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Closes issue #47 by storing each view in a separate file named with the

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view's name and created upon view creation.
This commit is contained in:
Celine Mercier
2016-06-30 11:41:30 +02:00
parent ad2af0b512
commit 0869b9ba3f
7 changed files with 526 additions and 649 deletions
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2
python/obitools3/obidms/_obidms.pxd
View File

@ -91,5 +91,5 @@ cdef class OBIDMS:
cpdef OBIView open_view(self, str view_name)
cpdef OBIView new_view(self, str view_name, object view_to_clone=*, list line_selection=*, str view_type=*, str comments=*)
cpdef dict read_view_infos(self, str view_name)
cpdef dict read_views(self)
# cpdef dict read_views(self) TODO

137
python/obitools3/obidms/_obidms.pyx
View File

@ -54,16 +54,15 @@ from ._obidmscolumn_seq cimport OBIDMS_column_seq, \
OBIDMS_column_multi_elts_seq
from .capi.obiview cimport Obiview_p, \
Obiviews_infos_all_p, \
Obiview_infos_p, \
Column_reference_p, \
obi_new_view_nuc_seqs, \
obi_new_view, \
obi_new_view_cloned_from_name, \
obi_new_view_nuc_seqs_cloned_from_name, \
obi_view_map_file, \
obi_view_unmap_file, \
obi_open_view, \
obi_read_view_infos, \
obi_close_view_infos, \
obi_view_delete_column, \
obi_view_add_column, \
obi_view_get_column, \
@ -291,11 +290,11 @@ cdef class OBIView :
raise Exception("Error creating/opening a view")
self.pointer = view
self.name = bytes2str(view.name)
self.name = bytes2str(view.infos.name)
# Go through columns to build list of corresponding python instances
self.columns = {}
for i in range(view.column_count) :
for i in range(view.infos.column_count) :
column_p = <OBIDMS_column_p> (view.columns)[i]
header = (column_p).header
col_name = bytes2str(header.name)
@ -305,7 +304,7 @@ cdef class OBIView :
def __repr__(self) :
cdef str s
s = str(self.name) + ", " + str(self.comments) + ", " + str(self.pointer.line_count) + " lines\n"
s = str(self.name) + ", " + str(self.comments) + ", " + str(self.pointer.infos.line_count) + " lines\n"
for column_name in self.columns :
s = s + self.columns[column_name].__repr__() + '\n'
return s
@ -402,7 +401,7 @@ cdef class OBIView :
cdef OBIView_line line # TODO Check that this works for NUC SEQ views
# Yield each line
lines_used = (self.pointer).line_count
lines_used = self.pointer.infos.line_count
for line_nb in range(lines_used) :
line = self[line_nb]
@ -486,12 +485,12 @@ cdef class OBIView_NUC_SEQS(OBIView):
raise Exception("Error creating/opening view")
self.pointer = view
self.name = bytes2str(view.name)
self.comments = bytes2str(view.comments)
self.name = bytes2str(view.infos.name)
self.comments = bytes2str(view.infos.comments)
# Go through columns to build list of corresponding python instances
self.columns = {}
for i in range(view.column_count) :
for i in range(view.infos.column_count) :
column_p = <OBIDMS_column_p> (view.columns)[i]
header = (column_p).header
col_name = bytes2str(header.name)
@ -603,7 +602,7 @@ cdef class OBIDMS :
view_class = OBIView_NUC_SEQS
else :
view_class = OBIView
return view_class(self, view_name)
@ -621,54 +620,84 @@ cdef class OBIDMS :
cpdef dict read_view_infos(self, str view_name) :
all_views = self.read_views()
return all_views[view_name]
cpdef dict read_views(self) : # TODO function that prints the dic nicely and function that prints 1 view nicely. Add column type in col ref
cdef Obiviews_infos_all_p all_views_p
cdef Obiview_infos_p view_p
cdef Obiview_infos_p view_infos_p
cdef dict view_infos_d
cdef Column_reference_p column_refs
cdef int nb_views
cdef int i, j
cdef str view_name
cdef str column_name
cdef dict views
cdef bytes name_b
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_refs = view_infos_p.column_references
for j in range(view_infos_d["column_count"]) :
column_name = bytes2str((column_refs[j]).column_name)
view_infos_d["column_references"][column_name] = {}
view_infos_d["column_references"][column_name]["version"] = column_refs[j].version
views = {}
all_views_p = obi_read_view_infos(self.pointer)
if all_views_p == NULL :
raise Exception("No views to read")
nb_views = <int> (all_views_p.header).view_count
for i in range(nb_views) :
view_p = (<Obiview_infos_p> (all_views_p.view_infos)) + i
view_name = bytes2str(view_p.name)
views[view_name] = {}
views[view_name]["comments"] = bytes2str(view_p.comments)
views[view_name]["view_type"] = bytes2str(view_p.view_type)
views[view_name]["column_count"] = <int> view_p.column_count
views[view_name]["line_count"] = <int> view_p.line_count
views[view_name]["view_number"] = <int> view_p.view_number
views[view_name]["created_from"] = bytes2str(view_p.created_from)
views[view_name]["creation_date"] = bytes2str(obi_format_date(view_p.creation_date))
if (view_p.all_lines) :
views[view_name]["line_selection"] = None
else :
views[view_name]["line_selection"] = {}
views[view_name]["line_selection"]["column_name"] = bytes2str((view_p.line_selection).column_name)
views[view_name]["line_selection"]["version"] = <int> (view_p.line_selection).version
views[view_name]["column_references"] = {}
column_refs = view_p.column_references
for j in range(views[view_name]["column_count"]) :
column_name = bytes2str((column_refs[j]).column_name)
views[view_name]["column_references"][column_name] = {}
views[view_name]["column_references"][column_name]["version"] = column_refs[j].version
obi_close_view_infos(all_views_p);
return views
obi_view_unmap_file(self.pointer, view_infos_p)
return view_infos_d
# cpdef dict read_views(self) : # TODO function that prints the dic nicely and function that prints 1 view nicely. Add column type in col ref
#
# cdef Obiviews_infos_all_p all_views_p
# cdef Obiview_infos_p view_p
# cdef Column_reference_p column_refs
# cdef int nb_views
# cdef int i, j
# cdef str view_name
# cdef str column_name
# cdef dict views
# cdef bytes name_b
#
# views = {}
# all_views_p = obi_read_view_infos(self.pointer)
# if all_views_p == NULL :
# raise Exception("No views to read")
# nb_views = <int> (all_views_p.header).view_count
# for i in range(nb_views) :
# view_p = (<Obiview_infos_p> (all_views_p.view_infos)) + i
# view_name = bytes2str(view_p.name)
# views[view_name] = {}
# views[view_name]["comments"] = bytes2str(view_p.comments)
# views[view_name]["view_type"] = bytes2str(view_p.view_type)
# views[view_name]["column_count"] = <int> view_p.column_count
# views[view_name]["line_count"] = <int> view_p.line_count
# views[view_name]["view_number"] = <int> view_p.view_number
# views[view_name]["created_from"] = bytes2str(view_p.created_from)
# views[view_name]["creation_date"] = bytes2str(obi_format_date(view_p.creation_date))
# if (view_p.all_lines) :
# views[view_name]["line_selection"] = None
# else :
# views[view_name]["line_selection"] = {}
# views[view_name]["line_selection"]["column_name"] = bytes2str((view_p.line_selection).column_name)
# views[view_name]["line_selection"]["version"] = <int> (view_p.line_selection).version
# views[view_name]["column_references"] = {}
# column_refs = view_p.column_references
# for j in range(views[view_name]["column_count"]) :
# column_name = bytes2str((column_refs[j]).column_name)
# views[view_name]["column_references"][column_name] = {}
# views[view_name]["column_references"][column_name]["version"] = column_refs[j].version
#
# obi_close_view_infos(all_views_p);
#
# return views

44
python/obitools3/obidms/capi/obiview.pxd
View File

@ -23,21 +23,6 @@ cdef extern from "obiview.h" nogil:
extern const_char_p DEFINITION_COLUMN
extern const_char_p QUALITY_COLUMN
struct Obiview_t :
OBIDMS_p dms
const_char_p name
const_char_p created_from
const_char_p view_type
bint read_only
OBIDMS_column_p line_selection
OBIDMS_column_p new_line_selection
index_t line_count
int column_count
OBIDMS_column_p columns
const_char_p comments
ctypedef Obiview_t* Obiview_p
struct Column_reference_t :
const_char_p column_name
@ -47,7 +32,6 @@ cdef extern from "obiview.h" nogil:
struct Obiview_infos_t :
int view_number
time_t creation_date
const_char_p name
const_char_p created_from
@ -62,19 +46,15 @@ cdef extern from "obiview.h" nogil:
ctypedef Obiview_infos_t* Obiview_infos_p
struct Obiviews_header_t :
size_t header_size
size_t views_size
int view_count
ctypedef Obiviews_header_t* Obiviews_header_p
struct Obiview_t :
Obiview_infos_p infos
OBIDMS_p dms
bint read_only
OBIDMS_column_p line_selection
OBIDMS_column_p new_line_selection
OBIDMS_column_p columns
struct Obiviews_infos_all_t :
Obiviews_header_p header
Obiview_infos_p view_infos
ctypedef Obiviews_infos_all_t* Obiviews_infos_all_p
ctypedef Obiview_t* Obiview_p
Obiview_p obi_new_view_nuc_seqs(OBIDMS_p dms, const_char_p view_name, Obiview_p view_to_clone, index_t* line_selection, const_char_p comments)
@ -85,6 +65,10 @@ cdef extern from "obiview.h" nogil:
Obiview_p obi_new_view_nuc_seqs_cloned_from_name(OBIDMS_p dms, const_char_p view_name, const_char_p view_to_clone_name, index_t* line_selection, const_char_p comments)
Obiview_infos_p obi_view_map_file(OBIDMS_p dms, const char* view_name)
int obi_view_unmap_file(OBIDMS_p dms, Obiview_infos_p view_infos)
Obiview_p obi_open_view(OBIDMS_p dms, const_char_p view_name)
int obi_view_add_column(Obiview_p view,
@ -113,10 +97,6 @@ cdef extern from "obiview.h" nogil:
int obi_close_view(Obiview_p view)
int obi_save_and_close_view(Obiview_p view)
Obiviews_infos_all_p obi_read_view_infos(OBIDMS_p dms)
int obi_close_view_infos(Obiviews_infos_all_p views)
int obi_column_set_obiint_with_elt_name_in_view(Obiview_p view,
OBIDMS_column_p column,