Closed aguang closed 5 years ago
Merging #25 into devel will increase coverage by
18.45%
. The diff coverage is91.07%
.
@@ Coverage Diff @@
## devel #25 +/- ##
===========================================
+ Coverage 70.34% 88.79% +18.45%
===========================================
Files 10 11 +1
Lines 499 607 +108
===========================================
+ Hits 351 539 +188
+ Misses 148 68 -80
Impacted Files | Coverage Δ | |
---|---|---|
tests/test_sra.py | 100% <100%> (ø) |
|
qcdb/parsers/fastqc_parse.py | 95.55% <100%> (ø) |
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qcdb/sra_metadata.py | 100% <100%> (ø) |
|
qcdb/parsers/parse.py | 96.51% <100%> (+13.98%) |
:arrow_up: |
qcdb/db_create.py | 63.26% <45.83%> (+63.26%) |
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qcdb/parsers/picardtools_parse.py | 85.71% <50%> (ø) |
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qcdb/parsers/qckitfastq_parse.py | 87.5% <66.66%> (ø) |
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qcdb/db_load.py | 69.51% <80%> (+39.27%) |
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tests/test_db.py | 97.22% <97.82%> (+2.16%) |
:arrow_up: |
... and 4 more |
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Key changes:
samplemeta
samplemeta
,sample_id
has been renamed todb_id
, andsample_name
has been renamed tosample_id
. This is to match the fact the SRA has a column namedsample_id
(for SRX/ERX/DRX accessions) as well so that oursample_id
is equivalent to SRA'ssample_id
. All places referencingsample_id
orsample_name
should have been changed accordingly.tables_create.py
has been merged intodb_create.py
, so that when the db is created the tables are as wellThis PR closes #14.
Potential issues:
samplemeta
. In theory this should not be an issue since the limit is ~4 requests/second. In practice we'll see.