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import: Columns are now rewritten in OBI_FLOAT if a value is > INT32_MAX

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This commit is contained in:
MercierC
2021-03-29 09:00:52 +13:00
parent 6d445fe3ad
commit 3e93cfff7b
4 changed files with 10 additions and 5 deletions
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4
python/obitools3/commands/import.pyx
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@ -371,7 +371,7 @@ def run(config):
# Fill value # Fill value
dcols[tag][0][i] = value dcols[tag][0][i] = value
except IndexError : except (IndexError, OverflowError):
value_type = type(value) value_type = type(value)
old_column = dcols[tag][0] old_column = dcols[tag][0]
@ -419,7 +419,7 @@ def run(config):
dcols[tag][0][i] = value dcols[tag][0][i] = value
except Exception as e: except Exception as e:
print("\nCould not import sequence id:", entry.id, "(error raised:", e, ")") print("\nCould not import sequence:", entry, "(error raised:", e, ")")
if 'skiperror' in config['obi'] and not config['obi']['skiperror']: if 'skiperror' in config['obi'] and not config['obi']['skiperror']:
raise e raise e
else: else:

2
python/obitools3/dms/capi/obitypes.pxd
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@ -54,6 +54,8 @@ cdef extern from "obitypes.h" nogil:
extern uint8_t* OBIQual_int_NA extern uint8_t* OBIQual_int_NA
extern void* OBITuple_NA extern void* OBITuple_NA
extern obiint_t OBI_INT_MAX
const_char_p name_data_type(int data_type) const_char_p name_data_type(int data_type)
ctypedef OBIType_t obitype_t ctypedef OBIType_t obitype_t

5
python/obitools3/utils.pyx
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@ -9,7 +9,8 @@ from obitools3.dms.capi.obitypes cimport is_a_DNA_seq, \
OBI_QUAL, \ OBI_QUAL, \
OBI_SEQ, \ OBI_SEQ, \
OBI_STR, \ OBI_STR, \
index_t index_t, \
OBI_INT_MAX
from obitools3.dms.capi.obierrno cimport OBI_LINE_IDX_ERROR, \ from obitools3.dms.capi.obierrno cimport OBI_LINE_IDX_ERROR, \
OBI_ELT_IDX_ERROR, \ OBI_ELT_IDX_ERROR, \
@ -258,7 +259,7 @@ cdef obitype_t update_obitype(obitype_t obitype, object new_value) :
new_type = type(new_value) new_type = type(new_value)
if obitype == OBI_INT : if obitype == OBI_INT :
if new_type == float : if new_type == float or new_value > OBI_INT_MAX :
return OBI_FLOAT return OBI_FLOAT
# TODO BOOL vers INT/FLOAT # TODO BOOL vers INT/FLOAT
elif new_type == str or new_type == bytes : elif new_type == str or new_type == bytes :

2
src/obitypes.h
View File

@ -29,6 +29,8 @@
#define OBIQual_int_NA (NULL) /**< NA value for the type OBI_QUAL if the quality is in integer format */ #define OBIQual_int_NA (NULL) /**< NA value for the type OBI_QUAL if the quality is in integer format */
#define OBITuple_NA (NULL) /**< NA value for tuples of any type */ #define OBITuple_NA (NULL) /**< NA value for tuples of any type */
#define OBI_INT_MAX (INT32_MAX) /**< Maximum value for the type OBI_INT */
/** /**
* @brief enum for the boolean OBIType. * @brief enum for the boolean OBIType.