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Big refactoring 2

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This commit is contained in:
Eric Coissac
2016-12-26 13:56:31 +01:00
parent daacd0df76
commit e6db2086d5
3 changed files with 98 additions and 111 deletions
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107
python/obitools3/dms/_obidms.pyx
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@ -1,107 +0,0 @@
#cython: language_level=3
from obitools3.utils cimport bytes2str, str2bytes
from .capi.obidms cimport obi_dms, \
obi_close_dms
from .capi.obidmscolumn cimport obi_close_column, \
OBIDMS_column_p, \
OBIDMS_column_header_p
from .capi.obiutils cimport obi_format_date
from .capi.obiview cimport Obiview_p, \
Obiview_infos_p, \
Alias_column_pair_p, \
obi_view_map_file, \
obi_view_unmap_file
from .capi.obitypes cimport const_char_p, \
OBIType_t, \
OBI_INT, \
OBI_FLOAT, \
OBI_BOOL, \
OBI_CHAR, \
OBI_QUAL, \
OBI_STR, \
OBI_SEQ, \
name_data_type, \
only_ATGC # discuss
from ._obitaxo cimport OBI_Taxonomy
from libc.stdlib cimport malloc
cdef class OBIDMS :
def __init__(self, str dms_name) :
# Declarations
cdef bytes dms_name_b
# Format the character string to send to C function
dms_name_b = str2bytes(dms_name)
# Fill structure and create or open the DMS
self._pointer = obi_dms(<const_char_p> dms_name_b)
if self._pointer == NULL :
raise Exception("Failed opening or creating an OBIDMS")
# name property getter
@property
def name(self):
return bytes2str(self._pointer.dms_name)
cpdef close(self) :
if (obi_close_dms(self._pointer)) < 0 :
raise Exception("Problem closing an OBIDMS")
cpdef OBI_Taxonomy open_taxonomy(self, str taxo_name) :
return OBI_Taxonomy(self, taxo_name)
cpdef dict read_view_infos(self, str view_name) :
cdef Obiview_infos_p view_infos_p
cdef dict view_infos_d
cdef Alias_column_pair_p column_refs
cdef int i, j
cdef str column_name
view_infos_p = obi_view_map_file(self._pointer, str2bytes(view_name))
view_infos_d = {}
view_infos_d["name"] = bytes2str(view_infos_p.name)
view_infos_d["comments"] = bytes2str(view_infos_p.comments)
view_infos_d["view_type"] = bytes2str(view_infos_p.view_type)
view_infos_d["column_count"] = <int> view_infos_p.column_count
view_infos_d["line_count"] = <int> view_infos_p.line_count
view_infos_d["created_from"] = bytes2str(view_infos_p.created_from)
view_infos_d["creation_date"] = bytes2str(obi_format_date(view_infos_p.creation_date))
if (view_infos_p.all_lines) :
view_infos_d["line_selection"] = None
else :
view_infos_d["line_selection"] = {}
view_infos_d["line_selection"]["column_name"] = bytes2str((view_infos_p.line_selection).column_name)
view_infos_d["line_selection"]["version"] = <int> (view_infos_p.line_selection).version
view_infos_d["column_references"] = {}
column_references = view_infos_p.column_references
for j in range(view_infos_d["column_count"]) :
column_name = bytes2str((column_references[j]).alias)
view_infos_d["column_references"][column_name] = {}
view_infos_d["column_references"][column_name]["original_name"] = bytes2str((column_references[j]).column_refs.column_name)
view_infos_d["column_references"][column_name]["version"] = (column_references[j]).column_refs.version
obi_view_unmap_file(self._pointer, view_infos_p)
return view_infos_d

8
python/obitools3/dms/_obidms.pxd → python/obitools3/dms/dms.pxd
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@ -8,13 +8,13 @@ from ._obitaxo cimport OBI_Taxonomy
cdef class OBIDMS: cdef class DMS:
cdef OBIDMS_p _pointer cdef OBIDMS_p _pointer
cpdef close(self) cpdef close(self)
cpdef OBI_Taxonomy open_taxonomy(self, str taxo_name) cpdef Taxonomy open_taxonomy(self, str taxo_name)
cpdef dict read_view_infos(self, objec view_name)
cpdef dict read_view_infos(self, str view_name)
# cpdef dict read_views(self) TODO # cpdef dict read_views(self) TODO

94
python/obitools3/dms/dms.pyx Normal file
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@ -0,0 +1,94 @@
#cython: language_level=3
from libc.stdlib cimport malloc
from .capi.obidms cimport obi_dms, \
obi_close_dms
from .capi.obidmscolumn cimport obi_close_column, \
OBIDMS_column_p, \
OBIDMS_column_header_p
from .capi.obiutils cimport obi_format_date
from .capi.obiview cimport Obiview_p, \
Obiview_infos_p, \
Alias_column_pair_p, \
obi_view_map_file, \
obi_view_unmap_file
from .capi.obitypes cimport const_char_p, \
OBIType_t, \
OBI_INT, \
OBI_FLOAT, \
OBI_BOOL, \
OBI_CHAR, \
OBI_QUAL, \
OBI_STR, \
OBI_SEQ, \
name_data_type, \
only_ATGC # discuss
from obitools3.utils cimport bytes2str, \
str2bytes, \
tobytes
from .taxonomy cimport Taxonomy
cdef class DMS :
def __init__(self, object dms_name) :
'''
Constructor of a obitools3.dms.DMS instance.
@param dms_name: The name of the DMS
@type dms_name: a `str` or a `bytes` instance
'''
# Declarations
cdef bytes dms_name_b = tobytes(dms_name):
# Fill structure and create or open the DMS
self._pointer = obi_dms(<const_char_p> dms_name_b)
if self._pointer == NULL :
raise Exception("Failed opening or creating an OBIDMS")
def __dealloc__(self):
"""
Destructor of the DMS instance.
The destructor automatically call the `close` methode and
therefore free all the associated memory.
"""
self.close()
self._pointer=NULL
# name property getter
@property
def name(self):
"""
Returns the name of the DMS instance
"""
return bytes2str(self._pointer.dms_name)
cpdef close(self) :
"""
Closes the DNS instance and free the associated memory
the `close` method is automatically called by the object destructor.
"""
if (obi_close_dms(self._pointer)) < 0 :
raise Exception("Problem closing an OBIDMS")