyOptions(admin.ModelAdmin):
+ list_display = ('antigene','nickname','antibodies','catalog','source','biology','notes')
+ list_filter = ('antibodies','source')
+ fieldsets = (
+ (None, {
+ 'fields': (('antigene','nickname','antibodies'),('catalog','source'),('biology'),('notes'))
+ }),
+ )
+
+class SpeciesOptions(admin.ModelAdmin):
+ fieldsets = (
+ (None, {
+ 'fields': (('scientific_name', 'common_name'),)
+ }),
+ )
+
+class ConditionOptions(admin.ModelAdmin):
+ list_display = (('condition_name'), ('notes'),)
+ fieldsets = (
+ (None, {
+ 'fields': (('condition_name'),('nickname'),('notes'),)
+ }),
+ )
+
+class TagOptions(admin.ModelAdmin):
+ list_display = ('tag_name', 'context')
+ fieldsets = (
+ (None, {
+ 'fields': ('tag_name', 'context')
+ }),
+ )
+
+admin.site.register(Affiliation, AffiliationOptions)
+admin.site.register(Antibody, AntibodyOptions)
+admin.site.register(Cellline, CelllineOptions)
+admin.site.register(Condition, ConditionOptions)
+admin.site.register(Library, LibraryOptions)
+admin.site.register(Species, SpeciesOptions)
+admin.site.register(Tag, TagOptions)
from django.db import models
from django.contrib.auth.models import User
from htsworkflow.frontend import settings
-#from htsworkflow.reports.libinfopar import *
+from htsworkflow.frontend.reports.libinfopar import *
# Create your models here.
class Antibody(models.Model):
- antigene = models.CharField(max_length=500, db_index=True)
- # New field Aug/20/08
- # SQL to add column: alter table fctracker_antibody add column "nickname" varchar(20) NULL;
- nickname = models.CharField(max_length=20,blank=True,null=True, db_index=True,verbose_name = 'Short Name')
- catalog = models.CharField(max_length=50, unique=True, db_index=True)
- antibodies = models.CharField(max_length=500, db_index=True)
- source = models.CharField(max_length=500, blank=True, db_index=True)
- biology = models.TextField(blank=True)
- notes = models.TextField(blank=True)
- def __str__(self):
- return '%s - %s (%s)' % (self.antigene, self.antibodies, self.catalog)
- class Meta:
- verbose_name_plural = "antibodies"
- ordering = ["antigene"]
- class Admin:
- list_display = ('antigene','nickname','antibodies','catalog','source','biology','notes')
- list_filter = ('antibodies','source')
- fields = (
- (None, {
- 'fields': (('antigene','nickname','antibodies'),('catalog','source'),('biology'),('notes'))
- }),
- )
+ antigene = models.CharField(max_length=500, db_index=True)
+ # New field Aug/20/08
+ # SQL to add column:
+ # alter table fctracker_antibody add column "nickname" varchar(20) NULL;
+ nickname = models.CharField(
+ max_length=20,
+ blank=True,
+ null=True,
+ db_index=True,
+ verbose_name = 'Short Name'
+ )
+ catalog = models.CharField(max_length=50, unique=True, db_index=True)
+ antibodies = models.CharField(max_length=500, db_index=True)
+ source = models.CharField(max_length=500, blank=True, db_index=True)
+ biology = models.TextField(blank=True)
+ notes = models.TextField(blank=True)
+ def __unicode__(self):
+ return u'%s - %s (%s)' % (self.antigene, self.antibodies, self.catalog)
+ class Meta:
+ verbose_name_plural = "antibodies"
+ ordering = ["antigene"]
class Cellline(models.Model):
- cellline_name = models.CharField(max_length=100, unique=True, db_index=True)
- notes = models.TextField(blank=True)
- def __str__(self):
- return '%s' % (self.cellline_name)
-
- class Meta:
- ordering = ["cellline_name"]
-
- class Admin:
- fields = (
- (None, {
- 'fields': (('cellline_name'),('notes'),)
- }),
- )
+ cellline_name = models.CharField(max_length=100, unique=True, db_index=True)
+ nickname = models.CharField(max_length=20,
+ blank=True,
+ null=True,
+ db_index=True,
+ verbose_name = 'Short Name')
+ notes = models.TextField(blank=True)
+ def __unicode__(self):
+ return unicode(self.cellline_name)
+
+ class Meta:
+ ordering = ["cellline_name"]
class Condition(models.Model):
- condition_name = models.CharField(max_length=2000, unique=True, db_index=True)
- notes = models.TextField(blank=True)
- def __str__(self):
- return '%s' % (self.condition_name)
-
- class Meta:
- ordering = ["condition_name"]
-
- class Admin:
- fields = (
- (None, {
- 'fields': (('condition_name'),('notes'),)
- }),
- )
-
+ condition_name = models.CharField(
+ max_length=2000, unique=True, db_index=True)
+ nickname = models.CharField(max_length=20,
+ blank=True,
+ null=True,
+ db_index=True,
+ verbose_name = 'Short Name')
+ notes = models.TextField(blank=True)
+
+ def __unicode__(self):
+ return unicode(self.condition_name)
+
+ class Meta:
+ ordering = ["condition_name"]
+
+class Tag(models.Model):
+ tag_name = models.CharField(max_length=100, db_index=True,blank=False,null=False)
+ TAG_CONTEXT = (
+ #('Antibody','Antibody'),
+ #('Cellline', 'Cellline'),
+ #('Condition', 'Condition'),
+ ('Library', 'Library'),
+ ('ANY','ANY'),
+ )
+ context = models.CharField(max_length=50,
+ choices=TAG_CONTEXT, default='Library')
+
+ def __unicode__(self):
+ return u'%s' % (self.tag_name)
+
+ class Meta:
+ ordering = ["context","tag_name"]
+
class Species(models.Model):
-
- scientific_name = models.CharField(max_length=256, unique=False, db_index=True)
+ scientific_name = models.CharField(max_length=256,
+ unique=False,
+ db_index=True
+ )
common_name = models.CharField(max_length=256, blank=True)
- use_genome_build = models.CharField(max_length=100, 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)
+ def __unicode__(self):
+ return u'%s (%s)' % (self.scientific_name, self.common_name)
class Meta:
verbose_name_plural = "species"
ordering = ["scientific_name"]
- class Admin:
- fields = (
- (None, {
- 'fields': (('scientific_name', 'common_name'), ('use_genome_build'))
- }),
- )
-
class Affiliation(models.Model):
name = models.CharField(max_length=256, db_index=True, verbose_name='Group Name')
contact = models.CharField(max_length=256, null=True, blank=True,verbose_name='Contact Name')
email = models.EmailField(null=True,blank=True)
- def __str__(self):
- str = self.name
- if self.contact != '':
- str += ' ('+self.contact+')'
+ def __unicode__(self):
+ str = unicode(self.name)
+ if len(self.contact) != 0:
+ str += u' ('+self.contact+u')'
return str
class Meta:
ordering = ["name","contact"]
unique_together = (("name", "contact"),)
- class Admin:
- list_display = ('name','contact','email')
- fields = (
- (None, {
- 'fields': (('name','contact','email'))
- }),
- )
-
class Library(models.Model):
library_id = models.CharField(max_length=30, primary_key=True, db_index=True)
condition = models.ForeignKey(Condition)
antibody = models.ForeignKey(Antibody,blank=True,null=True)
# New field Aug/25/08. SQL: alter table fctracker_library add column "lib_affiliation" varchar(256) NULL;
- affiliations = models.ManyToManyField(Affiliation,related_name='library_affiliations',null=True,filter_interface=models.HORIZONTAL)
+ affiliations = models.ManyToManyField(Affiliation,related_name='library_affiliations',null=True)
+ # new field Nov/14/08
+ tags = models.ManyToManyField(Tag,related_name='library_tags',blank=True,null=True)
# New field Aug/19/08
# SQL to add column: alter table fctracker_library add column "replicate" smallint unsigned NULL;
REPLICATE_NUM = ((1,1),(2,2),(3,3),(4,4))
default='RNA-seq')
creation_date = models.DateField(blank=True, null=True)
- made_for = models.ForeignKey(User, edit_inline=models.TABULAR)
+ made_for = models.ForeignKey(User)
made_by = models.CharField(max_length=50, blank=True, default="Lorian")
PROTOCOL_END_POINTS = (
avg_lib_size = models.IntegerField(default=225, blank=True, null=True)
notes = models.TextField(blank=True)
- def __str__(self):
- return '#%s: %s' % (self.library_id, self.library_name)
+ def __unicode__(self):
+ return u'#%s: %s' % (self.library_id, self.library_name)
class Meta:
verbose_name_plural = "libraries"
ordering = ["-creation_date"] #["-library_id"]
def antibody_name(self):
- return self.antibody.nickname
+ str ='<a target=_self href="/admin/samples/antibody/'+self.antibody.id.__str__()+'/" title="'+self.antibody.__str__()+'">'+self.antibody.nickname+'</a>'
+ return str
+ antibody_name.allow_tags = True
- def org(self):
+ def organism(self):
return self.library_species.common_name
def affiliation(self):
tstr = ''
ar = []
for t in affs:
- ar.append(t.__str__())
+ ar.append(t.__unicode__())
return '%s' % (", ".join(ar))
+ def libtags(self):
+ affs = self.tags.all().order_by('tag_name')
+ ar = []
+ for t in affs:
+ ar.append(t.__unicode__())
+ return u'%s' % ( ", ".join(ar))
+
+ def DataRun(self):
+ str ='<a target=_self href="/admin/experiments/datarun/?q='+self.library_id+'" title="Check All Data Runs for This Specific Library ..." ">Data Run</a>'
+ return str
+ DataRun.allow_tags = True
+
+ def aligned_m_reads(self):
+ return getLibReads(self.library_id)
def aligned_reads(self):
res = getLibReads(self.library_id)
+
+ # Check data sanity
+ if res[2] != "OK":
+ return u'<div style="border:solid red 2px">'+res[2]+'</div>'
+
rc = "%1.2f" % (res[1]/1000000.0)
# Color Scheme: green is more than 10M, blue is more than 5M, orange is more than 3M and red is less. For RNAseq, all those thresholds should be doubled
if res[0] > 0:
if res[1] > rc_thr[2]:
bgcolor ='#ffcc33' # Orange
tstr = '<div style="background-color:'+bgcolor+';color:black">'
- tstr += res[0].__str__()+' Lanes, '+rc+' M Reads'
+ tstr += res[0].__unicode__()+' Lanes, '+rc+' M Reads'
tstr += '</div>'
else: tstr = 'not processed yet'
return tstr
aligned_reads.allow_tags = True
- class Admin:
- date_hierarchy = "creation_date"
- save_as = True
- save_on_top = True
- ##search_fields = ['library_id','library_name','affiliations__name','affiliations__contact','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']
- search_fields = ['library_id','library_name','cell_line__cellline_name','library_species__scientific_name','library_species__common_name','library_species__use_genome_build']
- #list_display = ('affiliation','library_id','aligned_reads','library_name','experiment_type','org','replicate','antibody_name','cell_line','made_by','creation_date')
- list_display = ('library_id','library_name','experiment_type','replicate','antibody_name','made_by','creation_date')
- #list_display_links = ('library_id', 'library_name')
-
- list_filter = ('experiment_type','affiliations','library_species', 'made_by','replicate')
- fields = (
- (None, {
- 'fields': (('replicate','library_id','library_name'),('library_species'),('experiment_type'),('cell_line','condition','antibody'),)
- }),
- ('Creation Information:', {
- 'fields' : (('made_for', 'made_by', 'creation_date'), ('stopping_point', 'amplified_from_sample'), ('undiluted_concentration', 'library_size'), 'notes',)
- }),
- ('Library/Project Affiliation:', {
- 'fields' : (('affiliations'),)
- }),
- )
-
# Put strings here, like "/home/html/django_templates" or "C:/www/django/templates".
# Always use forward slashes, even on Windows.
# Don't forget to use absolute paths, not relative paths.
- os.path.abspath("../templates"),
+ os.path.join(os.path.split(__file__)[0], 'templates'),
)
INSTALLED_APPS = (
--- /dev/null
+{% extends "admin/base.html" %}
+{% load i18n %}
+
+{% block title %}
+{{ title }}|{%trans "dev site admin" %}
+{% endblock %}
+
+{% block branding %}
+<h1 id="site-name" style="background-color:#cccccc;color:black">
+ {%block sitename %}
+ {% trans 'HTS Workflow Dev Server' %}
+ {%endblock%}
+</h1>
+{% endblock %}
+
+{% block nav-global %}{% endblock %}
--- /dev/null
+{% if run_f %}
+ <ul>
+ RUN FOLDER: <li>{{ run_f.run_folder }}</li>
+ </ul>
+{% else %}
+ <p>Run folder not found.</p>
+{% endif %}
--- /dev/null
+<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+<html>
+<head>
+<title>{{ fc.flowcell_id }} - GA SEQUENCING (SOLEXA) LOG</title>
+
+<style type="text/css">
+ table, td
+ {
+ border-color: #600;
+ border-style: solid;
+ }
+ table
+ {
+ border-width: 0 0 1px 1px;
+ border-spacing: 0;
+ border-collapse: collapse;
+ }
+ td
+ {
+ margin:0 ;
+ padding: 4px;
+ border-width: 1px 1px 0 0;
+ }
+</style>
+</head>
+<body>
+ <p>{% if fc %}</p>
+<table>
+<thead>
+ <td colspan="3"><b>GA SEQUENCING (SOLEXA) LOG</b></td>
+</thead>
+<tbody>
+<tr>
+<td>Date Run Started</td>
+<td colspan="2">{{ fc.run_date }}</td>
+</tr>
+<tr>
+<td>Cluster station used</td>
+<td colspan="2" nowrap>{{ fc.cluster_mac_id }}</td>
+</tr>
+<tr>
+<td>GA used</td>
+<td colspan="2" nowrap>{{ fc.seq_mac_id }}</td>
+</tr>
+<tr>
+<td>Flowcell number</td>
+<td colspan="2" nowrap>{{ fc.flowcell_id }}</td>
+</tr>
+<tr>
+<td>Number of Tiles per Lane</td>
+<td>100</td>
+</tr>
+<tr>
+<td>Number of Cycles</td>
+<td>{{ fc.read_length }}</td>
+</tr>
+</tbody>
+</table>
+<br/>
+<table>
+<thead>
+ <td>
+ <font point-size="9" face="Arial">
+ <b>SAMPLE INFORMATION</b>
+ </font>
+</thead>
+<tbody>
+<tr>
+<td> </td>
+<td>FC#</td>
+<td> </td>
+<td> </td>
+<td> </td>
+<td> </td>
+<td> </td>
+<td colspan="2" nowrap>FC bar code</td>
+</tr>
+<tr>
+<td valign="middle" nowrap>Lane</td>
+<td>1</td>
+<td>2</td>
+<td>3</td>
+<td>4</td>
+<td>5</td>
+<td>6</td>
+<td>7</td>
+<td>8</td>
+</tr>
+<tr>
+<td valign="middle" nowrap>Solexa Library Number</td>
+<td bgcolor="#CCFFCC">{{ fc.lane_1_library.library_id }}</td>
+<td bgcolor="#CCFFCC">{{ fc.lane_2_library.library_id }}</td>
+<td bgcolor="#CCFFCC">{{ fc.lane_3_library.library_id }}</td>
+<td bgcolor="#CCFFCC">{{ fc.lane_4_library.library_id }}</td>
+<td bgcolor="#CCFFCC">{{ fc.lane_5_library.library_id }}</td>
+<td bgcolor="#CCFFCC">{{ fc.lane_6_library.library_id }}</td>
+<td bgcolor="#CCFFCC">{{ fc.lane_7_library.library_id }}</td>
+<td bgcolor="#CCFFCC">{{ fc.lane_8_library.library_id }}</td>
+</tr>
+<tr>
+<td valign="middle" nowrap>Sample Name</td>
+<td bgcolor="#CCFFCC">{{ fc.lane_1_library.library_name }}</td>
+<td bgcolor="#CCFFCC">{{ fc.lane_2_library.library_name }}</td>
+<td bgcolor="#CCFFCC">{{ fc.lane_3_library.library_name }}</td>
+<td bgcolor="#CCFFCC">{{ fc.lane_4_library.library_name }}</td>
+<td bgcolor="#CCFFCC">{{ fc.lane_5_library.library_name }}</td>
+<td bgcolor="#CCFFCC">{{ fc.lane_6_library.library_name }}</td>
+<td bgcolor="#CCFFCC">{{ fc.lane_7_library.library_name }}</td>
+<td bgcolor="#CCFFCC">{{ fc.lane_8_library.library_name }}</td>
+</tr>
+<tr>
+<td valign="middle" nowrap>Organism</td>
+<td bgcolor="#CCFFCC">{{
+fc.lane_1_library.library_species.common_name }}</td>
+<td bgcolor="#CCFFCC">{{
+fc.lane_2_library.library_species.common_name }}</td>
+<td bgcolor="#CCFFCC">{{
+fc.lane_3_library.library_species.common_name }}</td>
+<td bgcolor="#CCFFCC">{{
+fc.lane_4_library.library_species.common_name }}</td>
+<td bgcolor="#CCFFCC">{{
+fc.lane_5_library.library_species.common_name }}</td>
+<td bgcolor="#CCFFCC">{{
+fc.lane_6_library.library_species.common_name }}</td>
+<td bgcolor="#CCFFCC">{{
+fc.lane_7_library.library_species.common_name }}</td>
+<td bgcolor="#CCFFCC">{{
+fc.lane_8_library.library_species.common_name }}</td>
+</tr>
+<tr>
+<td valign="middle" nowrap>Submitter</td>
+<td bgcolor="#CCFFCC">{{ fc.lane_1_library.made_by }}</td>
+<td bgcolor="#CCFFCC">{{ fc.lane_2_library.made_by }}</td>
+<td bgcolor="#CCFFCC">{{ fc.lane_3_library.made_by }}</td>
+<td bgcolor="#CCFFCC">{{ fc.lane_4_library.made_by }}</td>
+<td bgcolor="#CCFFCC">{{ fc.lane_5_library.made_by }}</td>
+<td bgcolor="#CCFFCC">{{ fc.lane_6_library.made_by }}</td>
+<td bgcolor="#CCFFCC">{{ fc.lane_7_library.made_by }}</td>
+<td bgcolor="#CCFFCC">{{ fc.lane_8_library.made_by }}</td>
+</tr>
+<tr>
+<td valign="middle" nowrap>First time run?</td>
+<td bgcolor="#CCFFCC"></td>
+<td bgcolor="#CCFFCC"></td>
+<td bgcolor="#CCFFCC"></td>
+<td bgcolor="#CCFFCC"></td>
+<td bgcolor="#CCFFCC"></td>
+<td bgcolor="#CCFFCC"></td>
+<td bgcolor="#CCFFCC"></td>
+<td bgcolor="#CCFFCC"></td>
+</tr>
+<tr>
+<td valign="middle" nowrap>Average Library Size (bp)</td>
+<td bgcolor="#CCFFCC">{{ fc.lane_1_library.avg_lib_size }}</td>
+<td bgcolor="#CCFFCC">{{ fc.lane_2_library.avg_lib_size }}</td>
+<td bgcolor="#CCFFCC">{{ fc.lane_3_library.avg_lib_size }}</td>
+<td bgcolor="#CCFFCC">{{ fc.lane_4_library.avg_lib_size }}</td>
+<td bgcolor="#CCFFCC">{{ fc.lane_5_library.avg_lib_size }}</td>
+<td bgcolor="#CCFFCC">{{ fc.lane_6_library.avg_lib_size }}</td>
+<td bgcolor="#CCFFCC">{{ fc.lane_7_library.avg_lib_size }}</td>
+<td bgcolor="#CCFFCC">{{ fc.lane_8_library.avg_lib_size }}</td>
+</tr>
+<tr>
+<td valign="middle" nowrap>Template Concentration (ng/ul)</td>
+<td bgcolor="#CCFFCC">{{ fc.lane_1_library.undiluted_concentration
+}}</td>
+<td bgcolor="#CCFFCC">{{ fc.lane_2_library.undiluted_concentration
+}}</td>
+<td bgcolor="#CCFFCC">{{ fc.lane_3_library.undiluted_concentration
+}}</td>
+<td bgcolor="#CCFFCC">{{ fc.lane_4_library.undiluted_concentration
+}}</td>
+<td bgcolor="#CCFFCC">{{ fc.lane_5_library.undiluted_concentration
+}}</td>
+<td bgcolor="#CCFFCC">{{ fc.lane_6_library.undiluted_concentration
+}}</td>
+<td bgcolor="#CCFFCC">{{ fc.lane_7_library.undiluted_concentration
+}}</td>
+<td bgcolor="#CCFFCC">{{ fc.lane_8_library.undiluted_concentration
+}}</td>
+</tr>
+<tr>
+<td valign="middle" nowrap>Run Concentration (pM)</td>
+<td bgcolor="#CCFFCC">{{ fc.lane_1_pM }}</td>
+<td bgcolor="#CCFFCC">{{ fc.lane_2_pM }}</td>
+<td bgcolor="#CCFFCC">{{ fc.lane_3_pM }}</td>
+<td bgcolor="#CCFFCC">{{ fc.lane_4_pM }}</td>
+<td bgcolor="#CCFFCC">{{ fc.lane_5_pM }}</td>
+<td bgcolor="#CCFFCC">{{ fc.lane_6_pM }}</td>
+<td bgcolor="#CCFFCC">{{ fc.lane_7_pM }}</td>
+<td bgcolor="#CCFFCC">{{ fc.lane_8_pM }}</td>
+</tr>
+</tbody>
+</table>
+{% else %}
+<p>Flowcell object missing. Can't create sheet.</p>
+{% endif %}
+</body>
+</html>
--- /dev/null
+{% if data_run_list %}
+ <ul>
+ {% for run in data_run_list %}
+ <li>{{ run.run_folder }}</li>
+ {% endfor %}
+ </ul>
+{% else %}
+ <p>No data runs are available.</p>
+{% endif %}
from django.conf.urls.defaults import *
+from django.contrib import admin
+admin.autodiscover()
# Databrowser:
-from django.contrib import databrowse
-from htsworkflow.frontend.samples.models import Library
-databrowse.site.register(Library)
+#from django.contrib import databrowse
+#from htsworkflow.frontend.samples.models import Library
+#databrowse.site.register(Library)
#databrowse.site.register(FlowCell)
urlpatterns = patterns('',
# Base:
(r'^eland_config/', include('htsworkflow.frontend.eland_config.urls')),
# Admin:
- (r'^admin/', include('django.contrib.admin.urls')),
- # ExpTrack:
- (r'^experiments/', include('htsworkflow.frontend.experiments.urls')),
+ (r'^admin/(.*)', admin.site.root),
+ # Experiments:
+ (r'^experiments/', include('htsworkflow.frontend.experiments.urls')),
# AnalysTrack:
- (r'^analysis/', include('htsworkflow.frontend.analysis.urls')),
+ #(r'^analysis/', include('htsworkflow.frontend.analysis.urls')),
# Report Views:
# (r'^reports/', include('gaworkflow.frontend....urls')),
# databrowser
- (r'^databrowse/(.*)', databrowse.site.root)
+ #(r'^databrowse/(.*)', databrowse.site.root)
)
projects / htsworkflow.git / commitdiff