htsworkflow/frontend/reports/models.py

   1 from django.db import models
   2 from django.db.models import Q
   3 from django.core.exceptions import ObjectDoesNotExist
   4 from datetime import datetime
   5 from htsworkflow.frontend.samples.models import *
   6 from htsworkflow.frontend.analysis.models import *
   7 from htsworkflow.frontend.experiments.models import *
   8 from string import *
   9 from htsworkflow.frontend.reports.utils import *
  10 import re
  11 ##from p1 import LibInfo
  12 from .libinfopar import *
  13
  14 ## This is a table based REPORT generator. The goal is to display a Progress Report for all the ENCODE projects, based on Study Name (e.g. NRSF, FOXP2, Methy-Seq on .. etc).
  15
  16 class ProgressReport(models.Model):
  17   st_sbj = models.ForeignKey(Project,limit_choices_to = Q(project_name__startswith='ENCODE '),related_name='project',db_index=True,verbose_name="Studied Subject")
  18   interactome_complete = models.BooleanField(default=False)
  19
  20   def Study(self):
  21     str = self.st_sbj.__str__()
  22     str += '<br/><br/>'
  23     str += '<a title="open Project record" href="/admin/analys_track/project/'+self.st_sbj.id.__str__()+'/" target=_self style="font-size:85%">Edit Project</a>'
  24     return str
  25   Study.allow_tags = True
  26
  27   def submit_to_DCC(self):
  28     varText = ''
  29     if self.note_about_DCC:
  30       varText += '<br/><u>Note:</u><br/>'+self.note_about_DCC
  31     return '%s<br/>%s' % (self.submitted_to_DCC,varText)
  32   submit_to_DCC.allow_tags = True
  33
  34   def submit_to_NCBI(self):
  35     varText = ''
  36     if self.note_about_NCBI:
  37       varText += '<br/><u>Note:</u><br/>'+self.note_about_NCBI
  38     return '%s<br/>%s' % (self.submitted_to_NCBI,varText)
  39   submit_to_NCBI.allow_tags = True
  40
  41   ## -- Utility functions <-- This method was transfered to untils.py
  42
  43   ## --- LIBARAY PREPARATION SECTION
  44   def getLibIds(self):
  45     ptasks = self.st_sbj.tasks.distinct()
  46     arLibs = []
  47     for t in ptasks:
  48       if t.subject1 is not None:
  49         arLibs.append(t.subject1.library_id)
  50       if t.subject2 is not None:
  51         arLibs.append(t.subject2.library_id)
  52     arLibs = unique(arLibs)
  53     return arLibs #.sort()
  54
  55   def getFCInfo(self,libid):   ## This is the haviest function
  56     arFCLanes = []
  57     ##Test return arFCLanes
  58     # can't get this to work: FC_L1 = FlowCell.objects.filter(lane_5_library__exact=libid)
  59     allFCs = FlowCell.objects.all()
  60     for f in allFCs:
  61       entry = ''
  62       lanes = []
  63       #found = False
  64 #      for i in range(1,9):
  65 #        if eval('f.lane_'+i.__str__()+'_library.library_id==libid'):
  66 #          lanes.append(i.__str__())
  67 #          found = True
  68
  69 # maybe a bit faster this way:
  70       if f.lane_1_library.library_id==libid:
  71           lanes.append('1')
  72           #found = True
  73       if f.lane_2_library.library_id==libid:
  74           lanes.append('2')
  75           #found = True
  76       if f.lane_3_library.library_id==libid:
  77           lanes.append('3')
  78           #found = True
  79       if f.lane_4_library.library_id==libid:
  80           lanes.append('4')
  81           #found = True
  82       if f.lane_5_library.library_id==libid:
  83           lanes.append('5')
  84           #found = True
  85       if f.lane_6_library.library_id==libid:
  86           lanes.append('6')
  87           #found = True
  88       if f.lane_7_library.library_id==libid:
  89           lanes.append('7')
  90           #found = True
  91       if f.lane_8_library.library_id==libid:
  92           lanes.append('8')
  93           #found = True
  94
  95
  96       #if found:
  97       if len(lanes)>0:
  98         rundate = re.sub(pattern="\s.*$",repl="",string=f.run_date.__str__())
  99         entry = '<b>'+f.flowcell_id + '</b> Lanes No.: '+','.join(lanes)+' ('+rundate+')'
 100         arFCLanes.append(entry)
 101     if len(arFCLanes)==0:
 102       arFCLanes.append('<font color=red>Flowcell not found.</font>')
 103     return arFCLanes
 104
 105   def ab_batch(self):
 106     ##  To have the Company's lot number, apearing on the (source) tube, we need to add new Field in Library.
 107     arlibs = self.getLibIds()
 108     tstr = '<ul>' ##<u><b>Ab</b> from '+len(arlibs).__str__()+' libs</u>: '
 109     arRows = []
 110     for l in arlibs:
 111       try:
 112         rec = Library.objects.get(library_id=l,antibody__isnull=False)
 113         arRows.append('<li>'+rec.antibody.antibodies+' for <b>'+rec.antibody.antigene+'</b> (src:'+rec.antibody.source+', cat:'+rec.antibody.catalog+')</li>')
 114       except ObjectDoesNotExist:
 115         tstr += ""
 116     tstr += "".join(unique(arRows))+'</ul>'
 117     return tstr
 118   ab_batch.allow_tags = True
 119
 120   def cell_line(self):
 121     arlibs = self.getLibIds()
 122     tstr = '<ul>'
 123     arRows = []
 124     for l in arlibs:
 125       try:
 126         rec = Library.objects.get(library_id=l)
 127         arRows.append('<li><b>'+rec.cell_line.cellline_name+'</b> ('+rec.condition.condition_name+')</li>')
 128       except ObjectDoesNotExist:
 129         tstr += ""
 130     tstr += "".join(unique(arRows))+'</ul>'
 131     return tstr
 132   cell_line.allow_tags = True
 133
 134   def cell_harvest_batch(self): # <- data now displayed in "cell_line"
 135     ## name + date
 136     arlibs = self.getLibIds()
 137     tstr = '<ul>'
 138     arRows = []
 139     for l in arlibs:
 140       try:
 141         rec = Library.objects.get(library_id=l)
 142         arRows.append('<li><b>'+rec.condition.condition_name+'</b></li>')
 143       except ObjectDoesNotExist:
 144         tstr += ""
 145     tstr += "".join(unique(arRows))+'</ul>'
 146     return tstr
 147   cell_harvest_batch.allow_tags = True
 148
 149   def ChIP_made(self):
 150     ## person + date
 151     return '...'
 152
 153   def library(self):
 154     ## Lib Id + Date + Person
 155     tstr = '<script>'
 156     tstr += 'function togit(eid){'
 157     tstr += 'f=document.getElementById(eid);'
 158     tstr += 'if(f.style.display==\'none\'){'
 159     tstr += 'f.style.display=\'block\';'
 160     tstr += '}else{'
 161     tstr += 'f.style.display=\'none\';'
 162     tstr += '}'
 163     tstr += '}'
 164     tstr += '</script>'
 165     arlibs = self.getLibIds() ##.sort()
 166     arlibs = arlibs
 167     tstr +='<a href=# onClick="togit(\'libInfo'+self.st_sbj.project_name+'\')">view /hide</a>'
 168     tstr += '<div id="libInfo'+self.st_sbj.project_name+'" style="display:block;border:solid #cccccc 1px;width:200px;height:300px;overflow:auto"><ul>'
 169     arRows = []
 170     for l in arlibs:
 171       try:
 172         rec = Library.objects.get(library_id=l)
 173         arRows.append('<li><b>'+rec.library_id+'</b>: '+rec.library_name+'.<br/>Made By: '+rec.made_by+', On: '+ rec.creation_date.__str__()+'</li>')
 174       except ObjectDoesNotExist:
 175         tstr += ""
 176     tstr += "".join(unique(arRows))+'</ul></div>'
 177     return tstr
 178   library.allow_tags = True
 179
 180
 181   ## -- SEQUENCING SECTION
 182   def sequencing(self):
 183     ## FCId + Lane + Date
 184     arlibs = self.getLibIds()
 185     tstr ='<a href=# onClick="togit(\'seqInfo'+self.st_sbj.project_name+'\')">view /hide</a>'
 186     tstr += '<div id="seqInfo'+self.st_sbj.project_name+'" style="display:block;border:solid #cccccc 1px;width:200px;height:300px;overflow:auto"><ul>'
 187     for l in arlibs:
 188       tstr += '<li><b>'+l+'</b>:<br/>'+(' / '.join(self.getFCInfo(l)))+'</li>'
 189     tstr += '</ul></div>'
 190     return tstr
 191   sequencing.allow_tags = True
 192
 193   def aligned_reads(self):
 194     ## Mega reads/lane
 195     arlibs = self.getLibIds()
 196     tstr = '<a href=# onClick="togit(\'readsInfo'+self.st_sbj.project_name+'\')">view /hide</a>'
 197     tstr += '<div id="readsInfo'+self.st_sbj.project_name+'" style="display:block;border:solid #cccccc 1px;width:200px;height:300px;overflow:auto">'
 198     tstr += '<table><tr><td>Library Id</td><td>Total Lanes</td><td>M Reads</td></tr>'
 199     LanesCnt, ReadsCnt = 0, 0
 200     for l in arlibs:
 201       res = getLibReads(l)
 202       LanesCnt += res[0]
 203       ReadsCnt += res[1]
 204       rc = "%1.2f" % (res[1]/1000000.0)
 205       tstr += '<tr><td><b>'+l+'</b></td><td>'+res[0].__str__()+'</td></td><td>'+rc+'</td></tr>'
 206     tstr += '</table>'
 207     #tstr += '<a target=_blank href="'+settings.TASKS_PROJS_SERVER+'/projects/'+self.st_sbj.id.__str__()+'">Project results page</a>'
 208     tstr += '</div>'
 209     myNum = (ReadsCnt/1000000.0)
 210     myNum  = "%1.2f" % (myNum)
 211     tstr += '<div>Total: <b>'+LanesCnt.__str__()+'</b> lanes and <b>'+myNum+'</b> M Reads</div>'
 212     tstr += '<a target=_blank href="'+settings.TASKS_PROJS_SERVER+'/projects/'+self.st_sbj.id.__str__()+'">Project results page</a>'
 213     return tstr
 214   aligned_reads.allow_tags = True
 215
 216   def peak_calling(self):
 217     # date + what etc..
 218     return 'coming up ..'
 219
 220   QPCR = models.CharField(max_length=500,blank=True,null=True)
 221   submitted_to_DCC = models.DateTimeField(blank=True,null=True)
 222   submitted_to_NCBI = models.DateTimeField(blank=True,null=True)
 223   note_about_DCC =  models.TextField(blank=True)
 224   note_about_NCBI = models.TextField(blank=True)
 225
 226   def __str__(self):
 227       return '"%s" - %s' % (self.st_sbj,self.interactome_complete)
 228
 229   class Meta:
 230     #verbose_name_plural = "Reports"
 231     ordering = ["id"]
 232
 233   class Admin:
 234     list_display = ('Study','ab_batch','cell_line','library','sequencing','aligned_reads','QPCR','submit_to_DCC','submit_to_NCBI','interactome_complete')
 235     ## list_filter = ('interactome_complete')
 236
 237
 238 #############################################