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Fix code for samples with missing location #22

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Fix code for samples with missing location #22

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16 changes: 10 additions & 6 deletions genomeuploader/genome_upload.py
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Original file line number Diff line number Diff line change
Expand Up @@ -409,10 +409,14 @@ def extract_ENA_info(genomeInfo, uploadDir, webin, password):
latitude = '-' + location.split('S')[0].strip()
longitude = location.split('S')[1].strip()

if 'W' in longitude:
longitude = '-' + longitude.split('W')[0].strip()
elif longitude.endswith('E'):
longitude = longitude.split('E')[0].strip()
try:
if 'W' in longitude:
longitude = '-' + longitude.split('W')[0].strip()
elif longitude.endswith('E'):
longitude = longitude.split('E')[0].strip()
except TypeError:
# NoneType is not iterable
pass

if latitude:
latitude = "{:.{}f}".format(round(float(latitude), GEOGRAPHY_DIGIT_COORDS), GEOGRAPHY_DIGIT_COORDS)
Expand Down Expand Up @@ -492,12 +496,12 @@ def combine_ENA_info(genomeInfo, ENADict):
latitude = latitList[0]
if multipleElementSet(latitList):
latitude = "not provided"
genomeInfo[g]["latitude"] = str(round(float(latitude), GEOGRAPHY_DIGIT_COORDS))
genomeInfo[g]["latitude"] = str(round(float(latitude), GEOGRAPHY_DIGIT_COORDS)) if latitude != "not provided" else latitude

longitude = longList[0]
if multipleElementSet(longList):
longitude = "not provided"
genomeInfo[g]["longitude"] = str(round(float(longitude), GEOGRAPHY_DIGIT_COORDS))
genomeInfo[g]["longitude"] = str(round(float(longitude), GEOGRAPHY_DIGIT_COORDS)) if longitude != "not provided" else longitude

samples = samplesList[0]
if multipleElementSet(samplesList):
Expand Down