# Path: chanjo_report/server/constants.py
# LEVELS = OrderedDict([
#     (10, 'completeness_10'),
#     (15, 'completeness_15'),
#     (20, 'completeness_20'),
#     (50, 'completeness_50'),
#     (100, 'completeness_100'),
# ])
# 
# Path: chanjo_report/server/extensions.py



import itertools
import logging
from flask import abort, flash
from sqlalchemy.exc import OperationalError
from sqlalchemy import func
from chanjo.store.models import Transcript, TranscriptStat, Sample
from chanjo.sex import predict_sex
from chanjo_report.server.constants import LEVELS
from chanjo_report.server.extensions import api
                      .filter(Transcript.gene_id.in_(genes)))
    return query


def transcripts_rows(sample_ids, genes=None, level=10):
    """Generate metrics rows for transcripts."""
    for sample_id in sample_ids:
        sample_obj = Sample.query.get(sample_id)
        all_tx = TranscriptStat.query.filter_by(sample_id=sample_id)
        if genes:
            all_tx = (all_tx.join(TranscriptStat.transcript)
                            .filter(Transcript.gene_id.in_(genes)))
        tx_count = all_tx.count()
        stat_field = getattr(TranscriptStat, LEVELS[level])
        missed_tx = all_tx.filter(stat_field < 100)
        missed_count = missed_tx.count()
        if tx_count == 0:
            tx_yield = 0
            flash("no matching transcripts found!")
        else:
            tx_yield = 100 - (missed_count / tx_count * 100)
        yield {
            'sample': sample_obj,
            'yield': tx_yield,
            'missed': missed_tx,
            'missed_count': missed_count,
            'total': tx_count,
        }



# Path: chanjo_report/server/constants.py
# LEVELS = OrderedDict([
#     (10, 'completeness_10'),
#     (15, 'completeness_15'),
#     (20, 'completeness_20'),
#     (50, 'completeness_50'),
#     (100, 'completeness_100'),
# ])
# 
# Path: chanjo_report/server/extensions.py



# Path: chanjo_report/server/blueprints/report/utils.py
import itertools
import logging
from flask import abort, flash
from sqlalchemy.exc import OperationalError
from sqlalchemy import func
from chanjo.store.models import Transcript, TranscriptStat, Sample
from chanjo.sex import predict_sex
from chanjo_report.server.constants import LEVELS
from chanjo_report.server.extensions import api

                      .filter(Transcript.gene_id.in_(genes)))
    return query


def transcripts_rows(sample_ids, genes=None, level=10):
    """Generate metrics rows for transcripts."""
    for sample_id in sample_ids:
        sample_obj = Sample.query.get(sample_id)
        all_tx = TranscriptStat.query.filter_by(sample_id=sample_id)
        if genes:
            all_tx = (all_tx.join(TranscriptStat.transcript)
                            .filter(Transcript.gene_id.in_(genes)))
        tx_count = all_tx.count()
        stat_field = getattr(TranscriptStat, LEVELS[level])
        missed_tx = all_tx.filter(stat_field < 100)
        missed_count = missed_tx.count()
        if tx_count == 0:
            tx_yield = 0
            flash("no matching transcripts found!")
        else:
            tx_yield = 100 - (missed_count / tx_count * 100)
        yield {
            'sample': sample_obj,
            'yield': tx_yield,
            'missed': missed_tx,
            'missed_count': missed_count,
            'total': tx_count,
        }



def diagnostic_yield(api, genes=None, samples=None, group=None, level=10):