def attach_bams_to_vcfs(vcfs):
"""Attach tumor_bam and normal_bam to all VCFs."""
with tables(db.engine, 'bams') as (con, bams):
q = select(bams.c)
bams = [dict(b) for b in con.execute(q).fetchall()]
for vcf in vcfs:
normal_bam_id = vcf.get('normal_bam_id')
tumor_bam_id = vcf.get('tumor_bam_id')
vcf['tumor_bam'] = (
dict(find(bams, lambda x: x.get('id') == tumor_bam_id) or {}))
vcf['normal_bam'] = (
dict(find(bams, lambda x: x.get('id') == normal_bam_id) or {}))
def test_home(self, *mocks):
cycledash.views.home()
project_trees = mocked.call_args[1]['project_trees']
last_comments = mocked.call_args[1]['last_comments']
asserts.eq_(len(project_trees), 2)
project = find(project_trees, lambda p: p['name'] == PROJECT_NAME)
asserts.ok_(project)
vcfs = project.get('vcfs')
asserts.ok_(vcfs)
asserts.eq_(len(vcfs), 2)
asserts.eq_(set([v['uri'] for v in vcfs]),
set([self.run['uri'], self.run2['uri']]))
bams = project.get('bams')
asserts.ok_(bams)
asserts.eq_(len(bams), 2)
asserts.eq_(len(last_comments), 2)
comment2_found = find(last_comments, lambda c: c['vcfId'] == self.run['id'])
asserts.eq_(comment2_found['commentText'], self.comment2['comment_text'])
def get_projects_tree():
"""Return a list of all projects, with their respective vcfs and bams.
{ "projects": [
{ "name": "Project Name",
"notes": "Some test notes"
"vcfs": [...]
"bams": [
{ "name": "a dataset", ... }, ...
]}, ...
]}
"""
with tables(db.engine, 'vcfs', 'user_comments', 'bams', 'projects') as \
(con, vcfs, user_comments, bams_table, projects):
joined = (vcfs
.outerjoin(user_comments, vcfs.c.id == user_comments.c.vcf_id))
num_comments = func.count(user_comments.c.vcf_id).label('num_comments')
q = (select(vcfs.c + [num_comments])
.select_from(joined)
.group_by(vcfs.c.id)
.order_by(desc(vcfs.c.id)))
vcfs = [dict(v) for v in con.execute(q).fetchall()]
q = select(bams_table.c)
all_bams = [dict(b) for b in con.execute(q).fetchall()]
q = select(projects.c)
projects = [dict(b) for b in con.execute(q).fetchall()]
bams.attach_bams_to_vcfs(vcfs)
for vcf in vcfs:
project_id = vcf.get('project_id')
vcf['project'] = dict(find(projects,
lambda x: x.get('id') == project_id) or {})
_join_task_states(vcfs)
for project in projects:
project_id = project['id']
project_bams = [bam for bam in all_bams
if bam.get('project_id') == project_id]
project_vcfs = [vcf for vcf in vcfs
if vcf.get('project_id') == project_id]
project['bams'] = project_bams
project['vcfs'] = project_vcfs
return projects
def get_from_variant(variant):
sample = find(variant.samples, lambda x: x.sample == sample_name)
return getattr(sample.data, attr)
