Merge pull request #113 from lehtiolab/dia_longit_qc

Include DIA in longitudinal qc

src/backend/analysis/jobs.py

@@ -104,14 +104,12 @@ def process(self, **kwargs):
             analysis=analysis)
         run = {'timestamp': timestamp,
                'analysis_id': analysis.id,
+               'qcrun_id': kwargs['qcrun_id'],
                'token': analysis.nextflowsearch.token,
-               'rf_id': raw.rawfile_id,
                'wf_commit': nfwf.commit,
                'nxf_wf_fn': nfwf.filename,
                'repo': nfwf.nfworkflow.repo,
                'runname': f'{analysis.id}_longqc_{raw.rawfile.producer.name}_rawfile{raw.rawfile_id}_{timestamp}',
-               'filename': raw.filename,
-               'instrument': raw.rawfile.producer.name,
                }
         self.run_tasks.append(((run, params, stagefiles, ','.join(nfwf.profiles), nfwf.nfversion), {}))
         analysis.log.append('[{}] Job queued'.format(datetime.strftime(timezone.now(), '%Y-%m-%d %H:%M:%S')))

src/backend/analysis/tasks.py

@@ -428,9 +428,8 @@ def execute_normal_nf(run, params, rundir, gitwfdir, taskid, nf_version, profile
 def run_nextflow_longitude_qc(self, run, params, stagefiles, profiles, nf_version):
     print('Got message to run QC workflow, preparing')
     reporturl = urljoin(settings.KANTELEHOST, reverse('jobs:storelongqc'))
-    postdata = {'client_id': settings.APIKEY, 'rf_id': run['rf_id'], 'plots': {},
-                'analysis_id': run['analysis_id'], 'task': self.request.id,
-                'instrument': run['instrument'], 'filename': run['filename']}
+    postdata = {'client_id': settings.APIKEY, 'qcrun_id': run['qcrun_id'], 'plots': {},
+            'task': self.request.id}
     rundir = create_runname_dir(run)
     params, gitwfdir, no_stagedir = prepare_nextflow_run(run, self.request.id, rundir, stagefiles, [], params)
     # QC has no stagedir, we put the raw in rundir to stage

src/backend/dashboard/migrations/0003_lineplotdata_plottype.py

@@ -0,0 +1,95 @@
+# Generated by Django 4.2.13 on 2025-01-09 13:53
+
+from django.db import migrations, models
+from django.db.models import F
+
+from dashboard import models as dm
+
+
+dtmap = {
+        'psms': dm.LineDataTypes.NRPSMS,
+        'scans': dm.LineDataTypes.NRSCANS,
+        'peptides': dm.LineDataTypes.NRPEPTIDES,
+        'unique_peptides': dm.LineDataTypes.NRPEPTIDES_UNI,
+        'proteins': dm.LineDataTypes.NRPROTEINS,
+        'miscleav1': dm.LineDataTypes.MISCLEAV1,
+        'miscleav2': dm.LineDataTypes.MISCLEAV2,
+        'peaks_fwhm': dm.LineDataTypes.PEAKS_FWHM,
+
+        'perror': dm.QuartileDataTypes.MASSERROR,
+        'msgfscore': dm.QuartileDataTypes.SCORE,
+        'rt': dm.QuartileDataTypes.RT,
+        'peparea': dm.QuartileDataTypes.PEPMS1AREA,
+        'ionmob': dm.QuartileDataTypes.IONMOB,
+        'fwhms': dm.QuartileDataTypes.FWHM,
+        'ioninj': dm.QuartileDataTypes.IONINJ,
+        'matched_peaks': dm.QuartileDataTypes.MATCHED_PEAKS,
+        }
+
+
+def fill_datatypes_remove_old(a, s):
+    Box = a.get_model('dashboard', 'BoxplotData')
+    Box.objects.filter(shortname='sagescores').delete()
+    for b in Box.objects.all():
+        b.datatype = dtmap[b.shortname]
+        b.save()
+    Line = a.get_model('dashboard', 'LineplotData')
+    Line.objects.filter(shortname='miscleav3').delete()
+    Line.objects.filter(shortname='miscleav0').delete()
+    for l in Line.objects.all():
+        l.datatype = dtmap[l.shortname]
+        l.save()
+    # Remove thermo ion mob plots
+    Box.objects.filter(datatype=dm.QuartileDataTypes.IONMOB, q2=F('q3'), q1=0.0).delete()
+
+def fake(a,s):
+    pass
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('dashboard', '0002_qcdata_is_ok_qcdata_message'),
+    ]
+
+    operations = [
+        migrations.AddField(
+            model_name='boxplotdata',
+            name='datatype',
+            field=models.IntegerField(choices=[(1, 'FWHM'), (2, 'Peptide MS1 area'), (3, 'Mass error'), (4, 'Retention time'), (5, 'Score'), (6, 'Ion mobility'), (7, 'Ion injection time(ms)'), (8, 'Amount MS2 peaks matched')]),
+            preserve_default=False,
+        ),
+
+        migrations.AddField(
+            model_name='lineplotdata',
+            name='datatype',
+            field=models.IntegerField(choices=[(1, 'Nr of proteins'), (2, 'Nr of peptides'), (3, 'Nr of peptides mapping uniquely'), (4, 'Nr of PSMs'), (5, 'Nr of scans'), (6, 'Nr of PSMs with 1 missed cleavage'), (7, 'Nr of PSMs with 2 missed cleavage'), (8, 'Amount scans FWHM')]),
+            preserve_default=False,
+        ),
+
+        migrations.AddField(
+            model_name='qcdata',
+            name='runtype',
+            field=models.IntegerField(choices=[(1, 'DDA'), (2, 'DIA')], default=1),
+            preserve_default=False,
+        ),
+
+        migrations.RunPython(fill_datatypes_remove_old, fake),
+
+        migrations.AlterField(
+            model_name='qcdata',
+            name='analysis',
+            field=models.OneToOneField(on_delete=models.deletion.CASCADE, to='analysis.analysis'),
+        ),
+        migrations.AlterField(
+            model_name='qcdata',
+            name='rawfile',
+            field=models.OneToOneField(on_delete=models.deletion.CASCADE, to='rawstatus.rawfile'),
+        ),
+
+        migrations.RenameModel(
+            old_name='QCData',
+            new_name='QCRun',
+        ),
+
+    ]

src/backend/dashboard/migrations/0004_remove_lineplotdata_plottype_qcdata_runtype.py

@@ -0,0 +1,29 @@
+# Generated by Django 4.2.13 on 2025-01-13 14:47
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('dashboard', '0003_lineplotdata_plottype'),
+    ]
+
+    operations = [
+        migrations.RemoveField(
+            model_name='lineplotdata',
+            name='shortname',
+        ),
+        migrations.RemoveField(
+            model_name='boxplotdata',
+            name='shortname',
+        ),
+        migrations.RemoveField(
+            model_name='boxplotdata',
+            name='lower',
+        ),
+        migrations.RemoveField(
+            model_name='boxplotdata',
+            name='upper',
+        ),
+    ]

src/backend/dashboard/models.py

@@ -1,27 +1,49 @@
 from django.db import models
 
-from rawstatus import models as filemodels
-from analysis import models as analysismodels
+from rawstatus import models as rm
+from analysis import models as am
+from datasets import models as dm
 
 
-class QCData(models.Model):
-    rawfile = models.ForeignKey(filemodels.RawFile, on_delete=models.CASCADE)
-    analysis = models.ForeignKey(analysismodels.Analysis, on_delete=models.CASCADE)
+class QCRun(models.Model):
+    rawfile = models.OneToOneField(rm.RawFile, on_delete=models.CASCADE)
+    analysis = models.OneToOneField(am.Analysis, on_delete=models.CASCADE)
     is_ok = models.BooleanField(default=True)
     message = models.TextField()
+    runtype = models.IntegerField(choices=dm.AcquisistionMode.choices)
+
+
+class LineDataTypes(models.IntegerChoices):
+    NRPROTEINS = 1, 'Nr of proteins'
+    NRPEPTIDES = 2, 'Nr of peptides'
+    NRPEPTIDES_UNI = 3, 'Nr of peptides mapping uniquely'
+    NRPSMS = 4, 'Nr of PSMs'
+    NRSCANS = 5, 'Nr of scans'
+    MISCLEAV1 = 6, 'Nr of PSMs with 1 missed cleavage'
+    MISCLEAV2 = 7, 'Nr of PSMs with 2 missed cleavage'
+    PEAKS_FWHM = 8, 'Amount scans FWHM'
+
+
+class QuartileDataTypes(models.IntegerChoices):
+    FWHM = 1, 'FWHM'
+    PEPMS1AREA = 2, 'Peptide MS1 area'
+    MASSERROR = 3, 'Mass error'
+    RT = 4, 'Retention time'
+    SCORE = 5, 'Score'
+    IONMOB = 6, 'Ion mobility'
+    IONINJ = 7, 'Ion injection time(ms)'
+    MATCHED_PEAKS = 8, 'Amount MS2 peaks matched'
 
 
 class LineplotData(models.Model):
-    qcrun = models.ForeignKey(QCData, on_delete=models.CASCADE)
+    qcrun = models.ForeignKey(QCRun, on_delete=models.CASCADE)
     value = models.FloatField()
-    shortname = models.CharField(max_length=20)
+    datatype = models.IntegerField(choices=LineDataTypes.choices)
 
 
 class BoxplotData(models.Model):
-    shortname = models.CharField(max_length=15)
-    qcrun = models.ForeignKey(QCData, on_delete=models.CASCADE)
-    upper = models.FloatField()
-    lower = models.FloatField()
+    datatype = models.IntegerField(choices=QuartileDataTypes.choices)
+    qcrun = models.ForeignKey(QCRun, on_delete=models.CASCADE)
     q1 = models.FloatField()
     q2 = models.FloatField()
     q3 = models.FloatField()

src/backend/dashboard/templates/dashboard/dashboard.html

@@ -4,7 +4,6 @@
 
 {% block head %}
   <link rel='stylesheet' href='{% static "dashboard/bundle.css" %}'>
-  <script crossorigin="anonymous" src="https://polyfill.io/v3/polyfill.min.js?features=Object.fromEntries"></script>
   <script defer src='{% static "dashboard/bundle.js" %}'></script>
   <script>
     const instruments = [
@@ -16,6 +15,6 @@
 {% endblock head %}
 
 {% block content %}
-<section id="apps">
-</section>
+<div id="apps">
+</div>
 {% endblock %}