From db806096d761b67ade7d3253eff54712d51c6717 Mon Sep 17 00:00:00 2001 From: Rami Rauch Date: Sat, 3 May 2008 00:01:55 +0000 Subject: [PATCH] add stanfords experiment tracker component --- gaworkflow/frontend/exp_track/__init__.py | 0 gaworkflow/frontend/exp_track/et_urls.py | 10 ++ gaworkflow/frontend/exp_track/exptrack.py | 182 ++++++++++++++++++++++ gaworkflow/frontend/exp_track/models.py | 29 ++++ gaworkflow/frontend/exp_track/views.py | 22 +++ 5 files changed, 243 insertions(+) create mode 100644 gaworkflow/frontend/exp_track/__init__.py create mode 100644 gaworkflow/frontend/exp_track/et_urls.py create mode 100644 gaworkflow/frontend/exp_track/exptrack.py create mode 100644 gaworkflow/frontend/exp_track/models.py create mode 100644 gaworkflow/frontend/exp_track/views.py diff --git a/gaworkflow/frontend/exp_track/__init__.py b/gaworkflow/frontend/exp_track/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/gaworkflow/frontend/exp_track/et_urls.py b/gaworkflow/frontend/exp_track/et_urls.py new file mode 100644 index 0000000..6acea12 --- /dev/null +++ b/gaworkflow/frontend/exp_track/et_urls.py @@ -0,0 +1,10 @@ +from django.conf.urls.defaults import * + +urlpatterns = patterns('', + + (r'^$', 'gaworkflow.frontend.exp_track.views.index'), + (r'^(?P.+)/$', 'gaworkflow.frontend.exp_track.views.detail'), + (r'^updStatus$', 'gaworkflow.frontend.exp_track.exptrack.updStatus'), + (r'^getConfile$', 'gaworkflow.frontend.exp_track.exptrack.getConfile'), + (r'^getLanesNames$', 'gaworkflow.frontend.exp_track.exptrack.getLaneLibs') +) diff --git a/gaworkflow/frontend/exp_track/exptrack.py b/gaworkflow/frontend/exp_track/exptrack.py new file mode 100644 index 0000000..18ed709 --- /dev/null +++ b/gaworkflow/frontend/exp_track/exptrack.py @@ -0,0 +1,182 @@ +# some core functions of the exp tracker module +from django.http import HttpResponse +from datetime import datetime +from string import * +import re +from gaworkflow.frontend.exp_track.models import DataRun +from gaworkflow.frontend.fctracker.models import FlowCell, Library +from django.core.exceptions import ObjectDoesNotExist +from django.core.mail import send_mail, mail_admins + +def updStatus(request): + output='' + user = 'none' + pswd = '' + UpdatedStatus = 'unknown' + ClIP = 'unknown' + granted = False + fcid = 'none' + runfolder = 'unknown' + + if request.has_key('fcid'): + fcid = request['fcid'] + else: + return HttpResponse('missing fcid') + + if request.has_key('runf'): + runfolder = request['runf'] + else: + return HttpResponse('missing runf') + + if request.has_key('user'): + user = request['user'] + else: + return HttpResponse('access denied') + + #TO DO: pswd decode etc.. + #if request.has_key('pswd'): + # pswd = request['pswd'] + #else: + # return HttpResponse('access denied') + + ClIP = request.META['REMOTE_ADDR'] + + #Check permission to update + if (user == 'rami' and (ClIP == '171.65.76.167' or ClIP == '171.65.76.51' or (ClIP == '74.51.115.100' or ClIP == '64.89.97.100'))): ## or ClIP == '127.0.0.1')): + granted = True + + if granted: + if request.has_key('updst'): + UpdatedStatus = request['updst'] + else: + return HttpResponse('missing status') + + # Update Data Run status in DB + # Try get rec. If not found return 'entry not found + ', if found try update and return updated + try: + rec = DataRun.objects.get(run_folder=runfolder) + rec.run_status = UpdatedStatus + + #if there's a message update that too + mytimestamp = datetime.now().__str__() + mytimestamp = re.sub(pattern=":[^:]*$",repl="",string=mytimestamp) + if request.has_key('msg'): + rec.run_note += ", "+request['msg']+" ("+mytimestamp+")" + else : + if UpdatedStatus == '1': + rec.run_note = "Started ("+mytimestamp+")" + + rec.save() + output = "updated to:'"+DataRun.RUN_STATUS_CHOICES[int(UpdatedStatus)][1].__str__()+"'" + except ObjectDoesNotExist: + output = "entry not found: "+fcid+", "+runfolder + else: + output ="access denied.. u: "+user+", ClIP: "+ClIP + + #Notify researcher by email + # Doesn't work + #send_mail('Exp Tracker', 'Data Run Status '+output, 'rrauch@stanford.edu', ['rrrami@gmail.com'], fail_silently=False) + #mail_admins("test subject", "testing , testing", fail_silently=False) + # gives error: (49, "Can't assign requested address") + return HttpResponse(output) + +def generateConfile(fcid): + cnfgfile = 'READ_LENGTH 25\n' + cnfgfile += 'ANALYSIS eland\n' + cnfgfile += 'GENOME_FILE all_chr.fa\n' + cnfgfile += 'ELAND_MULTIPLE_INSTANCES 8\n' + genome_dir = 'GENOME_DIR /Volumes/Genomes/' + eland_genome = 'ELAND_GENOME /Volumes/Genomes/' + + try: + rec = FlowCell.objects.get(flowcell_id=fcid) + + cnfgfile += '1:'+genome_dir+rec.lane_1_library.library_species.use_genome_build+'\n' + cnfgfile += '1:'+eland_genome+rec.lane_1_library.library_species.use_genome_build+'\n' + + cnfgfile += '2:'+genome_dir+rec.lane_2_library.library_species.use_genome_build+'\n' + cnfgfile += '2:'+eland_genome+rec.lane_2_library.library_species.use_genome_build+'\n' + + cnfgfile += '3:'+genome_dir+rec.lane_3_library.library_species.use_genome_build+'\n' + cnfgfile += '3:'+eland_genome+rec.lane_3_library.library_species.use_genome_build+'\n' + + cnfgfile += '4:'+genome_dir+rec.lane_4_library.library_species.use_genome_build+'\n' + cnfgfile += '4:'+eland_genome+rec.lane_4_library.library_species.use_genome_build+'\n' + + cnfgfile += '5:'+genome_dir+rec.lane_5_library.library_species.use_genome_build+'\n' + cnfgfile += '5:'+eland_genome+rec.lane_5_library.library_species.use_genome_build+'\n' + + cnfgfile += '6:'+genome_dir+rec.lane_6_library.library_species.use_genome_build+'\n' + cnfgfile += '6:'+eland_genome+rec.lane_6_library.library_species.use_genome_build+'\n' + + cnfgfile += '7:'+genome_dir+rec.lane_7_library.library_species.use_genome_build+'\n' + cnfgfile += '7:'+eland_genome+rec.lane_7_library.library_species.use_genome_build+'\n' + + cnfgfile += '8:'+genome_dir+rec.lane_8_library.library_species.use_genome_build+'\n' + cnfgfile += '8:'+eland_genome+rec.lane_8_library.library_species.use_genome_build + + except ObjectDoesNotExist: + cnfgfile = 'Entry not found for runfolder = '+runfolder + + return cnfgfile + +def getConfile(request): + fcid = 'none' + cnfgfile = '' + runfolder = 'unknown' + if request.has_key('fcid'): + fcid = request['fcid'] + if request.has_key('runf'): + runfolder = request['runf'] + try: + rec = DataRun.objects.get(run_folder=runfolder) #,flowcell_id=fcid) + cnfgfile = rec.config_params + #match_str = re.compile(r"READ_LENGTH.+$") + match_str = re.compile('^READ_LENGTH.+') + if not match_str.search(cnfgfile): + cnfgfile = generateConfile(fcid) + if match_str.search(cnfgfile): + rec = DataRun.objects.get(run_folder=runfolder) #,flowcell_id=fcid) + rec.config_params = cnfgfile + rec.save() + else: + cnfgfile = 'Failed generating config params for RunFolder = '+runfolder +', Flowcell id = '+ fcid+ ' Config Text:\n'+cnfgfile + + except ObjectDoesNotExist: + cnfgfile = 'Entry not found for RunFolder = '+runfolder + + return HttpResponse(cnfgfile) + +def getLaneLibs(request): + fcid = 'none' + outputfile = '' + if request.has_key('fcid'): + fcid = request['fcid'] + try: + rec = FlowCell.objects.get(flowcell_id=fcid) + #Ex: 071211 + year = datetime.today().year.__str__() + year = replace(year,'20','') + month = datetime.today().month + if month < 10: month = "0"+month.__str__() + else: month = month.__str__() + day = datetime.today().day + if day < 10: day = "0"+day.__str__() + else: day = day.__str__() + mydate = year+month+day + outputfile = '' + outputfile += '\n' + outputfile += '\n' + outputfile += '\n' + outputfile += '\n' + outputfile += '\n' + outputfile += '\n' + outputfile += '\n' + outputfile += '\n' + outputfile += '\n' + outputfile += '\n' + except ObjectDoesNotExist: + outputfile = 'Flowcell entry not found for: '+fcid + else: outputfile = 'Missing input: flowcell id' + + return HttpResponse(outputfile) diff --git a/gaworkflow/frontend/exp_track/models.py b/gaworkflow/frontend/exp_track/models.py new file mode 100644 index 0000000..7bdaff7 --- /dev/null +++ b/gaworkflow/frontend/exp_track/models.py @@ -0,0 +1,29 @@ +from django.db import models +from gaworkflow.frontend.fctracker.models import FlowCell + +class DataRun(models.Model): + #ConfTemplate = "READ_LENGTH 25\nGENOME_DIR /Volumes/Genomes/hg18\nELAND_GENOME /Volumes/Genomes/hg18\nANALYSIS eland\nGENOME_FILE all_chr.fa\nELAND_MULTIPLE_INSTANCES 8" + ConfTemplate = "CONFIG PARAMS WILL BE GENERATED BY THE PIPELINE SCRIPT.\nYOU'LL BE ABLE TO EDIT AFTER IF NEEDED." + ##----- + run_folder = models.CharField(max_length=50,unique=True, db_index=True) + fcid = models.ForeignKey(FlowCell,verbose_name="Flowcell Id") #, null=True) + config_params = models.TextField(default=ConfTemplate) + run_start_time = models.DateTimeField(core=True) + RUN_STATUS_CHOICES = ( + (0, 'Solexa Pipeline Not Yet Started'), + (1, 'Solexa Pipeline Started'), + (2, 'Solexa Pipeline Interrupted'), + (3, 'Solexa Pipeline Finished'), + (4, 'CollectReads Started'), + (5, 'CollectReads Finished'), + ) + run_status = models.IntegerField(choices=RUN_STATUS_CHOICES, default=0) + run_note = models.CharField(max_length=500,blank=True) + + #def __unicode__(self): + # return ... + + class Admin: + list_display = ('run_folder','fcid','run_start_time','run_status','run_note') + list_filter = ('run_status','run_start_time') + diff --git a/gaworkflow/frontend/exp_track/views.py b/gaworkflow/frontend/exp_track/views.py new file mode 100644 index 0000000..1d9aa8d --- /dev/null +++ b/gaworkflow/frontend/exp_track/views.py @@ -0,0 +1,22 @@ +# Create your views here. +#from django.template import Context, loader +#shortcut to the above modules +from django.shortcuts import render_to_response, get_object_or_404 +from gaworkflow.frontend.exp_track.models import DataRun +from django.http import HttpResponse + +def index(request): + all_runs = DataRun.objects.all().order_by('-run_start_time') + #t = loader.get_template('exptrack/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}) + +def detail(request, run_folder): + html_str = '

Exp Track Details Page

' + 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}) -- 2.30.2