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Cython: Columns: added support for JSON formatted comments

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This commit is contained in:
Celine Mercier
2018-10-07 18:59:43 +02:00
parent 86bb582a17
commit 704d9b0474
4 changed files with 111 additions and 15 deletions
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5
python/obitools3/dms/column/column.pxd
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@ -22,13 +22,16 @@ cdef class Column(OBIWrapper) :
cdef inline OBIDMS_column_p pointer(self)
cdef read_elements_names(self)
@staticmethod
cdef type get_column_class(obitype_t obitype, bint multi_elts, bint tuples)
@staticmethod
cdef type get_python_type(obitype_t obitype, bint multi_elts)
cdef class Column_comments(dict):
cdef Column _column
cdef class Column_multi_elts(Column) :

117
python/obitools3/dms/column/column.pyx
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@ -13,7 +13,8 @@ from ..capi.obidms cimport obi_import_column
from ..capi.obidmscolumn cimport OBIDMS_column_header_p, \
obi_close_column, \
obi_get_elements_names
obi_get_elements_names, \
obi_column_write_comments
from ..capi.obiutils cimport obi_format_date
@ -26,7 +27,10 @@ from ..object cimport OBIDeactivatedInstanceError
from obitools3.utils cimport tobytes, \
bytes2str, \
str2bytes
str2bytes, \
str2bytes_object, \
bytes2str_object, \
clean_empty_values_from_object
from obitools3.dms.column import typed_column
@ -35,6 +39,8 @@ from libc.stdlib cimport free
import importlib
import inspect
import pkgutil
import json
cdef class Column(OBIWrapper) :
'''
@ -82,13 +88,13 @@ cdef class Column(OBIWrapper) :
bint to_eval=False,
object associated_column_name=b"",
int associated_column_version=-1,
object comments=b"",
object comments={},
object alias=b""):
# TODO indexer_name?
cdef bytes column_name_b = tobytes(column_name)
cdef bytes alias_b = tobytes(alias)
cdef bytes comments_b = tobytes(comments)
cdef bytes comments_b = str2bytes(json.dumps(bytes2str_object(comments)))
cdef bytes associated_column_name_b = tobytes(associated_column_name)
cdef list elements_names_s
cdef bytes elements_names_b
@ -159,7 +165,7 @@ cdef class Column(OBIWrapper) :
column_pp = obi_view_get_pointer_on_column_in_view(view.pointer(),
column_name_b)
if column_pp == NULL:
raise KeyError("Cannot access to column %s in view %s" % (
bytes2str(column_name_b),
@ -373,21 +379,104 @@ cdef class Column(OBIWrapper) :
raise OBIDeactivatedInstanceError()
return self.pointer().header.to_eval
# comments property getter
@property
def comments(self):
if not self.active() :
raise OBIDeactivatedInstanceError()
return self.pointer().header.comments
# creation_date property getter
@property
def creation_date(self):
if not self.active() :
raise OBIDeactivatedInstanceError()
return obi_format_date(self.pointer().header.creation_date)
# comments property getter
@property
def comments(self):
return Column_comments(self)
@comments.setter
def comments(self, object value):
Column_comments(self, value)
cdef class Column_comments(dict): # Not thread safe
def __init__(self, Column column, value=None) :
if not column.active() :
raise OBIDeactivatedInstanceError()
self._column = column
if value is not None:
self.update(value) # TODO test and discuss not overwriting (could use replace bool)
self._update_from_file()
def _update_from_file(self):
cdef bytes comments_json
cdef str comments_json_str
cdef OBIDMS_column_p column_p
cdef Column column
if not self._column.active() :
raise OBIDeactivatedInstanceError()
column = self._column
column_p = <OBIDMS_column_p>(column.pointer())
comments_json = <bytes> column_p.header.comments
comments_json_str = bytes2str(comments_json)
comments_dict = json.loads(comments_json_str)
str2bytes_object(comments_dict)
super(Column_comments, self).update(comments_dict)
def __getitem__(self, object key):
if not self._column.active() :
raise OBIDeactivatedInstanceError()
if type(key) == str:
key = str2bytes(key)
self._update_from_file()
return super(Column_comments, self).__getitem__(key)
def __setitem__(self, object key, object value):
cdef OBIDMS_column_p column_p
cdef Column column
if not self._column.active() :
raise OBIDeactivatedInstanceError()
column = self._column
column_p = <OBIDMS_column_p>(column.pointer())
# Remove virtually empty values from the object # TODO discuss
clean_empty_values_from_object(value)
# If value is virtually empty, don't add it # TODO discuss
if value is None or len(value) == 0:
return
# Convert to bytes
if type(key) == str:
key = str2bytes(key)
value_bytes = str2bytes_object(value)
# Update dict with comments already written in file
self._update_from_file()
# Add new element # TODO don't overwrite?
super(Column_comments, self).__setitem__(key, value_bytes)
# Convert to str because json library doens't like bytes
dict_str = {key:item for key,item in self.items()}
dict_str = bytes2str_object(dict_str)
# Convert to json string
comments_json = json.dumps(dict_str)
# Write new comments
if obi_column_write_comments(column_p, tobytes(comments_json)) < 0:
raise Exception("Could not write column comments: %s", comments_json)
def update(self, value):
for k,v in value.items():
self[k] = v
def __contains__(self, key):
return super(Column_comments, self).__contains__(tobytes(key))
def __str__(self):
return bytes2str(self._column.pointer().header.comments)
######################################################################################################

2
python/obitools3/dms/dms.cfiles
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@ -18,6 +18,8 @@
../../../src/libecoPCR/ecodna.c
../../../src/libecoPCR/ecoError.c
../../../src/libecoPCR/ecoMalloc.c
../../../src/libjson/cJSON.c
../../../src/libjson/json_utils.c
../../../src/obiavl.c
../../../src/obiblob_indexer.c
../../../src/obiblob.c

2
python/obitools3/utils.cfiles
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@ -18,6 +18,8 @@
../../src/libecoPCR/ecodna.c
../../src/libecoPCR/ecoError.c
../../src/libecoPCR/ecoMalloc.c
../../src/libjson/cJSON.c
../../src/libjson/json_utils.c
../../src/obiavl.c
../../src/obiblob_indexer.c
../../src/obiblob.c