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Merge branch 'master' of git@git.metabarcoding.org:obitools/obitools3.git

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This commit is contained in:
Eric Coissac
2016-07-03 09:22:22 +02:00
parent aff9831c13 0869b9ba3f
commit 000b9999ad
23 changed files with 1056 additions and 920 deletions
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2
python/obitools3/obidms/_obidms.pxd
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@ -91,5 +91,5 @@ cdef class OBIDMS:
cpdef OBIView open_view(self, str view_name) 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 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_view_infos(self, str view_name)
cpdef dict read_views(self) # cpdef dict read_views(self) TODO

173
python/obitools3/obidms/_obidms.pyx
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@ -44,7 +44,8 @@ from ._obidmscolumn_bool cimport OBIDMS_column_bool, \
from ._obidmscolumn_char cimport OBIDMS_column_char, \ from ._obidmscolumn_char cimport OBIDMS_column_char, \
OBIDMS_column_multi_elts_char OBIDMS_column_multi_elts_char
from ._obidmscolumn_qual cimport OBIDMS_column_qual from ._obidmscolumn_qual cimport OBIDMS_column_qual, \
OBIDMS_column_multi_elts_qual
from ._obidmscolumn_str cimport OBIDMS_column_str, \ from ._obidmscolumn_str cimport OBIDMS_column_str, \
OBIDMS_column_multi_elts_str OBIDMS_column_multi_elts_str
@ -53,16 +54,15 @@ from ._obidmscolumn_seq cimport OBIDMS_column_seq, \
OBIDMS_column_multi_elts_seq OBIDMS_column_multi_elts_seq
from .capi.obiview cimport Obiview_p, \ from .capi.obiview cimport Obiview_p, \
Obiviews_infos_all_p, \
Obiview_infos_p, \ Obiview_infos_p, \
Column_reference_p, \ Column_reference_p, \
obi_new_view_nuc_seqs, \ obi_new_view_nuc_seqs, \
obi_new_view, \ obi_new_view, \
obi_new_view_cloned_from_name, \ obi_new_view_cloned_from_name, \
obi_new_view_nuc_seqs_cloned_from_name, \ obi_new_view_nuc_seqs_cloned_from_name, \
obi_view_map_file, \
obi_view_unmap_file, \
obi_open_view, \ obi_open_view, \
obi_read_view_infos, \
obi_close_view_infos, \
obi_view_delete_column, \ obi_view_delete_column, \
obi_view_add_column, \ obi_view_add_column, \
obi_view_get_column, \ obi_view_get_column, \
@ -194,8 +194,8 @@ cdef class OBIDMS_column :
elif col_type == OBI_QUAL : elif col_type == OBI_QUAL :
if col_one_element_per_line : if col_one_element_per_line :
subclass = OBIDMS_column_qual subclass = OBIDMS_column_qual
# else : # TODO else :
# subclass = OBIDMS_column_multi_elts_qual subclass = OBIDMS_column_multi_elts_qual
elif col_type == OBI_STR : elif col_type == OBI_STR :
if col_one_element_per_line : if col_one_element_per_line :
subclass = OBIDMS_column_str subclass = OBIDMS_column_str
@ -290,11 +290,11 @@ cdef class OBIView :
raise Exception("Error creating/opening a view") raise Exception("Error creating/opening a view")
self.pointer = 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 # Go through columns to build list of corresponding python instances
self.columns = {} 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] column_p = <OBIDMS_column_p> (view.columns)[i]
header = (column_p).header header = (column_p).header
col_name = bytes2str(header.name) col_name = bytes2str(header.name)
@ -304,7 +304,7 @@ cdef class OBIView :
def __repr__(self) : def __repr__(self) :
cdef str s 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 : for column_name in self.columns :
s = s + self.columns[column_name].__repr__() + '\n' s = s + self.columns[column_name].__repr__() + '\n'
return s return s
@ -313,7 +313,7 @@ cdef class OBIView :
cpdef delete_column(self, str column_name) : cpdef delete_column(self, str column_name) :
cdef int i cdef int i
cdef Obiview_p view cdef Obiview_p view_p
cdef OBIDMS_column column cdef OBIDMS_column column
cdef OBIDMS_column_p column_p cdef OBIDMS_column_p column_p
cdef OBIDMS_column_header_p header cdef OBIDMS_column_header_p header
@ -321,7 +321,7 @@ cdef class OBIView :
view = self.pointer view = self.pointer
if obi_view_delete_column(view, str2bytes(column_name)) < 0 : if obi_view_delete_column(view_p, str2bytes(column_name)) < 0 :
raise Exception("Problem deleting a column from a view") raise Exception("Problem deleting a column from a view")
# Update the dictionaries of column pointers and column objects, and update pointers in column objects (make function?): # Update the dictionaries of column pointers and column objects, and update pointers in column objects (make function?):
@ -329,7 +329,7 @@ cdef class OBIView :
for column_n in self.columns : for column_n in self.columns :
(self.columns[column_n]).update_pointer() (self.columns[column_n]).update_pointer()
cpdef add_column(self, cpdef add_column(self,
str column_name, str column_name,
@ -401,7 +401,7 @@ cdef class OBIView :
cdef OBIView_line line # TODO Check that this works for NUC SEQ views cdef OBIView_line line # TODO Check that this works for NUC SEQ views
# Yield each line # Yield each line
lines_used = (self.pointer).line_count lines_used = self.pointer.infos.line_count
for line_nb in range(lines_used) : for line_nb in range(lines_used) :
line = self[line_nb] line = self[line_nb]
@ -485,12 +485,12 @@ cdef class OBIView_NUC_SEQS(OBIView):
raise Exception("Error creating/opening view") raise Exception("Error creating/opening view")
self.pointer = view self.pointer = view
self.name = bytes2str(view.name) self.name = bytes2str(view.infos.name)
self.comments = bytes2str(view.comments) self.comments = bytes2str(view.infos.comments)
# Go through columns to build list of corresponding python instances # Go through columns to build list of corresponding python instances
self.columns = {} 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] column_p = <OBIDMS_column_p> (view.columns)[i]
header = (column_p).header header = (column_p).header
col_name = bytes2str(header.name) col_name = bytes2str(header.name)
@ -501,28 +501,6 @@ cdef class OBIView_NUC_SEQS(OBIView):
self.sequences = self.columns[bytes2str(NUC_SEQUENCE_COLUMN)] self.sequences = self.columns[bytes2str(NUC_SEQUENCE_COLUMN)]
self.definitions = self.columns[bytes2str(DEFINITION_COLUMN)] self.definitions = self.columns[bytes2str(DEFINITION_COLUMN)]
self.qualities = self.columns[bytes2str(QUALITY_COLUMN)] self.qualities = self.columns[bytes2str(QUALITY_COLUMN)]
cpdef delete_column(self, str column_name) :
cdef int i
cdef Obiview_p view_p
cdef OBIDMS_column column
cdef OBIDMS_column_p column_p
cdef OBIDMS_column_header_p header
cdef str column_n
view_p = self.pointer
if obi_view_delete_column(view_p, str2bytes(column_name)) < 0 :
raise Exception("Problem deleting a column from a view")
# Remove instance from the dictionary
(self.columns).pop(column_name)
for column_n in self.columns :
(self.columns[column_n]).update_pointer()
def __getitem__(self, object item) : def __getitem__(self, object item) :
if type(item) == str : if type(item) == str :
@ -530,7 +508,6 @@ cdef class OBIView_NUC_SEQS(OBIView):
elif type(item) == int : elif type(item) == int :
return OBI_Nuc_Seq_Stored(self, item) return OBI_Nuc_Seq_Stored(self, item)
def __setitem__(self, index_t line_idx, OBI_Nuc_Seq sequence_obj) : def __setitem__(self, index_t line_idx, OBI_Nuc_Seq sequence_obj) :
for key in sequence_obj : for key in sequence_obj :
self[line_idx][key] = sequence_obj[key] self[line_idx][key] = sequence_obj[key]
@ -625,7 +602,7 @@ cdef class OBIDMS :
view_class = OBIView_NUC_SEQS view_class = OBIView_NUC_SEQS
else : else :
view_class = OBIView view_class = OBIView
return view_class(self, view_name) return view_class(self, view_name)
@ -643,54 +620,84 @@ cdef class OBIDMS :
cpdef dict read_view_infos(self, str view_name) : 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_infos_p
cdef Obiview_infos_p view_p cdef dict view_infos_d
cdef Column_reference_p column_refs cdef Column_reference_p column_refs
cdef int nb_views
cdef int i, j cdef int i, j
cdef str view_name
cdef str column_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 = {} obi_view_unmap_file(self.pointer, view_infos_p)
all_views_p = obi_read_view_infos(self.pointer)
if all_views_p == NULL : return view_infos_d
raise Exception("No views to read")
nb_views = <int> (all_views_p.header).view_count
for i in range(nb_views) : # 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
view_p = (<Obiview_infos_p> (all_views_p.view_infos)) + i #
view_name = bytes2str(view_p.name) # cdef Obiviews_infos_all_p all_views_p
views[view_name] = {} # cdef Obiview_infos_p view_p
views[view_name]["comments"] = bytes2str(view_p.comments) # cdef Column_reference_p column_refs
views[view_name]["view_type"] = bytes2str(view_p.view_type) # cdef int nb_views
views[view_name]["column_count"] = <int> view_p.column_count # cdef int i, j
views[view_name]["line_count"] = <int> view_p.line_count # cdef str view_name
views[view_name]["view_number"] = <int> view_p.view_number # cdef str column_name
views[view_name]["created_from"] = bytes2str(view_p.created_from) # cdef dict views
views[view_name]["creation_date"] = bytes2str(obi_format_date(view_p.creation_date)) # cdef bytes name_b
if (view_p.all_lines) : #
views[view_name]["line_selection"] = None # views = {}
else : # all_views_p = obi_read_view_infos(self.pointer)
views[view_name]["line_selection"] = {} # if all_views_p == NULL :
views[view_name]["line_selection"]["column_name"] = bytes2str((view_p.line_selection).column_name) # raise Exception("No views to read")
views[view_name]["line_selection"]["version"] = <int> (view_p.line_selection).version # nb_views = <int> (all_views_p.header).view_count
views[view_name]["column_references"] = {} # for i in range(nb_views) :
column_refs = view_p.column_references # view_p = (<Obiview_infos_p> (all_views_p.view_infos)) + i
for j in range(views[view_name]["column_count"]) : # view_name = bytes2str(view_p.name)
column_name = bytes2str((column_refs[j]).column_name) # views[view_name] = {}
views[view_name]["column_references"][column_name] = {} # views[view_name]["comments"] = bytes2str(view_p.comments)
views[view_name]["column_references"][column_name]["version"] = column_refs[j].version # views[view_name]["view_type"] = bytes2str(view_p.view_type)
# views[view_name]["column_count"] = <int> view_p.column_count
obi_close_view_infos(all_views_p); # views[view_name]["line_count"] = <int> view_p.line_count
# views[view_name]["view_number"] = <int> view_p.view_number
return views # 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

13
python/obitools3/obidms/_obidmscolumn_qual.pxd
View File

@ -1,7 +1,7 @@
#cython: language_level=3 #cython: language_level=3
from .capi.obitypes cimport index_t from .capi.obitypes cimport index_t
from ._obidms cimport OBIDMS_column #, OBIDMS_column_multi_elts from ._obidms cimport OBIDMS_column , OBIDMS_column_multi_elts
cdef class OBIDMS_column_qual(OBIDMS_column): cdef class OBIDMS_column_qual(OBIDMS_column):
@ -11,7 +11,10 @@ cdef class OBIDMS_column_qual(OBIDMS_column):
cpdef set_str_line(self, index_t line_nb, object value) cpdef set_str_line(self, index_t line_nb, object value)
# cdef class OBIDMS_column_multi_elts_qual(OBIDMS_column_multi_elts): cdef class OBIDMS_column_multi_elts_qual(OBIDMS_column_multi_elts):
# cpdef object get_item(self, index_t line_nb, str element_name) cpdef object get_item(self, index_t line_nb, str element_name)
# cpdef object get_line(self, index_t line_nb) cpdef object get_str_item(self, index_t line_nb, str element_name)
# cpdef set_item(self, index_t line_nb, str element_name, object value) cpdef object get_line(self, index_t line_nb)
cpdef object get_str_line(self, index_t line_nb)
cpdef set_item(self, index_t line_nb, str element_name, object value)
cpdef set_str_item(self, index_t line_nb, str element_name, object value)

195
python/obitools3/obidms/_obidmscolumn_qual.pyx
View File

@ -32,7 +32,7 @@ cdef class OBIDMS_column_qual(OBIDMS_column):
value = obi_column_get_obiqual_int_with_elt_idx_in_view(self.view.pointer, (self.pointer)[0], line_nb, 0, &value_length) value = obi_column_get_obiqual_int_with_elt_idx_in_view(self.view.pointer, (self.pointer)[0], line_nb, 0, &value_length)
if obi_errno > 0 : if obi_errno > 0 :
raise IndexError(line_nb) raise IndexError(line_nb)
if value == NULL : # TODO if value == OBIQual_int_NA :
result = None result = None
else : else :
result = [] result = []
@ -47,7 +47,7 @@ cdef class OBIDMS_column_qual(OBIDMS_column):
value = obi_column_get_obiqual_char_with_elt_idx_in_view(self.view.pointer, (self.pointer)[0], line_nb, 0) value = obi_column_get_obiqual_char_with_elt_idx_in_view(self.view.pointer, (self.pointer)[0], line_nb, 0)
if obi_errno > 0 : if obi_errno > 0 :
raise IndexError(line_nb) raise IndexError(line_nb)
if strcmp(value, OBIQual_char_NA) == 0 : if value == OBIQual_char_NA :
result = None result = None
else : else :
result = bytes2str(value) result = bytes2str(value)
@ -58,94 +58,127 @@ cdef class OBIDMS_column_qual(OBIDMS_column):
cdef uint8_t* value_b cdef uint8_t* value_b
cdef int value_length cdef int value_length
if value is None : if value is None :
value_b = NULL # TODO if obi_column_set_obiqual_int_with_elt_idx_in_view(self.view.pointer, (self.pointer)[0], line_nb, 0, OBIQual_int_NA, 0) < 0:
value_length = 0 raise Exception("Problem setting a value in a column")
else : else :
value_length = len(value) value_length = len(value)
value_b = <uint8_t*> malloc(value_length * sizeof(uint8_t)) value_b = <uint8_t*> malloc(value_length * sizeof(uint8_t))
for i in range(value_length) : for i in range(value_length) :
value_b[i] = <uint8_t>value[i] value_b[i] = <uint8_t>value[i]
if obi_column_set_obiqual_int_with_elt_idx_in_view(self.view.pointer, (self.pointer)[0], line_nb, 0, value_b, value_length) < 0: if obi_column_set_obiqual_int_with_elt_idx_in_view(self.view.pointer, (self.pointer)[0], line_nb, 0, value_b, value_length) < 0:
raise Exception("Problem setting a value in a column") raise Exception("Problem setting a value in a column")
if value is not None :
free(value_b) free(value_b)
cpdef set_str_line(self, index_t line_nb, object value): cpdef set_str_line(self, index_t line_nb, object value):
cdef bytes value_b
if value is None : if value is None :
value_b = OBIQual_char_NA if obi_column_set_obiqual_char_with_elt_idx_in_view(self.view.pointer, (self.pointer)[0], line_nb, 0, OBIQual_char_NA) < 0:
raise Exception("Problem setting a value in a column")
else : else :
value_b = str2bytes(value) if obi_column_set_obiqual_char_with_elt_idx_in_view(self.view.pointer, (self.pointer)[0], line_nb, 0, str2bytes(value)) < 0:
if obi_column_set_obiqual_char_with_elt_idx_in_view(self.view.pointer, (self.pointer)[0], line_nb, 0, value_b) < 0: raise Exception("Problem setting a value in a column")
raise Exception("Problem setting a value in a column")
# TODO OR NOT? cdef class OBIDMS_column_multi_elts_qual(OBIDMS_column_multi_elts):
# cdef class OBIDMS_column_multi_elts_qual(OBIDMS_column_multi_elts):
# cpdef object get_item(self, index_t line_nb, str element_name):
# cdef const uint8_t* value
# cpdef object get_item(self, index_t line_nb, str element_name): cdef int value_length
# cdef const uint8_t* value cdef object result
# cdef int value_length cdef int i
# cdef object result value = obi_column_get_obiqual_int_with_elt_name_in_view(self.view.pointer, (self.pointer)[0], line_nb, str2bytes(element_name), &value_length)
# cdef int i if obi_errno > 0 :
# value = obi_column_get_obiqual_int_with_elt_name_in_view(self.view.pointer, (self.pointer)[0], line_nb, str2bytes(element_name), &value_length) raise IndexError(line_nb, element_name)
# if obi_errno > 0 : if value == OBIQual_int_NA :
# raise IndexError(line_nb, element_name) result = None
# if value == NULL: # TODO else :
# result = None result = []
# else : for i in range(value_length) :
# result = [] result.append(<int>value[i])
# for i in range(value_length) : return result
# result.append(<int>value[i])
# return result cpdef object get_str_item(self, index_t line_nb, str element_name):
# cdef char* value
# # cpdef object get_str_item(self, index_t line_nb, str element_name): cdef object result
# # pass value = obi_column_get_obiqual_char_with_elt_name_in_view(self.view.pointer, (self.pointer)[0], line_nb, str2bytes(element_name))
# # cdef char* value if obi_errno > 0 :
# # cdef object result raise IndexError(line_nb, element_name)
# # value = obi_column_get_obiseq_with_elt_name_in_view(self.view.pointer, (self.pointer)[0], line_nb, str2bytes(element_name)) if value == OBIQual_char_NA :
# # if obi_errno > 0 : result = None
# # raise IndexError(line_nb, element_name) else :
# # if strcmp(value, OBISeq_NA) == 0 : result = bytes2str(value)
# # result = None free(value)
# # else : return result
# # result = bytes2str(value)
# # free(value) cpdef object get_line(self, index_t line_nb) :
# # return result cdef const uint8_t* value
# cdef int value_length
# cpdef object get_line(self, index_t line_nb) : cdef object value_in_result
# pass cdef dict result
# # cdef char* value cdef index_t i
# # cdef object value_in_result cdef int j
# # cdef dict result cdef bint all_NA
# # cdef index_t i result = {}
# # cdef bint all_NA all_NA = True
# # result = {} for i in range(self.nb_elements_per_line) :
# # all_NA = True value = obi_column_get_obiqual_int_with_elt_idx_in_view(self.view.pointer, (self.pointer)[0], line_nb, i, &value_length)
# # for i in range(self.nb_elements_per_line) : if obi_errno > 0 :
# # value = obi_column_get_obiseq_with_elt_idx_in_view(self.view.pointer, (self.pointer)[0], line_nb, i) raise IndexError(line_nb)
# # if obi_errno > 0 : if value == OBIQual_int_NA :
# # raise IndexError(line_nb) value_in_result = None
# # if strcmp(value, OBISeq_NA) == 0 : else :
# # value_in_result = None value_in_result = []
# # else : for j in range(value_length) :
# # value_in_result = bytes2str(value) value_in_result.append(<int>value[j])
# # free(value) result[self.elements_names[i]] = value_in_result
# # result[self.elements_names[i]] = value_in_result if all_NA and (value_in_result is not None) :
# # if all_NA and (value_in_result is not None) : all_NA = False
# # all_NA = False if all_NA :
# # if all_NA : result = None
# # result = None return result
# # return result
# cpdef object get_str_line(self, index_t line_nb) :
# cpdef set_item(self, index_t line_nb, str element_name, object value): cdef char* value
# pass cdef object value_in_result
# # cdef bytes value_b cdef dict result
# # if value is None : cdef index_t i
# # value_b = OBISeq_NA cdef bint all_NA
# # else : result = {}
# # value_b = str2bytes(value) all_NA = True
# # if obi_column_set_obiseq_with_elt_name_in_view(self.view.pointer, (self.pointer)[0], line_nb, str2bytes(element_name), value_b) < 0: for i in range(self.nb_elements_per_line) :
# # raise Exception("Problem setting a value in a column") value = obi_column_get_obiqual_char_with_elt_idx_in_view(self.view.pointer, (self.pointer)[0], line_nb, i)
# # if obi_errno > 0 :
raise IndexError(line_nb)
if value == OBIQual_char_NA :
value_in_result = None
else :
value_in_result = bytes2str(value)
free(value)
result[self.elements_names[i]] = value_in_result
if all_NA and (value_in_result is not None) :
all_NA = False
if all_NA :
result = None
return result
cpdef set_item(self, index_t line_nb, str element_name, object value):
cdef uint8_t* value_b
cdef int value_length
if value is None :
if obi_column_set_obiqual_int_with_elt_name_in_view(self.view.pointer, (self.pointer)[0], line_nb, str2bytes(element_name), OBIQual_int_NA, 0) < 0:
raise Exception("Problem setting a value in a column")
else :
value_length = len(value)
value_b = <uint8_t*> malloc(value_length * sizeof(uint8_t))
for i in range(value_length) :
value_b[i] = <uint8_t>value[i]
if obi_column_set_obiqual_int_with_elt_name_in_view(self.view.pointer, (self.pointer)[0], line_nb, str2bytes(element_name), value_b, value_length) < 0:
raise Exception("Problem setting a value in a column")
free(value_b)
cpdef set_str_item(self, index_t line_nb, str element_name, object value):
if value is None :
if obi_column_set_obiqual_char_with_elt_name_in_view(self.view.pointer, (self.pointer)[0], line_nb, str2bytes(element_name), OBIQual_char_NA) < 0:
raise Exception("Problem setting a value in a column")
else :
if obi_column_set_obiqual_char_with_elt_name_in_view(self.view.pointer, (self.pointer)[0], line_nb, str2bytes(element_name), str2bytes(value)) < 0:
raise Exception("Problem setting a value in a column")

16
python/obitools3/obidms/_obidmscolumn_seq.pyx
View File

@ -13,7 +13,6 @@ from ._obidms cimport OBIView
from obitools3.utils cimport str2bytes, bytes2str from obitools3.utils cimport str2bytes, bytes2str
from libc.stdlib cimport free from libc.stdlib cimport free
from libc.string cimport strcmp
cdef class OBIDMS_column_seq(OBIDMS_column): cdef class OBIDMS_column_seq(OBIDMS_column):
@ -24,7 +23,7 @@ cdef class OBIDMS_column_seq(OBIDMS_column):
value = obi_column_get_obiseq_with_elt_idx_in_view(self.view.pointer, (self.pointer)[0], line_nb, 0) value = obi_column_get_obiseq_with_elt_idx_in_view(self.view.pointer, (self.pointer)[0], line_nb, 0)
if obi_errno > 0 : if obi_errno > 0 :
raise IndexError(line_nb) raise IndexError(line_nb)
if strcmp(value, OBISeq_NA) == 0 : if value == OBISeq_NA :
result = None result = None
else : else :
result = bytes2str(value) result = bytes2str(value)
@ -32,13 +31,12 @@ cdef class OBIDMS_column_seq(OBIDMS_column):
return result return result
cpdef set_line(self, index_t line_nb, object value): cpdef set_line(self, index_t line_nb, object value):
cdef bytes value_b
if value is None : if value is None :
value_b = OBISeq_NA if obi_column_set_obiseq_with_elt_idx_in_view(self.view.pointer, (self.pointer)[0], line_nb, 0, OBISeq_NA) < 0:
raise Exception("Problem setting a value in a column")
else : else :
value_b = str2bytes(value) if obi_column_set_obiseq_with_elt_idx_in_view(self.view.pointer, (self.pointer)[0], line_nb, 0, str2bytes(value)) < 0:
if obi_column_set_obiseq_with_elt_idx_in_view(self.view.pointer, (self.pointer)[0], line_nb, 0, value_b) < 0: raise Exception("Problem setting a value in a column")
raise Exception("Problem setting a value in a column")
# TODO choose alignment type (lcs or other) with supplementary argument # TODO choose alignment type (lcs or other) with supplementary argument
cpdef align(self, cpdef align(self,
@ -61,7 +59,7 @@ cdef class OBIDMS_column_multi_elts_seq(OBIDMS_column_multi_elts):
value = obi_column_get_obiseq_with_elt_name_in_view(self.view.pointer, (self.pointer)[0], line_nb, str2bytes(element_name)) value = obi_column_get_obiseq_with_elt_name_in_view(self.view.pointer, (self.pointer)[0], line_nb, str2bytes(element_name))
if obi_errno > 0 : if obi_errno > 0 :
raise IndexError(line_nb, element_name) raise IndexError(line_nb, element_name)
if strcmp(value, OBISeq_NA) == 0 : if value == OBISeq_NA :
result = None result = None
else : else :
result = bytes2str(value) result = bytes2str(value)
@ -80,7 +78,7 @@ cdef class OBIDMS_column_multi_elts_seq(OBIDMS_column_multi_elts):
value = obi_column_get_obiseq_with_elt_idx_in_view(self.view.pointer, (self.pointer)[0], line_nb, i) value = obi_column_get_obiseq_with_elt_idx_in_view(self.view.pointer, (self.pointer)[0], line_nb, i)
if obi_errno > 0 : if obi_errno > 0 :
raise IndexError(line_nb) raise IndexError(line_nb)
if strcmp(value, OBISeq_NA) == 0 : if value == OBISeq_NA :
value_in_result = None value_in_result = None
else : else :
value_in_result = bytes2str(value) value_in_result = bytes2str(value)

17
python/obitools3/obidms/_obidmscolumn_str.pyx
View File

@ -9,8 +9,6 @@ from .capi.obitypes cimport OBIStr_NA, const_char_p
from obitools3.utils cimport str2bytes, bytes2str from obitools3.utils cimport str2bytes, bytes2str
from libc.string cimport strcmp
cdef class OBIDMS_column_str(OBIDMS_column): cdef class OBIDMS_column_str(OBIDMS_column):
@ -20,7 +18,7 @@ cdef class OBIDMS_column_str(OBIDMS_column):
value = obi_column_get_obistr_with_elt_idx_in_view(self.view.pointer, (self.pointer)[0], line_nb, 0) value = obi_column_get_obistr_with_elt_idx_in_view(self.view.pointer, (self.pointer)[0], line_nb, 0)
if obi_errno > 0 : if obi_errno > 0 :
raise IndexError(line_nb) raise IndexError(line_nb)
if strcmp(value, OBIStr_NA) == 0 : if value == OBIStr_NA :
result = None result = None
else : else :
result = bytes2str(value) result = bytes2str(value)
@ -28,13 +26,12 @@ cdef class OBIDMS_column_str(OBIDMS_column):
return result return result
cpdef set_line(self, index_t line_nb, object value): cpdef set_line(self, index_t line_nb, object value):
cdef bytes value_b
if value is None : if value is None :
value_b = OBIStr_NA if obi_column_set_obistr_with_elt_idx_in_view(self.view.pointer, (self.pointer)[0], line_nb, 0, OBIStr_NA) < 0:
raise Exception("Problem setting a value in a column")
else : else :
value_b = str2bytes(value) if obi_column_set_obistr_with_elt_idx_in_view(self.view.pointer, (self.pointer)[0], line_nb, 0, str2bytes(value)) < 0:
if obi_column_set_obistr_with_elt_idx_in_view(self.view.pointer, (self.pointer)[0], line_nb, 0, value_b) < 0: raise Exception("Problem setting a value in a column")
raise Exception("Problem setting a value in a column")
cdef class OBIDMS_column_multi_elts_str(OBIDMS_column_multi_elts): cdef class OBIDMS_column_multi_elts_str(OBIDMS_column_multi_elts):
@ -45,7 +42,7 @@ cdef class OBIDMS_column_multi_elts_str(OBIDMS_column_multi_elts):
value = obi_column_get_obistr_with_elt_name_in_view(self.view.pointer, (self.pointer)[0], line_nb, str2bytes(element_name)) value = obi_column_get_obistr_with_elt_name_in_view(self.view.pointer, (self.pointer)[0], line_nb, str2bytes(element_name))
if obi_errno > 0 : if obi_errno > 0 :
raise IndexError(line_nb, element_name) raise IndexError(line_nb, element_name)
if strcmp(value, OBIStr_NA) == 0 : if value == OBIStr_NA :
result = None result = None
else : else :
result = bytes2str(value) result = bytes2str(value)
@ -64,7 +61,7 @@ cdef class OBIDMS_column_multi_elts_str(OBIDMS_column_multi_elts):
value = obi_column_get_obistr_with_elt_idx_in_view(self.view.pointer, (self.pointer)[0], line_nb, i) value = obi_column_get_obistr_with_elt_idx_in_view(self.view.pointer, (self.pointer)[0], line_nb, i)
if obi_errno > 0 : if obi_errno > 0 :
raise IndexError(line_nb) raise IndexError(line_nb)
if strcmp(value, OBIStr_NA) == 0 : if value == OBIStr_NA :
value_in_result = None value_in_result = None
else : else :
value_in_result = bytes2str(value) value_in_result = bytes2str(value)

40
python/obitools3/obidms/_obiseq.pxd
View File

@ -4,35 +4,35 @@ from ._obidms cimport OBIView_line
cdef class OBI_Seq(dict) : cdef class OBI_Seq(dict) :
cdef str id cdef object id
cdef str definition cdef object definition
cdef str sequence cdef object sequence
cpdef set_id(self, str id) cpdef set_id(self, object id)
cpdef get_id(self) cpdef object get_id(self)
cpdef set_definition(self, str definition) cpdef set_definition(self, object definition)
cpdef get_definition(self) cpdef object get_definition(self)
cpdef get_sequence(self) cpdef object get_sequence(self)
cdef class OBI_Nuc_Seq(OBI_Seq) : cdef class OBI_Nuc_Seq(OBI_Seq) :
cdef object quality cdef object quality
#cpdef str reverse_complement(self) #cpdef object reverse_complement(self)
cpdef set_sequence(self, str sequence) cpdef set_sequence(self, object sequence)
cpdef set_quality(self, object quality) cpdef set_quality(self, object quality)
cpdef get_quality(self) cpdef object get_quality(self)
cdef class OBI_Nuc_Seq_Stored(OBIView_line) : cdef class OBI_Nuc_Seq_Stored(OBIView_line) :
cpdef set_id(self, str id) cpdef set_id(self, object id)
cpdef get_id(self) cpdef object get_id(self)
cpdef set_definition(self, str definition) cpdef set_definition(self, object definition)
cpdef get_definition(self) cpdef object get_definition(self)
cpdef set_sequence(self, str sequence) cpdef set_sequence(self, object sequence)
cpdef get_sequence(self) cpdef object get_sequence(self)
cpdef set_quality(self, object quality) cpdef set_quality(self, object quality)
cpdef get_quality(self) cpdef object get_quality(self)
cpdef get_str_quality(self) cpdef object get_str_quality(self)
# cpdef str reverse_complement(self) # cpdef object reverse_complement(self)

26
python/obitools3/obidms/_obiseq.pyx
View File

@ -9,20 +9,20 @@ from .capi.obiview cimport NUC_SEQUENCE_COLUMN, \
cdef class OBI_Seq(dict) : cdef class OBI_Seq(dict) :
def __init__(self, str id, str seq, str definition=None) : def __init__(self, object id, object seq, object definition=None) :
self.set_id(id) self.set_id(id)
self.set_sequence(seq) self.set_sequence(seq)
if definition is not None : if definition is not None :
self.set_definition(definition) self.set_definition(definition)
cpdef set_id(self, str id) : cpdef set_id(self, object id) :
self.id = id self.id = id
self[bytes2str(ID_COLUMN)] = id self[bytes2str(ID_COLUMN)] = id
cpdef get_id(self) : cpdef get_id(self) :
return self.id return self.id
cpdef set_definition(self, str definition) : cpdef set_definition(self, object definition) :
self.definition = definition self.definition = definition
self[bytes2str(DEFINITION_COLUMN)] = definition self[bytes2str(DEFINITION_COLUMN)] = definition
@ -38,7 +38,7 @@ cdef class OBI_Seq(dict) :
cdef class OBI_Nuc_Seq(OBI_Seq) : cdef class OBI_Nuc_Seq(OBI_Seq) :
cpdef set_sequence(self, str sequence) : cpdef set_sequence(self, object sequence) :
self.sequence = sequence self.sequence = sequence
self[bytes2str(NUC_SEQUENCE_COLUMN)] = sequence self[bytes2str(NUC_SEQUENCE_COLUMN)] = sequence
@ -57,34 +57,34 @@ cdef class OBI_Nuc_Seq_Stored(OBIView_line) :
# TODO store the str version of column name macros # TODO store the str version of column name macros
cpdef set_id(self, str id) : cpdef set_id(self, object id) :
self[bytes2str(ID_COLUMN)] = id self[bytes2str(ID_COLUMN)] = id
cpdef get_id(self) : cpdef object get_id(self) :
return self[bytes2str(ID_COLUMN)] return self[bytes2str(ID_COLUMN)]
cpdef set_definition(self, str definition) : cpdef set_definition(self, object definition) :
self[bytes2str(DEFINITION_COLUMN)] = definition self[bytes2str(DEFINITION_COLUMN)] = definition
cpdef get_definition(self) : cpdef object get_definition(self) :
return self[bytes2str(DEFINITION_COLUMN)] return self[bytes2str(DEFINITION_COLUMN)]
cpdef set_sequence(self, str sequence) : cpdef set_sequence(self, object sequence) :
self[bytes2str(NUC_SEQUENCE_COLUMN)] = sequence self[bytes2str(NUC_SEQUENCE_COLUMN)] = sequence
cpdef get_sequence(self) : cpdef object get_sequence(self) :
return self[bytes2str(NUC_SEQUENCE_COLUMN)] return self[bytes2str(NUC_SEQUENCE_COLUMN)]
cpdef set_quality(self, object quality) : cpdef set_quality(self, object quality) :
if type(quality) == list : if (type(quality) == list) or (quality is None) :
self[bytes2str(QUALITY_COLUMN)] = quality self[bytes2str(QUALITY_COLUMN)] = quality
else : # Quality is in str form else : # Quality is in str form
(((self.view).columns)[bytes2str(QUALITY_COLUMN)]).set_str_line(self.index, quality) (((self.view).columns)[bytes2str(QUALITY_COLUMN)]).set_str_line(self.index, quality)
cpdef get_quality(self) : cpdef object get_quality(self) :
return self[bytes2str(QUALITY_COLUMN)] return self[bytes2str(QUALITY_COLUMN)]
cpdef get_str_quality(self) : cpdef object get_str_quality(self) :
return ((self.view).columns)[bytes2str(QUALITY_COLUMN)].get_str_line(self.index) return ((self.view).columns)[bytes2str(QUALITY_COLUMN)].get_str_line(self.index)
# def __str__(self) : # def __str__(self) :

5
python/obitools3/obidms/capi/obitypes.pxd
View File

@ -1,7 +1,8 @@
#cython: language_level=3 #cython: language_level=3
from libc.stdint cimport int32_t, int64_t from libc.stdint cimport int32_t, int64_t, uint8_t
from posix.types cimport time_t from posix.types cimport time_t
@ -47,8 +48,8 @@ cdef extern from "obitypes.h" nogil:
extern obibool_t OBIBool_NA extern obibool_t OBIBool_NA
extern const_char_p OBISeq_NA extern const_char_p OBISeq_NA
extern const_char_p OBIStr_NA extern const_char_p OBIStr_NA
extern const_char_p OBIQual_int_NA
extern const_char_p OBIQual_char_NA extern const_char_p OBIQual_char_NA
extern uint8_t* OBIQual_int_NA
const_char_p name_data_type(int data_type) const_char_p name_data_type(int data_type)

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 DEFINITION_COLUMN
extern const_char_p QUALITY_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 : struct Column_reference_t :
const_char_p column_name const_char_p column_name
@ -47,7 +32,6 @@ cdef extern from "obiview.h" nogil:
struct Obiview_infos_t : struct Obiview_infos_t :
int view_number
time_t creation_date time_t creation_date
const_char_p name const_char_p name
const_char_p created_from const_char_p created_from
@ -62,19 +46,15 @@ cdef extern from "obiview.h" nogil:
ctypedef Obiview_infos_t* Obiview_infos_p ctypedef Obiview_infos_t* Obiview_infos_p
struct Obiviews_header_t : struct Obiview_t :
size_t header_size Obiview_infos_p infos
size_t views_size OBIDMS_p dms
int view_count bint read_only
OBIDMS_column_p line_selection
ctypedef Obiviews_header_t* Obiviews_header_p OBIDMS_column_p new_line_selection
OBIDMS_column_p columns
ctypedef Obiview_t* Obiview_p
struct Obiviews_infos_all_t :
Obiviews_header_p header
Obiview_infos_p view_infos
ctypedef Obiviews_infos_all_t* Obiviews_infos_all_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) 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_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) Obiview_p obi_open_view(OBIDMS_p dms, const_char_p view_name)
int obi_view_add_column(Obiview_p view, 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_close_view(Obiview_p view)
int obi_save_and_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, int obi_column_set_obiint_with_elt_name_in_view(Obiview_p view,
OBIDMS_column_p column, OBIDMS_column_p column,

2
src/obi_align.c
View File

@ -25,7 +25,7 @@
// TODO // TODO
// use openMP pragmas : garder scores en memoire et ecrire a la fin? // use openMP pragmas : garder scores en memoire et ecrire a la fin? (normalement c bon avec index)
// tout ecrire en stdint? // tout ecrire en stdint?
// check NUC_SEQS and score type (int or float if normalize) // check NUC_SEQS and score type (int or float if normalize)
// what's with multiple sequence/line columns? // what's with multiple sequence/line columns?

256
src/obiavl.c
View File

@ -107,6 +107,42 @@ static char* build_avl_file_name(const char* avl_name);
static char* build_avl_data_file_name(const char* avl_name); static char* build_avl_data_file_name(const char* avl_name);
/**
* @brief Internal function building the full path of an AVL tree file.
*
* @warning The returned pointer has to be freed by the caller.
*
* @param dms A pointer to the OBIDMS to which the AVL tree belongs.
* @param avl_name The name of the AVL tree.
* @param avl_idx The index of the AVL if it's part of an AVL group, or -1 if not.
*
* @returns A pointer to the full path of the file where the AVL tree is stored.
* @retval NULL if an error occurred.
*
* @since May 2016
* @author Celine Mercier (celine.mercier@metabarcoding.org)
*/
static char* get_full_path_of_avl_file_name(OBIDMS_p dms, const char* avl_name, int avl_idx);
/**
* @brief Internal function building the file name for an AVL data file.
*
* @warning The returned pointer has to be freed by the caller.
*
* @param dms A pointer to the OBIDMS to which the AVL tree belongs.
* @param avl_name The name of the AVL tree.
* @param avl_idx The index of the AVL if it's part of an AVL group, or -1 if not.
*
* @returns A pointer to the full path of the file where the data referred to by the AVL tree is stored.
* @retval NULL if an error occurred.
*
* @since May 2016
* @author Celine Mercier (celine.mercier@metabarcoding.org)
*/
static char* get_full_path_of_avl_data_file_name(OBIDMS_p dms, const char* avl_name, int avl_idx);
/** /**
* @brief Internal function returning the size of an AVL tree header on this platform, * @brief Internal function returning the size of an AVL tree header on this platform,
* including the size of the bloom filter associated with the AVL tree. * including the size of the bloom filter associated with the AVL tree.
@ -253,9 +289,12 @@ int remap_an_avl(OBIDMS_avl_p avl);
/** /**
* @brief Internal function (re)mapping the tree and data parts of an AVL tree structure. * @brief Internal function creating and adding a new AVL in an AVL group.
* *
* @param avl A pointer to the AVL tree group structure. * @warning The previous AVL in the list of the group is unmapped,
* if it's not the 1st AVL being added.
*
* @param avl A pointer on the AVL tree group structure.
* *
* @retval 0 if the operation was successfully completed. * @retval 0 if the operation was successfully completed.
* @retval -1 if an error occurred. * @retval -1 if an error occurred.
@ -547,6 +586,102 @@ static char* build_avl_data_file_name(const char* avl_name)
} }
static char* get_full_path_of_avl_file_name(OBIDMS_p dms, const char* avl_name, int avl_idx)
{
char* complete_avl_name;
char* full_path;
char* avl_file_name;
if (avl_idx >= 0)
{
complete_avl_name = build_avl_name_with_idx(avl_name, avl_idx);
if (complete_avl_name == NULL)
return NULL;
}
else
{
complete_avl_name = (char*) malloc((strlen(avl_name)+1)*sizeof(char));
if (complete_avl_name == NULL)
{
obi_set_errno(OBI_MALLOC_ERROR);
obidebug(1, "\nError allocating memory for an AVL name");
return NULL;
}
strcpy(complete_avl_name, avl_name);
}
avl_file_name = build_avl_file_name(complete_avl_name);
if (avl_file_name == NULL)
{
free(complete_avl_name);
return NULL;
}
full_path = get_full_path_of_avl_dir(dms, avl_name);
if (full_path == NULL)
{
free(complete_avl_name);
free(avl_file_name);
return NULL;
}
strcat(full_path, "/");
strcat(full_path, avl_file_name);
free(complete_avl_name);
return full_path;
}
static char* get_full_path_of_avl_data_file_name(OBIDMS_p dms, const char* avl_name, int avl_idx)
{
char* complete_avl_name;
char* full_path;
char* avl_data_file_name;
if (avl_idx >= 0)
{
complete_avl_name = build_avl_name_with_idx(avl_name, avl_idx);
if (complete_avl_name == NULL)
return NULL;
}
else
{
complete_avl_name = (char*) malloc((strlen(avl_name)+1)*sizeof(char));
if (complete_avl_name == NULL)
{
obi_set_errno(OBI_MALLOC_ERROR);
obidebug(1, "\nError allocating memory for an AVL name");
return NULL;
}
strcpy(complete_avl_name, avl_name);
}
avl_data_file_name = build_avl_data_file_name(complete_avl_name);
if (avl_data_file_name == NULL)
{
free(complete_avl_name);
return NULL;
}
full_path = get_full_path_of_avl_dir(dms, avl_name);
if (full_path == NULL)
{
free(complete_avl_name);
free(avl_data_file_name);
return NULL;
}
strcat(full_path, "/");
strcat(full_path, avl_data_file_name);
free(complete_avl_name);
return full_path;
}
size_t get_avl_header_size() size_t get_avl_header_size()
{ {
size_t header_size; size_t header_size;
@ -646,7 +781,6 @@ int truncate_avl_to_size_used(OBIDMS_avl_p avl) // TODO is it necessary to unmap
file_descriptor, file_descriptor,
(avl->header)->header_size (avl->header)->header_size
); );
if (avl->tree == MAP_FAILED) if (avl->tree == MAP_FAILED)
{ {
obi_set_errno(OBI_AVL_ERROR); obi_set_errno(OBI_AVL_ERROR);
@ -930,9 +1064,10 @@ int add_new_avl_in_group(OBIDMS_avl_group_p avl_group)
return -1; return -1;
} }
// Unmap the previous AVL // Unmap the previous AVL if it's not the 1st
if (unmap_an_avl((avl_group->sub_avls)[avl_group->last_avl_idx]) < 0) if (avl_group->last_avl_idx > 0)
return -1; if (unmap_an_avl((avl_group->sub_avls)[avl_group->last_avl_idx]) < 0)
return -1;
// Increment current AVL index // Increment current AVL index
(avl_group->last_avl_idx)++; (avl_group->last_avl_idx)++;
@ -949,6 +1084,36 @@ int add_new_avl_in_group(OBIDMS_avl_group_p avl_group)
} }
// TODO doc
int add_existing_avl_in_group(OBIDMS_avl_group_p avl_group_dest, OBIDMS_avl_group_p avl_group_source, int avl_idx)
{
if (link(get_full_path_of_avl_file_name(avl_group_source->dms, avl_group_source->name, avl_idx), get_full_path_of_avl_file_name(avl_group_dest->dms, avl_group_dest->name, avl_idx)) < 0)
{
obi_set_errno(OBI_AVL_ERROR);
obidebug(1, "\nError creating a hard link to an existing AVL tree file");
return -1;
}
if (link(get_full_path_of_avl_data_file_name(avl_group_source->dms, avl_group_source->name, avl_idx), get_full_path_of_avl_data_file_name(avl_group_dest->dms, avl_group_dest->name, avl_idx)) < 0)
{
obi_set_errno(OBI_AVL_ERROR);
obidebug(1, "\nError creating a hard link to an existing AVL data file");
return -1;
}
// Increment current AVL index
(avl_group_dest->last_avl_idx)++;
// Open AVL for that group TODO ideally not needed, but needed for now
avl_group_dest->sub_avls[avl_group_dest->last_avl_idx] = obi_open_avl(avl_group_source->dms, avl_group_source->name, avl_idx);
if ((avl_group_dest->sub_avls)[avl_group_dest->last_avl_idx] == NULL)
{
obidebug(1, "\nError opening an AVL to add in an AVL group");
return -1;
}
return 0;
}
int maybe_in_avl(OBIDMS_avl_p avl, Obi_blob_p value) int maybe_in_avl(OBIDMS_avl_p avl, Obi_blob_p value)
{ {
return (bloom_check(&((avl->header)->bloom_filter), value, obi_blob_sizeof(value))); return (bloom_check(&((avl->header)->bloom_filter), value, obi_blob_sizeof(value)));
@ -1529,8 +1694,7 @@ OBIDMS_avl_p obi_create_avl(OBIDMS_p dms, const char* avl_name, int avl_idx)
// Bloom filter // Bloom filter
bloom_init(&((avl->header)->bloom_filter), MAX_NODE_COUNT_PER_AVL); bloom_init(&((avl->header)->bloom_filter), MAX_NODE_COUNT_PER_AVL);
if (avl_idx >= 0) free(complete_avl_name);
free(complete_avl_name);
return avl; return avl;
} }
@ -1777,8 +1941,7 @@ OBIDMS_avl_p obi_open_avl(OBIDMS_p dms, const char* avl_name, int avl_idx)
avl->dir_fd = avl_dir_file_descriptor; avl->dir_fd = avl_dir_file_descriptor;
avl->avl_fd = avl_file_descriptor; avl->avl_fd = avl_file_descriptor;
if (avl_idx >= 0) free(complete_avl_name);
free(complete_avl_name);
return avl; return avl;
} }
@ -1806,6 +1969,7 @@ OBIDMS_avl_group_p obi_avl_group(OBIDMS_p dms, const char* avl_name)
OBIDMS_avl_group_p obi_create_avl_group(OBIDMS_p dms, const char* avl_name) OBIDMS_avl_group_p obi_create_avl_group(OBIDMS_p dms, const char* avl_name)
{ {
OBIDMS_avl_group_p avl_group; OBIDMS_avl_group_p avl_group;
char* avl_dir_name;
avl_group = (OBIDMS_avl_group_p) malloc(sizeof(OBIDMS_avl_group_t)); avl_group = (OBIDMS_avl_group_p) malloc(sizeof(OBIDMS_avl_group_t));
if (avl_group == NULL) if (avl_group == NULL)
@ -1815,18 +1979,22 @@ OBIDMS_avl_group_p obi_create_avl_group(OBIDMS_p dms, const char* avl_name)
return NULL; return NULL;
} }
// Create 1st avl avl_group->last_avl_idx = -1;
(avl_group->sub_avls)[0] = obi_create_avl(dms, avl_name, 0); avl_group->dms = dms;
if ((avl_group->sub_avls)[0] == NULL)
{
obidebug(1, "\nError creating the first AVL of an AVL group");
return NULL;
}
avl_group->last_avl_idx = 0;
strcpy(avl_group->name, avl_name); strcpy(avl_group->name, avl_name);
avl_group->dms = dms; // Create the directory for that AVL group
avl_dir_name = get_full_path_of_avl_dir(dms, avl_name);
if (avl_dir_name == NULL)
return NULL;
if (mkdirat(dms->indexer_dir_fd, avl_dir_name, 00777) < 0)
{
obi_set_errno(OBI_AVL_ERROR);
obidebug(1, "\nError creating an AVL directory");
free(avl_dir_name);
return NULL;
}
// Add in the list of open indexers // Add in the list of open indexers
obi_dms_list_indexer(dms, avl_group); obi_dms_list_indexer(dms, avl_group);
@ -1926,20 +2094,23 @@ OBIDMS_avl_group_p obi_clone_avl_group(OBIDMS_avl_group_p avl_group, const char*
// Create the new AVL group // Create the new AVL group
new_avl_group = obi_create_avl_group(avl_group->dms, new_avl_name); new_avl_group = obi_create_avl_group(avl_group->dms, new_avl_name);
// Copy the data from each old AVL to the new ones // Create hard links to all the full AVLs that won't be modified: all but the last one
for (i=0; i<=(avl_group->last_avl_idx); i++) for (i=0; i<(avl_group->last_avl_idx); i++)
{ {
if (i > 0) // Don't need to create the 1st AVL if (add_existing_avl_in_group(new_avl_group, avl_group, i) < 0)
{ return NULL;
if (add_new_avl_in_group(new_avl_group) < 0)
{
obi_close_avl_group(new_avl_group);
return NULL;
}
}
obi_clone_avl((avl_group->sub_avls)[i], (new_avl_group->sub_avls)[i]);
} }
// Create the last AVL to copy data in it
if (add_new_avl_in_group(new_avl_group) < 0)
{
obi_close_avl_group(new_avl_group);
return NULL;
}
// Copy the data from the last AVL to a new one that can be modified
obi_clone_avl((avl_group->sub_avls)[avl_group->last_avl_idx], (new_avl_group->sub_avls)[new_avl_group->last_avl_idx]);
// Close old AVL group // Close old AVL group
if (obi_close_avl_group(avl_group) < 0) if (obi_close_avl_group(avl_group) < 0)
{ {
@ -1959,7 +2130,7 @@ int obi_close_avl(OBIDMS_avl_p avl)
ret_val = truncate_avl_to_size_used(avl); ret_val = truncate_avl_to_size_used(avl);
if (munmap(avl->tree, (((avl->header)->nb_items_max) * sizeof(AVL_node_t))) < 0) if (munmap(avl->tree, (avl->header)->avl_size) < 0)
{ {
obi_set_errno(OBI_AVL_ERROR); obi_set_errno(OBI_AVL_ERROR);
obidebug(1, "\nError munmapping the tree of an AVL tree file"); obidebug(1, "\nError munmapping the tree of an AVL tree file");
@ -1996,9 +2167,17 @@ int obi_close_avl_group(OBIDMS_avl_group_p avl_group)
ret_val = obi_dms_unlist_indexer(avl_group->dms, avl_group); ret_val = obi_dms_unlist_indexer(avl_group->dms, avl_group);
// Close each AVL of the group // Close each AVL of the group
for (i=0; i < (avl_group->last_avl_idx); i++) for (i=0; i <= (avl_group->last_avl_idx); i++)
{
// Remap all but the last AVL (already mapped) before closing to truncate and close properly
if (i < (avl_group->last_avl_idx))
{
if (remap_an_avl((avl_group->sub_avls)[i]) < 0)
ret_val = -1;
}
if (obi_close_avl((avl_group->sub_avls)[i]) < 0) if (obi_close_avl((avl_group->sub_avls)[i]) < 0)
ret_val = -1; ret_val = -1;
}
free(avl_group); free(avl_group);
} }
@ -2207,6 +2386,16 @@ index_t obi_avl_group_add(OBIDMS_avl_group_p avl_group, Obi_blob_p value)
index_t index_with_avl; index_t index_with_avl;
int i; int i;
// Create 1st AVL if group is empty
if (avl_group->last_avl_idx == -1)
{
if (add_new_avl_in_group(avl_group) < 0)
{
obidebug(1, "\nError creating the first AVL of an AVL group");
return -1;
}
}
if (maybe_in_avl((avl_group->sub_avls)[avl_group->last_avl_idx], value)) if (maybe_in_avl((avl_group->sub_avls)[avl_group->last_avl_idx], value))
{ {
index_in_avl = (int32_t) obi_avl_find((avl_group->sub_avls)[avl_group->last_avl_idx], value); index_in_avl = (int32_t) obi_avl_find((avl_group->sub_avls)[avl_group->last_avl_idx], value);
@ -2218,6 +2407,7 @@ index_t obi_avl_group_add(OBIDMS_avl_group_p avl_group, Obi_blob_p value)
return index_with_avl; return index_with_avl;
} }
} }
for (i=0; i < (avl_group->last_avl_idx); i++) for (i=0; i < (avl_group->last_avl_idx); i++)
{ {
if (maybe_in_avl((avl_group->sub_avls)[i], value)) if (maybe_in_avl((avl_group->sub_avls)[i], value))

6
src/obiavl.h
View File

@ -73,7 +73,7 @@ typedef struct AVL_node {
* @brief OBIDMS AVL tree data header structure. * @brief OBIDMS AVL tree data header structure.
*/ */
typedef struct OBIDMS_avl_data_header { typedef struct OBIDMS_avl_data_header {
int header_size; /**< Size of the header in bytes. size_t header_size; /**< Size of the header in bytes.
*/ */
index_t data_size_used; /**< Size of the data used in bytes. index_t data_size_used; /**< Size of the data used in bytes.
*/ */
@ -105,7 +105,7 @@ typedef struct OBIDMS_avl_data {
* @brief OBIDMS AVL tree header structure. * @brief OBIDMS AVL tree header structure.
*/ */
typedef struct OBIDMS_avl_header { typedef struct OBIDMS_avl_header {
int header_size; /**< Size of the header in bytes. size_t header_size; /**< Size of the header in bytes.
*/ */
size_t avl_size; /**< Size of the AVL tree in bytes. size_t avl_size; /**< Size of the AVL tree in bytes.
*/ */
@ -160,7 +160,7 @@ typedef struct OBIDMS_avl {
typedef struct OBIDMS_avl_group { typedef struct OBIDMS_avl_group {
OBIDMS_avl_p sub_avls[MAX_NB_OF_AVLS_IN_GROUP]; /**< Array containing the pointers to the AVL trees of the group. OBIDMS_avl_p sub_avls[MAX_NB_OF_AVLS_IN_GROUP]; /**< Array containing the pointers to the AVL trees of the group.
*/ */
int last_avl_idx; /**< Index in the sub_avls array of the AVL tree currently being filled. int last_avl_idx; /**< Index in the sub_avls array of the AVL tree currently being filled.
*/ */
char name[AVL_MAX_NAME+1]; /**< Base name of the AVL group. The AVL trees in it have names of the form basename_idx. char name[AVL_MAX_NAME+1]; /**< Base name of the AVL group. The AVL trees in it have names of the form basename_idx.
*/ */

43
src/obidms.c
View File

@ -252,7 +252,7 @@ OBIDMS_p obi_create_dms(const char* dms_path)
return NULL; return NULL;
} }
// Get file descriptor of DMS directory to create the indexer directory // Get file descriptor of DMS directory to create other directories
dms_dir = opendir(directory_name); dms_dir = opendir(directory_name);
if (dms_dir == NULL) if (dms_dir == NULL)
{ {
@ -280,6 +280,14 @@ OBIDMS_p obi_create_dms(const char* dms_path)
return NULL; return NULL;
} }
// Create the view directory
if (mkdirat(dms_file_descriptor, VIEW_DIR_NAME, 00777) < 0)
{
obi_set_errno(OBIVIEW_ERROR);
obidebug(1, "\nProblem creating a view directory");
return NULL;
}
// Isolate the dms name // Isolate the dms name
j = 0; j = 0;
for (i=0; i<strlen(dms_path); i++) for (i=0; i<strlen(dms_path); i++)
@ -447,6 +455,30 @@ OBIDMS_p obi_open_dms(const char* dms_path)
return NULL; return NULL;
} }
// Open the view directory
dms->view_directory = opendir_in_dms(dms, VIEW_DIR_NAME);
if (dms->view_directory == NULL)
{
obi_set_errno(OBIDMS_UNKNOWN_ERROR);
obidebug(1, "\nError opening the view directory");
closedir(dms->indexer_directory);
closedir(dms->directory);
free(dms);
return NULL;
}
// Store the view directory's file descriptor
dms->view_dir_fd = dirfd(dms->view_directory);
if (dms->view_dir_fd < 0)
{
obi_set_errno(OBIDMS_UNKNOWN_ERROR);
obidebug(1, "\nError getting the file descriptor of the view directory");
closedir(dms->view_directory);
closedir(dms->directory);
free(dms);
return NULL;
}
// Initialize the list of opened columns // Initialize the list of opened columns
dms->opened_columns = (Opened_columns_list_p) malloc(sizeof(Opened_columns_list_t)); dms->opened_columns = (Opened_columns_list_p) malloc(sizeof(Opened_columns_list_t));
(dms->opened_columns)->nb_opened_columns = 0; (dms->opened_columns)->nb_opened_columns = 0;
@ -486,7 +518,7 @@ int obi_close_dms(OBIDMS_p dms)
while ((dms->opened_columns)->nb_opened_columns > 0) while ((dms->opened_columns)->nb_opened_columns > 0)
obi_close_column(*((dms->opened_columns)->columns)); obi_close_column(*((dms->opened_columns)->columns));
// Close dms and indexer directories // Close dms, and view and indexer directories
if (closedir(dms->directory) < 0) if (closedir(dms->directory) < 0)
{ {
obi_set_errno(OBIDMS_MEMORY_ERROR); obi_set_errno(OBIDMS_MEMORY_ERROR);
@ -501,6 +533,13 @@ int obi_close_dms(OBIDMS_p dms)
free(dms); free(dms);
return -1; return -1;
} }
if (closedir(dms->view_directory) < 0)
{
obi_set_errno(OBIVIEW_ERROR);
obidebug(1, "\nError closing a view directory");
free(dms);
return -1;
}
free(dms); free(dms);
} }

8
src/obidms.h
View File

@ -30,6 +30,8 @@
*/ */
#define INDEXER_DIR_NAME "OBIBLOB_INDEXERS" /**< The name of the Obiblob indexer directory. #define INDEXER_DIR_NAME "OBIBLOB_INDEXERS" /**< The name of the Obiblob indexer directory.
*/ */
#define VIEW_DIR_NAME "VIEWS" /**< The name of the view directory.
*/
#define TAXONOMY_DIR_NAME "TAXONOMY" /**< The name of the taxonomy directory. #define TAXONOMY_DIR_NAME "TAXONOMY" /**< The name of the taxonomy directory.
*/ */
#define MAX_NB_OPENED_COLUMNS (100) /**< The maximum number of columns open at the same time. #define MAX_NB_OPENED_COLUMNS (100) /**< The maximum number of columns open at the same time.
@ -98,6 +100,12 @@ typedef struct OBIDMS {
int indexer_dir_fd; /**< The file descriptor of the directory entry int indexer_dir_fd; /**< The file descriptor of the directory entry
* usable to refer and scan the indexer directory. * usable to refer and scan the indexer directory.
*/ */
DIR* view_directory; /**< A directory entry usable to
* refer and scan the view directory.
*/
int view_dir_fd; /**< The file descriptor of the directory entry
* usable to refer and scan the view directory.
*/
bool little_endian; /**< Endianness of the database. bool little_endian; /**< Endianness of the database.
*/ */
Opened_columns_list_p opened_columns; /**< List of opened columns. Opened_columns_list_p opened_columns; /**< List of opened columns.

2
src/obidmscolumn.c
View File

@ -940,8 +940,6 @@ OBIDMS_column_p obi_clone_column(OBIDMS_p dms,
size_t line_size; size_t line_size;
index_t i, index; index_t i, index;
obidebug(1, "\nline_selection == NULL = %d\n", (line_selection == NULL));
column_to_clone = obi_open_column(dms, column_name, version_number); column_to_clone = obi_open_column(dms, column_name, version_number);
if (column_to_clone == NULL) if (column_to_clone == NULL)
{ {

69
src/obidmscolumn_qual.c
View File

@ -33,16 +33,22 @@ int obi_column_set_obiqual_char_with_elt_idx(OBIDMS_column_p column, index_t lin
int i; int i;
int ret_value; int ret_value;
int_value_length = strlen(value); // Check NA value
int_value = (uint8_t*) malloc(int_value_length * sizeof(uint8_t)); if (value == OBIQual_char_NA)
{
ret_value = obi_column_set_obiqual_int_with_elt_idx(column, line_nb, element_idx, OBIQual_int_NA, 0);
}
else
{
int_value_length = strlen(value);
int_value = (uint8_t*) malloc(int_value_length * sizeof(uint8_t));
// Convert in uint8_t array to index in that format // Convert in uint8_t array to index in that format
for (i=0; i<int_value_length; i++) for (i=0; i<int_value_length; i++)
int_value[i] = ((uint8_t)(value[i])) - QUALITY_ASCII_BASE; int_value[i] = ((uint8_t)(value[i])) - QUALITY_ASCII_BASE;
ret_value = obi_column_set_obiqual_int_with_elt_idx(column, line_nb, element_idx, int_value, int_value_length);
ret_value = obi_column_set_obiqual_int_with_elt_idx(column, line_nb, element_idx, int_value, int_value_length); free(int_value);
}
free(int_value);
return ret_value; return ret_value;
} }
@ -56,25 +62,38 @@ int obi_column_set_obiqual_int_with_elt_idx(OBIDMS_column_p column, index_t line
if (obi_column_prepare_to_set_value(column, line_nb) < 0) if (obi_column_prepare_to_set_value(column, line_nb) < 0)
return -1; return -1;
// Add the value in the indexer if (value == OBIQual_int_NA)
idx = obi_index_uint8(column->indexer, value, value_length);
if (idx == -1) // An error occurred
{ {
if (obi_errno == OBI_READ_ONLY_INDEXER_ERROR) idx = OBIIdx_NA;
}
else
{
// Add the value in the indexer
idx = obi_index_uint8(column->indexer, value, value_length);
if (idx == -1) // An error occurred
{ {
// If the error is that the indexer is read-only, clone it if (obi_errno == OBI_READ_ONLY_INDEXER_ERROR)
new_indexer_name = obi_build_indexer_name((column->header)->name, (column->header)->version); {
if (new_indexer_name == NULL) // TODO PUT IN A COLUMN FUNCTION
return -1; // If the error is that the indexer is read-only, clone it
column->indexer = obi_clone_indexer(column->indexer, new_indexer_name); // TODO Need to lock this somehow? new_indexer_name = obi_build_indexer_name((column->header)->name, (column->header)->version);
// Add the value in the new indexer if (new_indexer_name == NULL)
idx = obi_index_uint8(column->indexer, value, value_length); return -1;
if (idx == -1) column->indexer = obi_clone_indexer(column->indexer, new_indexer_name); // TODO Need to lock this somehow?
strcpy((column->header)->indexer_name, new_indexer_name);
free(new_indexer_name);
obi_set_errno(0);
// Add the value in the new indexer
idx = obi_index_uint8(column->indexer, value, value_length);
if (idx == -1)
return -1;
}
else
return -1; return -1;
} }
else
return -1;
} }
// Add the value's index in the column // Add the value's index in the column
*(((index_t*) (column->data)) + (line_nb * ((column->header)->nb_elements_per_line)) + element_idx) = idx; *(((index_t*) (column->data)) + (line_nb * ((column->header)->nb_elements_per_line)) + element_idx) = idx;
@ -91,6 +110,10 @@ char* obi_column_get_obiqual_char_with_elt_idx(OBIDMS_column_p column, index_t l
int_value = obi_column_get_obiqual_int_with_elt_idx(column, line_nb, element_idx, &int_value_length); int_value = obi_column_get_obiqual_int_with_elt_idx(column, line_nb, element_idx, &int_value_length);
// Check NA
if (int_value == OBIQual_int_NA)
return OBIQual_char_NA;
value = (char*) malloc((int_value_length + 1) * sizeof(char)); value = (char*) malloc((int_value_length + 1) * sizeof(char));
// Encode int quality to char quality // Encode int quality to char quality

4
src/obidmscolumn_qual.h
View File

@ -86,7 +86,7 @@ int obi_column_set_obiqual_int_with_elt_idx(OBIDMS_column_p column, index_t line
* @param element_idx The index of the element that should be recovered in the line. * @param element_idx The index of the element that should be recovered in the line.
* *
* @returns The recovered value, in the character string format. * @returns The recovered value, in the character string format.
* @retval OBIQual_str_NA the NA value of the type if an error occurred and obi_errno is set. * @retval OBIQual_char_NA the NA value of the type if an error occurred and obi_errno is set.
* *
* @since May 2016 * @since May 2016
* @author Celine Mercier (celine.mercier@metabarcoding.org) * @author Celine Mercier (celine.mercier@metabarcoding.org)
@ -172,7 +172,7 @@ int obi_column_set_obiqual_int_with_elt_name(OBIDMS_column_p column, index_t lin
* @param element_name The name of the element that should be recovered in the line. * @param element_name The name of the element that should be recovered in the line.
* *
* @returns The recovered value, in the character string format. * @returns The recovered value, in the character string format.
* @retval OBIQual_str_NA the NA value of the type if an error occurred and obi_errno is set. * @retval OBIQual_char_NA the NA value of the type if an error occurred and obi_errno is set.
* *
* @since May 2016 * @since May 2016
* @author Celine Mercier (celine.mercier@metabarcoding.org) * @author Celine Mercier (celine.mercier@metabarcoding.org)

41
src/obidmscolumn_seq.c
View File

@ -32,25 +32,38 @@ int obi_column_set_obiseq_with_elt_idx(OBIDMS_column_p column, index_t line_nb,
if (obi_column_prepare_to_set_value(column, line_nb) < 0) if (obi_column_prepare_to_set_value(column, line_nb) < 0)
return -1; return -1;
// Add the value in the indexer if (value == OBISeq_NA)
idx = obi_index_dna_seq(column->indexer, value);
if (idx == -1) // An error occurred
{ {
if (obi_errno == OBI_READ_ONLY_INDEXER_ERROR) idx = OBIIdx_NA;
}
else
{
// Add the value in the indexer
idx = obi_index_dna_seq(column->indexer, value);
if (idx == -1) // An error occurred
{ {
// If the error is that the indexer is read-only, clone it if (obi_errno == OBI_READ_ONLY_INDEXER_ERROR)
new_indexer_name = obi_build_indexer_name((column->header)->name, (column->header)->version); {
if (new_indexer_name == NULL) // TODO PUT IN A COLUMN FUNCTION
return -1; // If the error is that the indexer is read-only, clone it
column->indexer = obi_clone_indexer(column->indexer, new_indexer_name); // TODO Need to lock this somehow? new_indexer_name = obi_build_indexer_name((column->header)->name, (column->header)->version);
// Add the value in the new indexer if (new_indexer_name == NULL)
idx = obi_index_dna_seq(column->indexer, value); return -1;
if (idx == -1) column->indexer = obi_clone_indexer(column->indexer, new_indexer_name); // TODO Need to lock this somehow?
strcpy((column->header)->indexer_name, new_indexer_name);
free(new_indexer_name);
obi_set_errno(0);
// Add the value in the new indexer
idx = obi_index_dna_seq(column->indexer, value);
if (idx == -1)
return -1;
}
else
return -1; return -1;
} }
else
return -1;
} }
// Add the value's index in the column // Add the value's index in the column
*(((index_t*) (column->data)) + (line_nb * ((column->header)->nb_elements_per_line)) + element_idx) = idx; *(((index_t*) (column->data)) + (line_nb * ((column->header)->nb_elements_per_line)) + element_idx) = idx;

42
src/obidmscolumn_str.c
View File

@ -32,24 +32,36 @@ int obi_column_set_obistr_with_elt_idx(OBIDMS_column_p column, index_t line_nb,
if (obi_column_prepare_to_set_value(column, line_nb) < 0) if (obi_column_prepare_to_set_value(column, line_nb) < 0)
return -1; return -1;
// Add the value in the indexer if (value == OBIStr_NA)
idx = obi_index_char_str(column->indexer, value);
if (idx == -1) // An error occurred
{ {
if (obi_errno == OBI_READ_ONLY_INDEXER_ERROR) idx = OBIIdx_NA;
}
else
{
// Add the value in the indexer
idx = obi_index_char_str(column->indexer, value);
if (idx == -1) // An error occurred
{ {
// If the error is that the indexer is read-only, clone it if (obi_errno == OBI_READ_ONLY_INDEXER_ERROR)
new_indexer_name = obi_build_indexer_name((column->header)->name, (column->header)->version); {
if (new_indexer_name == NULL) // TODO PUT IN A COLUMN FUNCTION
return -1; // If the error is that the indexer is read-only, clone it
column->indexer = obi_clone_indexer(column->indexer, new_indexer_name); // TODO Need to lock this somehow? new_indexer_name = obi_build_indexer_name((column->header)->name, (column->header)->version);
// Add the value in the new indexer if (new_indexer_name == NULL)
idx = obi_index_char_str(column->indexer, value); return -1;
if (idx == -1) column->indexer = obi_clone_indexer(column->indexer, new_indexer_name); // TODO Need to lock this somehow?
strcpy((column->header)->indexer_name, new_indexer_name);
free(new_indexer_name);
obi_set_errno(0);
// Add the value in the new indexer
idx = obi_index_char_str(column->indexer, value);
if (idx == -1)
return -1;
}
else
return -1; return -1;
} }
else
return -1;
} }
// Add the value's index in the column // Add the value's index in the column
@ -64,7 +76,7 @@ const char* obi_column_get_obistr_with_elt_idx(OBIDMS_column_p column, index_t l
index_t idx; index_t idx;
if (obi_column_prepare_to_get_value(column, line_nb) < 0) if (obi_column_prepare_to_get_value(column, line_nb) < 0)
return OBISeq_NA; return OBIStr_NA;
idx = *(((index_t*) (column->data)) + (line_nb * ((column->header)->nb_elements_per_line)) + element_idx); idx = *(((index_t*) (column->data)) + (line_nb * ((column->header)->nb_elements_per_line)) + element_idx);

8
src/obitypes.h
View File

@ -22,10 +22,10 @@
#define OBIIdx_NA (INT64_MIN) /**< NA value for indices */ #define OBIIdx_NA (INT64_MIN) /**< NA value for indices */
#define OBIFloat_NA (float_NA()) /**< NA value for the type OBI_FLOAT */ #define OBIFloat_NA (float_NA()) /**< NA value for the type OBI_FLOAT */
#define OBIChar_NA (0) /**< NA value for the type OBI_CHAR */ // TODO not sure about this one as it can be impossible to distinguish from uninitialized values #define OBIChar_NA (0) /**< NA value for the type OBI_CHAR */ // TODO not sure about this one as it can be impossible to distinguish from uninitialized values
#define OBISeq_NA ("\0") /**< NA value for the type OBI_SEQ */ // TODO discuss #define OBISeq_NA (NULL) /**< NA value for the type OBI_SEQ */ // TODO discuss
#define OBIStr_NA ("\0") /**< NA value for the type OBI_STR */ // TODO discuss #define OBIStr_NA (NULL) /**< NA value for the type OBI_STR */ // TODO discuss
#define OBIQual_char_NA ("\0") /**< NA value for the type OBI_QUAL if the quality is in character string format */ // TODO test and discuss #define OBIQual_char_NA (NULL) /**< NA value for the type OBI_QUAL if the quality is in character string format */
#define OBIQual_int_NA (NULL) /**< NA value for the type OBI_QUAL if the quality is in integer format */ // TODO test and discuss #define OBIQual_int_NA (NULL) /**< NA value for the type OBI_QUAL if the quality is in integer format */
/** /**

862
src/obiview.c
View File

File diff suppressed because it is too large Load Diff

102
src/obiview.h
View File

@ -34,8 +34,6 @@
*/ */
#define VIEW_TYPE_MAX_LENGTH (1024) /**< The maximum length of the type name of a view. #define VIEW_TYPE_MAX_LENGTH (1024) /**< The maximum length of the type name of a view.
*/ */
#define OBIVIEW_FILE_NAME "obiviews" /**< The default name of a view file.
*/
#define LINES_COLUMN_NAME "LINES" /**< The name of the column containing the line selections #define LINES_COLUMN_NAME "LINES" /**< The name of the column containing the line selections
* in all views. * in all views.
*/ */
@ -56,45 +54,6 @@
*/ */
/**
* @brief Structure for an opened view.
*/
typedef struct Obiview {
OBIDMS_p dms; /**< A pointer on the DMS to which the view belongs.
*/
char name[OBIVIEW_NAME_MAX_LENGTH+1]; /**< Name of the view.
*/
char created_from[OBIVIEW_NAME_MAX_LENGTH+1]; /**< Name of the view from which that view was cloned if the view was cloned.
*/
char view_type[VIEW_TYPE_MAX_LENGTH+1]; /**< Type of the view if there is one.
* Types existing: NUC_SEQS_VIEW.
*/
bool read_only; /**< Whether the view is read-only or can be modified.
*/
OBIDMS_column_p line_selection; /**< A pointer on the column containing the line selection
* associated with the view if there is one.
* This line selection is read-only, and when a line from the view is read,
* it is this line selection that is used.
*/
OBIDMS_column_p new_line_selection; /**< A pointer on the column containing the new line selection being built
* to associate with the view, if there is one.
* When a line is selected with obi_select_line() or obi_select_lines(),
* it is recorded in this line selection.
*/
index_t line_count; /**< The number of lines in the view. Refers to the number of lines in each
* column of the view if line_selection is NULL, or to the line count of
* line_selection if it is not NULL.
*/
int column_count; /**< The number of columns in the view.
*/
OBIDMS_column_p columns[MAX_NB_OPENED_COLUMNS]; /**< Array of pointers on all the columns of the view.
*/
char comments[OBIVIEW_COMMENTS_MAX_LENGTH+1]; /**< Comments, additional informations on the view.
*/
} Obiview_t, *Obiview_p;
/** /**
* @brief Structure referencing a column by its name and its version. * @brief Structure referencing a column by its name and its version.
*/ */
@ -112,8 +71,6 @@ typedef struct Column_reference {
* Once a view has been written in the view file, it can not be modified and can only be read. * Once a view has been written in the view file, it can not be modified and can only be read.
*/ */
typedef struct Obiview_infos { typedef struct Obiview_infos {
int view_number; /**< Number of the view in the view file.
*/
time_t creation_date; /**< Time at which the view was written in the view file. time_t creation_date; /**< Time at which the view was written in the view file.
*/ */
char name[OBIVIEW_NAME_MAX_LENGTH+1]; /**< Name of the view, used to identify it. char name[OBIVIEW_NAME_MAX_LENGTH+1]; /**< Name of the view, used to identify it.
@ -138,7 +95,29 @@ typedef struct Obiview_infos {
} Obiview_infos_t, *Obiview_infos_p; } Obiview_infos_t, *Obiview_infos_p;
// TODO : Combine the common elements of the Obiview_infos and Obiview structures in one structure used by both? /**
* @brief Structure for an opened view.
*/
typedef struct Obiview {
Obiview_infos_p infos; /**< A pointer on the mapped view informations.
*/
OBIDMS_p dms; /**< A pointer on the DMS to which the view belongs.
*/
bool read_only; /**< Whether the view is read-only or can be modified.
*/
OBIDMS_column_p line_selection; /**< A pointer on the column containing the line selection
* associated with the view if there is one.
* This line selection is read-only, and when a line from the view is read,
* it is this line selection that is used.
*/
OBIDMS_column_p new_line_selection; /**< A pointer on the column containing the new line selection being built
* to associate with the view, if there is one.
* When a line is selected with obi_select_line() or obi_select_lines(),
* it is recorded in this line selection.
*/
OBIDMS_column_p columns[MAX_NB_OPENED_COLUMNS]; /**< Array of pointers on all the columns of the view.
*/
} Obiview_t, *Obiview_p;
/** /**
@ -269,6 +248,37 @@ Obiview_p obi_new_view_nuc_seqs(OBIDMS_p dms, const char* view_name, Obiview_p v
Obiview_p obi_new_view_nuc_seqs_cloned_from_name(OBIDMS_p dms, const char* view_name, const char* view_to_clone_name, index_t* line_selection, const char* comments); Obiview_p obi_new_view_nuc_seqs_cloned_from_name(OBIDMS_p dms, const char* view_name, const char* view_to_clone_name, index_t* line_selection, const char* comments);
/**
* @brief Maps a view file and returns the mapped structure stored in it.
*
* @param dms A pointer on the OBIDMS.
* @param view_name The unique name identifying the view.
*
* @returns A pointer on the mapped view infos structure.
* @retval NULL if an error occurred.
*
* @since June 2016
* @author Celine Mercier (celine.mercier@metabarcoding.org)
*/
Obiview_infos_p obi_view_map_file(OBIDMS_p dms, const char* view_name);
/**
* @brief Unmaps a view file.
*
* @param dms A pointer on the OBIDMS.
* @param view_infos A pointer on the mapped view infos structure.
*
* @returns A value indicating the success of the operation.
* @retval 0 if the operation was successfully completed.
* @retval -1 if an error occurred.
*
* @since June 2016
* @author Celine Mercier (celine.mercier@metabarcoding.org)
*/
int obi_view_unmap_file(OBIDMS_p dms, Obiview_infos_p view_infos);
/** /**
* @brief Opens a view identified by its name stored in the view file. * @brief Opens a view identified by its name stored in the view file.
* *
@ -873,7 +883,7 @@ int obi_column_set_obiqual_int_with_elt_idx_in_view(Obiview_p view, OBIDMS_colum
* @param element_idx The index of the element that should be recovered in the line. * @param element_idx The index of the element that should be recovered in the line.
* *
* @returns The recovered value, in the character string format. * @returns The recovered value, in the character string format.
* @retval OBIQual_str_NA the NA value of the type if an error occurred and obi_errno is set. * @retval OBIQual_char_NA the NA value of the type if an error occurred and obi_errno is set.
* *
* @since May 2016 * @since May 2016
* @author Celine Mercier (celine.mercier@metabarcoding.org) * @author Celine Mercier (celine.mercier@metabarcoding.org)
@ -967,7 +977,7 @@ int obi_column_set_obiqual_int_with_elt_name_in_view(Obiview_p view, OBIDMS_colu
* @param element_name The name of the element that should be recovered in the line. * @param element_name The name of the element that should be recovered in the line.
* *
* @returns The recovered value, in the character string format. * @returns The recovered value, in the character string format.
* @retval OBIQual_str_NA the NA value of the type if an error occurred and obi_errno is set. * @retval OBIQual_char_NA the NA value of the type if an error occurred and obi_errno is set.
* *
* @since May 2016 * @since May 2016
* @author Celine Mercier (celine.mercier@metabarcoding.org) * @author Celine Mercier (celine.mercier@metabarcoding.org)