runs.py

import datetime
from flask import request
from flask.ext.restful import abort, fields
from sqlalchemy import select, desc, func
import voluptuous
from voluptuous import Schema, Any, Required, Exclusive, Coerce

from cycledash import db
from cycledash.helpers import get_id_where, get_where, abort_if_none_for
from cycledash.validations import Doc, expect_one_of, PathString
from common.helpers import tables
import workers.runner

from . import genotypes, bams, marshal_with, validate_with, projects, Resource


CreateRun = Schema({
    Required('uri'): PathString,

    # One of `project` is required, but not supported in voluptuous, so we
    # enforce this in code. cf. https://github.com/alecthomas/voluptuous/issues/115
    Exclusive('project_id', 'project'): Coerce(int),
    Exclusive('project_name', 'project'): unicode,

    Exclusive('normal_bam_id', 'normal_bam'): Coerce(int),
    Exclusive('normal_bam_uri', 'normal_bam'): PathString,
    Exclusive('tumor_bam_id', 'tumor_bam'): Coerce(int),
    Exclusive('tumor_bam_uri', 'tumor_bam'): PathString,

    'caller_name': unicode,
    'project_id': Coerce(int),
    'tumor_dataset_id': Coerce(int),
    'normal_dataset_id': Coerce(int),
    'truth_vcf_path': PathString,
    'is_validation': bool,
    'notes': unicode,
    'dataset': unicode,
    'project_name': unicode,
    'vcf_header': unicode,
    'vcf_release': Coerce(int)
})

UpdateRun = Schema({
    'caller_name': unicode,

    Exclusive('normal_bam_id', 'normal_bam'): Coerce(int),
    Exclusive('normal_bam_uri', 'normal_bam'): PathString,
    Exclusive('tumor_bam_id', 'tumor_bam'): Coerce(int),
    Exclusive('tumor_bam_uri', 'tumor_bam'): PathString,

    'notes': unicode,
    'vcf_header': unicode,
    'vcf_release': Coerce(int),

    'true_positive': Coerce(int),
    'false_positive': Coerce(int),
    'precision': Coerce(float),
    'recall': Coerce(float),
    'f1score': Coerce(float)
})

run_fields = {
    Doc('id', 'The internal ID of the Run.'):
        long,
    Doc('extant_columns', 'A list of all the columns the Run has.'):
        Any(basestring, None),
    Doc('uri', 'The HDFS or NFS URI of the VCF this run was based on.'):
        basestring,
    Doc('caller_name',
        'The name of the variant caller used to generate this Run.'):
        Any(basestring, None),
    Doc('genotype_count', 'The number of genotypes (calls) made in this Run.'):
        Any(long, None),
    Doc('created_at', 'Timestamp when the Run was created.'):
        datetime.datetime,
    Doc('notes', 'Any ancillary notes, parameters, etc of the Run.'):
        Any(basestring, None),
    Doc('vcf_header', 'The raw VCF text of the header.'):
        Any(basestring, None),
    Doc('vcf_release', 'ENSEMBL Release for the reference'):
        Any(int, None),
    Doc('project_id', 'The internal ID of the Project this Run belongs to.'):
        long,
    Doc('normal_bam_id',
        'The internal ID of the normal BAM associated with the Run.'):
        Any(long, None),
    Doc('tumor_bam_id',
        'The internal ID of the normal BAM associated with the Run.'):
        Any(long, None)
}

RunFields = Schema(run_fields)

# Used because on GET /runs/<id> we need some extra fields [for now].
thick_run_fields = run_fields.copy()
thick_run_fields.update({
    'spec': type,
    'contigs': list,
    'normal_bam': object,
    'tumor_bam': object
})
ThickRunFields = Schema(thick_run_fields)


class RunList(Resource):
    require_auth = True
    @marshal_with(RunFields, envelope='runs')
    def get(self):
        """Get list of all runs in order of recency."""
        with tables(db.engine, 'vcfs') as (con, runs):
            q = select(runs.c).order_by(desc(runs.c.id))
            return [dict(r) for r in q.execute().fetchall()]

    @validate_with(CreateRun)
    @marshal_with(RunFields)
    def post(self):
        """Create a new run.

        This will import the VCF's genotypes into the database in a worker, as
        well as annotate it with gene names.
        """
        run = request.validated_body
        try:
            expect_one_of(request.validated_body, 'project_name', 'project_id')
        except voluptuous.MultipleInvalid as e:
            errors = [str(err) for err in e.errors]
            abort(409, message='Validation error', errors=errors)
        try:
            projects.set_and_verify_project_id_on(run)
        except voluptuous.Invalid as e:
            abort(404, message='Project not found.', errors=[str(e)])
        try:
            _set_or_verify_bam_id_on(run, bam_type='normal')
            _set_or_verify_bam_id_on(run, bam_type='tumor')
        except voluptuous.Invalid as e:
            abort(404, message='BAM not found.', errors=[str(e)])

        with tables(db.engine, 'vcfs') as (con, runs):
            run = runs.insert(
                request.validated_body).returning(*runs.c).execute().fetchone()
        workers.runner.start_workers_for_vcf_id(run['id'])
        return dict(run), 201


class Run(Resource):
    require_auth = True
    @marshal_with(ThickRunFields)
    def get(self, run_id):
        """Return a vcf with a given ID."""
        with tables(db.engine, 'vcfs') as (con, runs):
            q = select(runs.c).where(runs.c.id == run_id)
            run = dict(_abort_if_none(q.execute().fetchone(), run_id))
        bams.attach_bams_to_vcfs([run])
        return run

    @validate_with(UpdateRun)
    @marshal_with(RunFields)
    def put(self, run_id):
        """Update the run by its ID."""
        with tables(db.engine, 'vcfs') as (con, runs):
            q = runs.update(runs.c.id == run_id).values(
                **request.validated_body
            ).returning(*runs.c)
            return dict(_abort_if_none(q.execute().fetchone(), run_id))

    @marshal_with(RunFields)
    def delete(self, run_id):
        """Delete a run by its ID."""
        with tables(db.engine, 'vcfs') as (con, runs):
            q = (runs.delete()
                 .where(runs.c.id == run_id)
                 .returning(*runs.c))
            # TODO: unattach BAMs and projects before deleting?
            # TODO: cascade tasks & genotypes deletion?
            return dict(_abort_if_none(q.execute().fetchone(), run_id))


_abort_if_none = abort_if_none_for('run')


def get_related_vcfs(run):
    """Return a list of vcfs in the same project as vcf."""
    with tables(db.engine, 'vcfs') as (con, runs):
        q = select(runs.c).where(
            runs.c.project_id == run['project_id']).where(
                runs.c.id != run['id'])
        return [dict(r) for r in q.execute().fetchall()]


def _set_or_verify_bam_id_on(run, bam_type):
    """After calling this, run['(bam_type)_bam_id'] will be set to a valid BAM ID.

    If there is not a matching BAM, it will raise voluptuous.Invalid.
    """
    id_key = bam_type + '_bam_id'
    uri_key = bam_type + '_bam_uri'
    bam_id = run.get(id_key)
    if bam_id:
        if get_where('bams', db, id=bam_id) is None:
            raise voluptuous.Invalid(
                'bam with id "{}" does not exist'.format(bam_id))
    elif run.get(uri_key):
        bam_id = get_id_where('bams', db, uri=run[uri_key])
        if bam_id is None:
            raise voluptuous.Invalid(
                'bam with uri "{}" does not exist'.format(run[uri_key]))
        run[id_key] = bam_id
        del run[uri_key]