updated models and load functions for almeida #18
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dfornika
requested changes
Sep 26, 2023
tb_db/parsers.py
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| with open(speciation_path, 'r') as f: | ||
| reader = csv.DictReader(f) | ||
| count = 0 | ||
| #count = 0 |
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Let's remove this count variable if it isn't going to be used rather than leaving it commented out
tb_db/parsers.py
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| #species.append(speci) | ||
| #count+=1 |
tb_db/parsers.py
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| qcs = [] | ||
| with open(qc_path, 'r') as f: | ||
| reader = csv.DictReader(f) | ||
| for row in reader: | ||
| qc = { | ||
| 'sample_id': row['sample_id'], | ||
| 'sample_name': row['sample_id'], | ||
| #'sample_name': row['sample_id'], | ||
| 'sequencing_run_id' : sequencing_run_id, | ||
| 'most_abundant_species_name':row['most_abundant_species_name'], | ||
| 'most_abundant_species_fraction_total_reads': float(row['most_abundant_species_fraction_total_reads']), |
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This is optional but I have a suggestion:
I try to wrap conversions to int and float in try / catch blocks like this:
try:
total_bases = int(row['total_bases'])
except ValueError as e:
total_bases = None
If there are several fields that need to be converted then I'll do something like this:
float_fields = [
'average_base_quality',
'percent_bases_above_q30',
'percent_gc',
]
for field in float_fields:
try:
row[field] = float(row[field])
except ValueError as e:
row[field] = None
tb_db/parsers.py
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| @@ -185,7 +185,7 @@ def parse_cgmlst(cgmlst_path: str, uncalled='-'): | |||
| reader = csv.DictReader(f) | |||
| for row in reader: | |||
| sample_id = row.pop('sample_id') | |||
| sample_id = sample_id[:6] | |||
| #sample_id = sample_id | |||
tb_db/models.py
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| #accession = Column(String) | ||
| #collection_date = Column(Date) |
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Let's remove these if they aren't being used
tb_db/models.py
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| @@ -71,9 +71,9 @@ class Library(Base): | |||
| """ | |||
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| sample_id = Column(Integer, ForeignKey("sample.id"), nullable=False) | |||
| sample_name = Column(String) | |||
| #sample_name = Column(String) | |||
tb_db/models.py
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| sequencing_run_id = Column(String) | ||
| library_id = Column(String) | ||
| #library_id = Column(String) |
| @@ -349,7 +349,7 @@ def create_cgmlst_profile(self, sample, profile,runid): | |||
| assert(created_cgmlst_profile.library_id == created_libraries[0].id) | |||
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| TestSampleCrudMachine = SampleCrudMachine.TestCase | |||
| #comment the below out as it says 'dict' object has no attribute 'startswith' that i am not sure how to fix, refer to line 305 in crud.py | |||
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We'll have to take a look at the overall testing processes and make sure everything passes, but I'm not going to let it block merging this. We can address that later.
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