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Mccalluc/unnecessary evals #1935

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merged 5 commits into from
Jul 24, 2017
Merged

Mccalluc/unnecessary evals #1935

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8376d5c
Replace eval with globals
mccalluc Jul 20, 2017
ed4f306
Get rid of one more eval
mccalluc Jul 20, 2017
2cdc655
Useless function call
mccalluc Jul 20, 2017
ab4be4f
Combine normal named params and splat
mccalluc Jul 20, 2017
88dea18
Get rid of the last eval
mccalluc Jul 20, 2017
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45 changes: 17 additions & 28 deletions refinery/annotation_server/management/commands/add_genome_annotation.py
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Original file line number Diff line number Diff line change
Expand Up @@ -53,16 +53,9 @@ def parse_gff_attribute(attr):
return ret_dict


def parse_db_string(attr, sym):
def parse_db_params(attr, sym):
"""Helper function for entering gff, gtf, files into models"""
ret_string = ''
for var in sym:
if var in attr:
if ret_string:
ret_string += ', %s="%s"' % (var, attr[var])
else:
ret_string += '%s="%s"' % (var, attr[var])
return ret_string
return {k: attr[k] for k in sym}


def getFileHandle(file_in):
Expand Down Expand Up @@ -171,7 +164,7 @@ def addWigAnnotation(self, wig_file, db_model, annot_type):
"""General function for adding Wig files into the annotation_server
specifically for Conservation and GC content
"""
current_table = eval(db_model)
current_table = globals()[db_model]
current_table.objects.all().delete()
handle = getFileHandle(wig_file)
for line in handle:
Expand All @@ -196,14 +189,13 @@ def addWigAnnotation(self, wig_file, db_model, annot_type):
ret_attr = parse_wig_attribute(line)
table_vals = ['name', 'altColor', 'color', 'visibility',
'priority', 'type', 'description']
db_string = "WigDescription(genome_build='%s', " \
"annotation_type='%s', %s)"
db_string = db_string % (
self.GENOME_BUILD, annot_type, parse_db_string(
ret_attr, table_vals)
params = parse_db_params(
ret_attr, table_vals
)
# saving to wigDescription model
item = eval(db_string)
item = WigDescription(
genome_build=self.GENOME_BUILD,
annotation_type=annot_type,
**params)
item.save()

elif t1[0] == 'fixedStep':
Expand Down Expand Up @@ -296,22 +288,19 @@ def addGeneAnnotation(self, gff_file, db_model, table_vals):
"""Function for adding additional gene annotation files
i.e hg19 gencode, dm3 flybase, ce10 wormbase
"""
current_table = eval(db_model)
current_table = globals()[db_model]
current_table.objects.all().delete()
handle = getFileHandle(gff_file)
for line in handle:
# TODO: what to do with additional description fields
if line[0] != '#':
t1 = line.strip().split('\t')
attrib = parse_gff_attribute(t1[8])
db_string = (
'current_table(chrom=t1[0], source=t1[1], feature=t1[2], '
'start=t1[3], end=t1[4], score=t1[5], strand=t1[6], '
'frame=t1[7], attribute=t1[8], %s)'
)
parse_db_string(attrib, table_vals)
db_string = db_string % (parse_db_string(attrib, table_vals))
item = eval(db_string)
params = parse_db_params(attrib, table_vals)
item = current_table(
chrom=t1[0], source=t1[1], feature=t1[2],
start=t1[3], end=t1[4], score=t1[5], strand=t1[6],
frame=t1[7], attribute=t1[8], **params)
item.save()

def addGapRegions(self, bed_file, db_model):
Expand All @@ -322,7 +311,7 @@ def addGapRegions(self, bed_file, db_model):
"genome: %s, file: %s table: %s",
self.GENOME_BUILD, bed_file, db_model)

current_table = eval(db_model)
current_table = globals()[db_model]
current_table.objects.all().delete()
handle = getFileHandle(bed_file)
for line in handle:
Expand All @@ -341,7 +330,7 @@ def addBedAnnotation(self, bed_file, db_model):
"genome: %s, file: %s table: %s",
self.GENOME_BUILD, bed_file, db_model)

current_table = eval(db_model)
current_table = globals()[db_model]
current_table.objects.all().delete()
handle = getFileHandle(bed_file)
for line in handle:
Expand Down
20 changes: 10 additions & 10 deletions refinery/annotation_server/views.py
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Original file line number Diff line number Diff line change
Expand Up @@ -20,7 +20,7 @@ def search_genes(request, genome, search_string):
genome, search_string)

if genome in SUPPORTED_GENOMES:
current_table = eval(genome + "_EnsGene")
current_table = globals()[genome + "_EnsGene"]
curr_vals = current_table.objects.filter(
Q(name__contains=search_string) | Q(name2__contains=search_string)
).values('name', 'chrom', 'strand', 'txStart', 'txEnd', 'cdsStart',
Expand Down Expand Up @@ -81,7 +81,7 @@ def get_length(request, genome):
logger.debug("annotation_server.get_length called for genome: %s", genome)

if genome in SUPPORTED_GENOMES:
current_table = eval(genome + "_ChromInfo")
current_table = globals()[genome + "_ChromInfo"]
data = ValuesQuerySetToDict(
current_table.objects.values('chrom', 'size'))
return HttpResponse(data, 'application/json')
Expand All @@ -95,7 +95,7 @@ def get_chrom_length(request, genome, chrom):
"%s chromosome: %s", genome, chrom)

if genome in SUPPORTED_GENOMES:
current_table = eval(genome + "_ChromInfo")
current_table = globals()[genome + "_ChromInfo"]
curr_vals = current_table.objects.filter(chrom__iexact=chrom).values(
'chrom', 'size')
data = ValuesQuerySetToDict(curr_vals)
Expand All @@ -112,7 +112,7 @@ def get_cytoband(request, genome, chrom):
"%s chromosome: %s", genome, chrom)

if genome in SUPPORTED_GENOMES:
current_table = eval(genome + "_CytoBand")
current_table = globals()[genome + "_CytoBand"]
curr_vals = current_table.objects.filter(chrom__iexact=chrom).values(
'chrom', 'chromStart', 'chromEnd', 'name', 'gieStain')
data = ValuesQuerySetToDict(curr_vals)
Expand All @@ -127,7 +127,7 @@ def get_genes(request, genome, chrom, start, end):
"%s chromosome: %s", genome, chrom)

if genome in SUPPORTED_GENOMES:
current_table = eval(genome + "_EnsGene")
current_table = globals()[genome + "_EnsGene"]
curr_vals = current_table.objects.filter(
Q(chrom__iexact=chrom),
Q(cdsStart__range=(start, end)) | Q(cdsEnd__range=(start, end))
Expand All @@ -145,7 +145,7 @@ def get_gc(request, genome, chrom, start, end):
"%s chromosome: %s:%s-%s", genome, chrom, start, end)

if genome in SUPPORTED_GENOMES:
current_table = eval(genome + "_GC")
current_table = globals()[genome + "_GC"]
curr_vals = current_table.objects.filter(
Q(chrom__iexact=chrom),
Q(position__range=(start, end)),
Expand All @@ -164,7 +164,7 @@ def get_maptheo(request, genome, chrom, start, end):
"%s chromosome: %s:%s-%s", genome, chrom, start, end)

if genome in MAPPABILITY_THEORETICAL:
current_table = eval(genome + "_MappabilityTheoretical")
current_table = globals()[genome + "_MappabilityTheoretical"]
curr_vals = current_table.objects.filter(
Q(chrom__iexact=chrom),
Q(chromStart__range=(start, end)) | Q(chromEnd__range=(start, end))
Expand All @@ -182,7 +182,7 @@ def get_mapemp(request, genome, chrom, start, end):
"%s chromosome: %s:%s-%s", genome, chrom, start, end)

if genome in SUPPORTED_GENOMES:
current_table = eval(genome + "_MappabilityEmpirial")
current_table = globals()[genome + "_MappabilityEmpirial"]
curr_vals = current_table.objects.filter(
Q(chrom__iexact=chrom),
Q(chromStart__range=(start, end)) | Q(chromEnd__range=(start, end))
Expand All @@ -199,7 +199,7 @@ def get_conservation(request, genome, chrom, start, end):
"%s chromosome: %s:%s-%s", genome, chrom, start, end)

if genome in SUPPORTED_GENOMES:
current_table = eval(genome + "_Conservation")
current_table = globals()[genome + "_Conservation"]
curr_vals = current_table.objects.filter(
Q(chrom__iexact=chrom),
Q(position__range=(start, end)),
Expand All @@ -217,7 +217,7 @@ def get_gapregion(request, genome, chrom, start, end):
"%s chromosome: %s:%s-%s", genome, chrom, start, end)

if genome in GAP_REGIONS:
current_table = eval(genome + "_GapRegions")
current_table = globals()[genome + "_GapRegions"]
curr_vals = current_table.objects.filter(
Q(chrom__iexact=chrom),
Q(chromStart__gte=start),
Expand Down