--- /dev/null
+from django.db import models
+from django.db.models import Q
+from django.core.exceptions import ObjectDoesNotExist
+from datetime import datetime
+from gaworkflow.frontend.fctracker.models import *
+from gaworkflow.frontend.analys_track.models import *
+from gaworkflow.frontend.exp_track.models import *
+from string import *
+import re
+##from p1 import LibInfo
+from libinfopar import *
+
+## 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).
+
+class ProgressReport(models.Model):
+ st_sbj = models.ForeignKey(Project,limit_choices_to = Q(project_name__startswith='ENCODE '),related_name='project',db_index=True,verbose_name="Studied Subject")
+ interactome_complete = models.BooleanField(default=False)
+
+ def Study(self):
+ str = self.st_sbj.__str__()
+ str += '<br/><br/>'
+ 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>'
+ return str
+ Study.allow_tags = True
+
+ def submit_to_DCC(self):
+ varText = ''
+ if self.note_about_DCC:
+ varText += '<br/><u>Note:</u><br/>'+self.note_about_DCC
+ return '%s<br/>%s' % (self.submitted_to_DCC,varText)
+ submit_to_DCC.allow_tags = True
+
+ def submit_to_NCBI(self):
+ varText = ''
+ if self.note_about_NCBI:
+ varText += '<br/><u>Note:</u><br/>'+self.note_about_NCBI
+ return '%s<br/>%s' % (self.submitted_to_NCBI,varText)
+ submit_to_NCBI.allow_tags = True
+
+ #REPS = ((1,1),(2,2),(3,3))
+ #replicate = models.PositiveSmallIntegerField(choices=REPS,verbose_name='Replicate Number')
+
+ ## -- Utility functions
+ def unique(self,s):
+ """Return a list of the elements in s, but without duplicates.
+ For example, unique([1,2,3,1,2,3]) is some permutation of [1,2,3],
+ unique("abcabc") some permutation of ["a", "b", "c"], and
+ unique(([1, 2], [2, 3], [1, 2])) some permutation of
+ [[2, 3], [1, 2]].
+ For best speed, all sequence elements should be hashable. Then
+ unique() will usually work in linear time.
+ If not possible, the sequence elements should enjoy a total
+ ordering, and if list(s).sort() doesn't raise TypeError it's
+ assumed that they do enjoy a total ordering. Then unique() will
+ usually work in O(N*log2(N)) time.
+ If that's not possible either, the sequence elements must support
+ equality-testing. Then unique() will usually work in quadratic
+ time.
+ """
+
+ n = len(s)
+ if n == 0:
+ return []
+
+ # Try using a dict first, as that's the fastest and will usually
+ # work. If it doesn't work, it will usually fail quickly, so it
+ # usually doesn't cost much to *try* it. It requires that all the
+ # sequence elements be hashable, and support equality comparison.
+ u = {}
+ try:
+ for x in s:
+ u[x] = 1
+ except TypeError:
+ del u # move on to the next method
+ else:
+ return u.keys()
+
+ # We can't hash all the elements. Second fastest is to sort,
+ # which brings the equal elements together; then duplicates are
+ # easy to weed out in a single pass.
+ # NOTE: Python's list.sort() was designed to be efficient in the
+ # presence of many duplicate elements. This isn't true of all
+ # sort functions in all languages or libraries, so this approach
+ # is more effective in Python than it may be elsewhere.
+ try:
+ t = list(s)
+ t.sort()
+ except TypeError:
+ del t # move on to the next method
+ else:
+ assert n > 0
+ last = t[0]
+ lasti = i = 1
+ while i < n:
+ if t[i] != last:
+ t[lasti] = last = t[i]
+ lasti += 1
+ i += 1
+ return t[:lasti]
+
+ # Brute force is all that's left.
+ u = []
+ for x in s:
+ if x not in u:
+ u.append(x)
+ return u
+
+
+ ## --- LIBARAY PREPARATION SECTION
+ def getLibIds(self):
+ ptasks = self.st_sbj.tasks.distinct()
+ arLibs = []
+ for t in ptasks:
+ if t.subject1 is not None:
+ arLibs.append(t.subject1.library_id)
+ if t.subject2 is not None:
+ arLibs.append(t.subject2.library_id)
+ arLibs = self.unique(arLibs)
+ return arLibs #.sort()
+
+ def getFCInfo(self,libid): ## This is the haviest function
+ arFCLanes = []
+ ##Test return arFCLanes
+ # can't get this to work: FC_L1 = FlowCell.objects.filter(lane_5_library__exact=libid)
+ allFCs = FlowCell.objects.all()
+ for f in allFCs:
+ entry = ''
+ lanes = []
+ #found = False
+# for i in range(1,9):
+# if eval('f.lane_'+i.__str__()+'_library.library_id==libid'):
+# lanes.append(i.__str__())
+# found = True
+
+# maybe a bit faster this way:
+ if f.lane_1_library.library_id==libid:
+ lanes.append('1')
+ #found = True
+ if f.lane_2_library.library_id==libid:
+ lanes.append('2')
+ #found = True
+ if f.lane_3_library.library_id==libid:
+ lanes.append('3')
+ #found = True
+ if f.lane_4_library.library_id==libid:
+ lanes.append('4')
+ #found = True
+ if f.lane_5_library.library_id==libid:
+ lanes.append('5')
+ #found = True
+ if f.lane_6_library.library_id==libid:
+ lanes.append('6')
+ #found = True
+ if f.lane_7_library.library_id==libid:
+ lanes.append('7')
+ #found = True
+ if f.lane_8_library.library_id==libid:
+ lanes.append('8')
+ #found = True
+
+
+ #if found:
+ if len(lanes)>0:
+ rundate = re.sub(pattern="\s.*$",repl="",string=f.run_date.__str__())
+ entry = '<b>'+f.flowcell_id + '</b> Lanes No.: '+','.join(lanes)+' ('+rundate+')'
+ arFCLanes.append(entry)
+ if len(arFCLanes)==0:
+ arFCLanes.append('<font color=red>Flowcell not found.</font>')
+ return arFCLanes
+
+ def ab_batch(self):
+ ## To have the Company's lot number, apearing on the (source) tube, we need to add new Field in Library.
+ arlibs = self.getLibIds()
+ tstr = '<ul>' ##<u><b>Ab</b> from '+len(arlibs).__str__()+' libs</u>: '
+ arRows = []
+ for l in arlibs:
+ try:
+ rec = Library.objects.get(library_id=l,antibody__isnull=False)
+ arRows.append('<li>'+rec.antibody.antibodies+' for <b>'+rec.antibody.antigene+'</b> (src:'+rec.antibody.source+', cat:'+rec.antibody.catalog+')</li>')
+ except ObjectDoesNotExist:
+ tstr += ""
+ tstr += "".join(self.unique(arRows))+'</ul>'
+ return tstr
+ ab_batch.allow_tags = True
+
+ def cell_line(self):
+ arlibs = self.getLibIds()
+ tstr = '<ul>'
+ arRows = []
+ for l in arlibs:
+ try:
+ rec = Library.objects.get(library_id=l)
+ arRows.append('<li><b>'+rec.cell_line.cellline_name+'</b> ('+rec.condition.condition_name+')</li>')
+ except ObjectDoesNotExist:
+ tstr += ""
+ tstr += "".join(self.unique(arRows))+'</ul>'
+ return tstr
+ cell_line.allow_tags = True
+
+ def cell_harvest_batch(self): # <- data now displayed in "cell_line"
+ ## name + date
+ arlibs = self.getLibIds()
+ tstr = '<ul>'
+ arRows = []
+ for l in arlibs:
+ try:
+ rec = Library.objects.get(library_id=l)
+ arRows.append('<li><b>'+rec.condition.condition_name+'</b></li>')
+ except ObjectDoesNotExist:
+ tstr += ""
+ tstr += "".join(self.unique(arRows))+'</ul>'
+ return tstr
+ cell_harvest_batch.allow_tags = True
+
+ def ChIP_made(self):
+ ## person + date
+ return '...'
+
+ def library(self):
+ ## Lib Id + Date + Person
+ tstr = '<script>'
+ tstr += 'function togit(eid){'
+ tstr += 'f=document.getElementById(eid);'
+ tstr += 'if(f.style.display==\'none\'){'
+ tstr += 'f.style.display=\'block\';'
+ tstr += '}else{'
+ tstr += 'f.style.display=\'none\';'
+ tstr += '}'
+ tstr += '}'
+ tstr += '</script>'
+ arlibs = self.getLibIds() ##.sort()
+ arlibs = arlibs
+ tstr +='<a href=# onClick="togit(\'libInfo'+self.st_sbj.project_name+'\')">view /hide</a>'
+ tstr += '<div id="libInfo'+self.st_sbj.project_name+'" style="display:block;border:solid #cccccc 1px;width:200px;height:300px;overflow:auto"><ul>'
+ arRows = []
+ for l in arlibs:
+ try:
+ rec = Library.objects.get(library_id=l)
+ arRows.append('<li><b>'+rec.library_id+'</b>: '+rec.library_name+'.<br/>Made By: '+rec.made_by+', On: '+ rec.creation_date.__str__()+'</li>')
+ except ObjectDoesNotExist:
+ tstr += ""
+ tstr += "".join(self.unique(arRows))+'</ul></div>'
+ return tstr
+ library.allow_tags = True
+
+
+ ## -- SEQUENCING SECTION
+ def sequencing(self):
+ ## FCId + Lane + Date
+ arlibs = self.getLibIds()
+ tstr ='<a href=# onClick="togit(\'seqInfo'+self.st_sbj.project_name+'\')">view /hide</a>'
+ tstr += '<div id="seqInfo'+self.st_sbj.project_name+'" style="display:block;border:solid #cccccc 1px;width:200px;height:300px;overflow:auto"><ul>'
+ for l in arlibs:
+ tstr += '<li><b>'+l+'</b>:<br/>'+(' / '.join(self.getFCInfo(l)))+'</li>'
+ tstr += '</ul></div>'
+ return tstr
+ sequencing.allow_tags = True
+
+ def aligned_reads(self):
+ ## Mega reads/lane
+ arlibs = self.getLibIds()
+ tstr = '<a href=# onClick="togit(\'readsInfo'+self.st_sbj.project_name+'\')">view /hide</a>'
+ tstr += '<div id="readsInfo'+self.st_sbj.project_name+'" style="display:block;border:solid #cccccc 1px;width:200px;height:300px;overflow:auto">'
+ tstr += '<table><tr><td>Library Id</td><td>Total Lanes</td><td>M Reads</td></tr>'
+ LanesCnt, ReadsCnt = 0, 0
+ for l in arlibs:
+ res = getLibReads(l)
+ LanesCnt += res[0]
+ ReadsCnt += res[1]
+ rc = "%1.2f" % (res[1]/1000000.0)
+ tstr += '<tr><td><b>'+l+'</b></td><td>'+res[0].__str__()+'</td></td><td>'+rc+'</td></tr>'
+ tstr += '</table>'
+ #tstr += '<a target=_blank href="http://m304-apple-server.stanford.edu/projects/'+self.st_sbj.id.__str__()+'">Project results page</a>'
+ tstr += '</div>'
+ myNum = (ReadsCnt/1000000.0)
+ myNum = "%1.2f" % (myNum)
+ tstr += '<div>Total: <b>'+LanesCnt.__str__()+'</b> lanes and <b>'+myNum+'</b> M Reads</div>'
+ tstr += '<a target=_blank href="http://m304-apple-server.stanford.edu/projects/'+self.st_sbj.id.__str__()+'">Project results page</a>'
+ return tstr
+ aligned_reads.allow_tags = True
+
+ def peak_calling(self):
+ # date + what etc..
+ return 'coming up ..'
+
+ QPCR = models.CharField(max_length=500,blank=True,null=True)
+ submitted_to_DCC = models.DateTimeField(core=True,blank=True,null=True)
+ submitted_to_NCBI = models.DateTimeField(core=True,blank=True,null=True)
+ note_about_DCC = models.TextField(blank=True)
+ note_about_NCBI = models.TextField(blank=True)
+
+ def __str__(self):
+ return '"%s" - %s' % (self.st_sbj,self.interactome_complete)
+
+ class Meta:
+ #verbose_name_plural = "Reports"
+ ordering = ["id"]
+
+ class Admin:
+ list_display = ('Study','ab_batch','cell_line','library','sequencing','aligned_reads','QPCR','submit_to_DCC','submit_to_NCBI','interactome_complete')
+ ## list_filter = ('interactome_complete')
+
projects / htsworkflow.git / blobdiff