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Update loadable refs to read_group refs #35

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merged 4 commits into from
Nov 1, 2024
Merged

Update loadable refs to read_group refs #35

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f528976
Update loadable refs to read_group refs
mellypop Feb 2, 2023
f8d7465
Merge branch 'main' into feature/update-loadable-refs-to-read_group
mellypop Mar 6, 2023
75d6a1f
Format query cleanly
mellypop Mar 7, 2023
e969838
Merge branch 'main' into feature/update-loadable-refs-to-read_group
mcrusch Nov 1, 2024
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23 changes: 11 additions & 12 deletions src/main/scripts/add_bam_pair_xenocp.py
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Original file line number Diff line number Diff line change
Expand Up @@ -89,22 +89,22 @@ def add_bam_pair_stp(raptr, sample, target, project, subproject, **kwargs):
formal_name = %s and target_name = %s and project_name = %s and subproject = %s;"""
stp_id = raptr.fetch_item_or_fail(query, (sample, target, project, subproject))

# Get loadables associated with old bam_tpl
# Get read groups associated with old bam_tpl
query = """select bam_tpl_id, bam_id from bam_and_tpl where sample_target_project_id = %s
and bam_status = 'Normal' and legacy = False"""
(bam_tpl_id, bam_id) = raptr.fetch_row_or_fail(query, (stp_id,))
query = """select loadable_id from bam_tpl_loadable where bam_tpl_id = %s;"""
loadable_ids = raptr.fetch_col_or_fail(query, (bam_tpl_id,))
query = """select read_group_id from bam_tpl_read_group where bam_tpl_id = %s;"""
rg_ids = raptr.fetch_col_or_fail(query, (bam_tpl_id,))

# Insert a new bam_tpl with qualifier 'xenocp'
query = """insert into bam_tpl (bam_tpl_id, qualifier, status, sample_target_project_id)
values (nextval('blt_id_seq'), 'xenocp', 'Default', %s) returning bam_tpl_id;"""
bam_tpl_id_xenocp = raptr.fetch_item_or_fail(query, (stp_id,))

# Associate loadables with new bam_tpl.
query = """insert into bam_tpl_loadable values (%s, %s)"""
for lid in loadable_ids:
raptr.execute(query, (bam_tpl_id_xenocp, lid))
query = """insert into bam_tpl_read_group values (%s, %s)"""
for rgid in rg_ids:
raptr.execute(query, (bam_tpl_id_xenocp, rgid))

# Get genome for old bam
query = """select genome_id from bam where bam_id = %s;"""
Expand All @@ -118,12 +118,11 @@ def add_bam_pair_stp(raptr, sample, target, project, subproject, **kwargs):
raptr.execute(query, (bam_id_xenocp, bam_tpl_id_xenocp))

# Get read_group_ids and insert into bam_read_group
query = """SELECT read_group_id, pu from read_group inner join (select loadable_id as lid,
project_id as pid, project_name, subproject, target_name from loadable inner join
(select * from sample_target_project_view where
formal_name = %s and target_name = %s and project_name = %s
and subproject = %s) using (sample_target_id))
on loadable_id = lid and project_id = pid where status = 'Normal';"""
query = """select rg.read_group_id, rg.pu
from read_group rg inner join sample_target_project_view stpv
on rg.sample_target_id = stpv.sample_target_id and rg.project_id = stpv.project_id
where status = 'Normal' and formal_name = %s and target_name = %s
and project_name = %s and subproject = %s;"""
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Let's take the opportunity to format this (i.e. newlines, indentation, etc.). It's already changed enough that the whole block is a diff, so no reason not to fix the lack of formatting of the query.

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Something like this?

    query = """select
            rg.read_group_id,
            rg.pu
        from
            read_group rg
            inner join sample_target_project_view stpv
                on rg.sample_target_id = stpv.sample_target_id and rg.project_id = stpv.project_id
        where
            status = 'Normal'
            and formal_name = %s
            and target_name = %s
            and project_name = %s
            and subproject = %s;"""

res = raptr.execute_fetch(query, (sample, target, project, subproject))
query = """insert into bam_read_group (bam_id, read_group_id, rgid)
values (%s, %s, %s);"""
Expand Down