Merge branch 'master' of git@git.metabarcoding.org:obitools/obitools3.git
This commit is contained in:
@ -91,5 +91,5 @@ cdef class OBIDMS:
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cpdef OBIView open_view(self, str view_name)
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cpdef OBIView new_view(self, str view_name, object view_to_clone=*, list line_selection=*, str view_type=*, str comments=*)
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cpdef dict read_view_infos(self, str view_name)
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cpdef dict read_views(self)
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# cpdef dict read_views(self) TODO
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@ -44,7 +44,8 @@ from ._obidmscolumn_bool cimport OBIDMS_column_bool, \
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from ._obidmscolumn_char cimport OBIDMS_column_char, \
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OBIDMS_column_multi_elts_char
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from ._obidmscolumn_qual cimport OBIDMS_column_qual
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from ._obidmscolumn_qual cimport OBIDMS_column_qual, \
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OBIDMS_column_multi_elts_qual
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from ._obidmscolumn_str cimport OBIDMS_column_str, \
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OBIDMS_column_multi_elts_str
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@ -53,16 +54,15 @@ from ._obidmscolumn_seq cimport OBIDMS_column_seq, \
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OBIDMS_column_multi_elts_seq
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from .capi.obiview cimport Obiview_p, \
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Obiviews_infos_all_p, \
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Obiview_infos_p, \
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Column_reference_p, \
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obi_new_view_nuc_seqs, \
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obi_new_view, \
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obi_new_view_cloned_from_name, \
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obi_new_view_nuc_seqs_cloned_from_name, \
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obi_view_map_file, \
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obi_view_unmap_file, \
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obi_open_view, \
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obi_read_view_infos, \
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obi_close_view_infos, \
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obi_view_delete_column, \
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obi_view_add_column, \
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obi_view_get_column, \
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@ -194,8 +194,8 @@ cdef class OBIDMS_column :
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elif col_type == OBI_QUAL :
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if col_one_element_per_line :
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subclass = OBIDMS_column_qual
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# else : # TODO
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# subclass = OBIDMS_column_multi_elts_qual
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else :
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subclass = OBIDMS_column_multi_elts_qual
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elif col_type == OBI_STR :
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if col_one_element_per_line :
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subclass = OBIDMS_column_str
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@ -290,11 +290,11 @@ cdef class OBIView :
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raise Exception("Error creating/opening a view")
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self.pointer = view
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self.name = bytes2str(view.name)
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self.name = bytes2str(view.infos.name)
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# Go through columns to build list of corresponding python instances
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self.columns = {}
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for i in range(view.column_count) :
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for i in range(view.infos.column_count) :
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column_p = <OBIDMS_column_p> (view.columns)[i]
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header = (column_p).header
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col_name = bytes2str(header.name)
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@ -304,7 +304,7 @@ cdef class OBIView :
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def __repr__(self) :
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cdef str s
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s = str(self.name) + ", " + str(self.comments) + ", " + str(self.pointer.line_count) + " lines\n"
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s = str(self.name) + ", " + str(self.comments) + ", " + str(self.pointer.infos.line_count) + " lines\n"
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for column_name in self.columns :
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s = s + self.columns[column_name].__repr__() + '\n'
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return s
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@ -313,7 +313,7 @@ cdef class OBIView :
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cpdef delete_column(self, str column_name) :
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cdef int i
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cdef Obiview_p view
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cdef Obiview_p view_p
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cdef OBIDMS_column column
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cdef OBIDMS_column_p column_p
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cdef OBIDMS_column_header_p header
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@ -321,7 +321,7 @@ cdef class OBIView :
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view = self.pointer
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if obi_view_delete_column(view, str2bytes(column_name)) < 0 :
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if obi_view_delete_column(view_p, str2bytes(column_name)) < 0 :
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raise Exception("Problem deleting a column from a view")
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# Update the dictionaries of column pointers and column objects, and update pointers in column objects (make function?):
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@ -401,7 +401,7 @@ cdef class OBIView :
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cdef OBIView_line line # TODO Check that this works for NUC SEQ views
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# Yield each line
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lines_used = (self.pointer).line_count
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lines_used = self.pointer.infos.line_count
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for line_nb in range(lines_used) :
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line = self[line_nb]
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@ -485,12 +485,12 @@ cdef class OBIView_NUC_SEQS(OBIView):
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raise Exception("Error creating/opening view")
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self.pointer = view
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self.name = bytes2str(view.name)
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self.comments = bytes2str(view.comments)
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self.name = bytes2str(view.infos.name)
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self.comments = bytes2str(view.infos.comments)
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# Go through columns to build list of corresponding python instances
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self.columns = {}
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for i in range(view.column_count) :
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for i in range(view.infos.column_count) :
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column_p = <OBIDMS_column_p> (view.columns)[i]
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header = (column_p).header
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col_name = bytes2str(header.name)
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@ -502,35 +502,12 @@ cdef class OBIView_NUC_SEQS(OBIView):
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self.definitions = self.columns[bytes2str(DEFINITION_COLUMN)]
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self.qualities = self.columns[bytes2str(QUALITY_COLUMN)]
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cpdef delete_column(self, str column_name) :
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cdef int i
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cdef Obiview_p view_p
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cdef OBIDMS_column column
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cdef OBIDMS_column_p column_p
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cdef OBIDMS_column_header_p header
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cdef str column_n
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view_p = self.pointer
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if obi_view_delete_column(view_p, str2bytes(column_name)) < 0 :
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raise Exception("Problem deleting a column from a view")
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# Remove instance from the dictionary
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(self.columns).pop(column_name)
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for column_n in self.columns :
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(self.columns[column_n]).update_pointer()
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def __getitem__(self, object item) :
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if type(item) == str :
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return (self.columns)[item]
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elif type(item) == int :
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return OBI_Nuc_Seq_Stored(self, item)
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def __setitem__(self, index_t line_idx, OBI_Nuc_Seq sequence_obj) :
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for key in sequence_obj :
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self[line_idx][key] = sequence_obj[key]
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@ -643,54 +620,84 @@ cdef class OBIDMS :
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cpdef dict read_view_infos(self, str view_name) :
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all_views = self.read_views()
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return all_views[view_name]
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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
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cdef Obiviews_infos_all_p all_views_p
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cdef Obiview_infos_p view_p
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cdef Obiview_infos_p view_infos_p
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cdef dict view_infos_d
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cdef Column_reference_p column_refs
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cdef int nb_views
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cdef int i, j
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cdef str view_name
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cdef str column_name
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cdef dict views
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cdef bytes name_b
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views = {}
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all_views_p = obi_read_view_infos(self.pointer)
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if all_views_p == NULL :
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raise Exception("No views to read")
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nb_views = <int> (all_views_p.header).view_count
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for i in range(nb_views) :
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view_p = (<Obiview_infos_p> (all_views_p.view_infos)) + i
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view_name = bytes2str(view_p.name)
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views[view_name] = {}
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views[view_name]["comments"] = bytes2str(view_p.comments)
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views[view_name]["view_type"] = bytes2str(view_p.view_type)
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views[view_name]["column_count"] = <int> view_p.column_count
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views[view_name]["line_count"] = <int> view_p.line_count
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views[view_name]["view_number"] = <int> view_p.view_number
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views[view_name]["created_from"] = bytes2str(view_p.created_from)
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views[view_name]["creation_date"] = bytes2str(obi_format_date(view_p.creation_date))
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if (view_p.all_lines) :
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views[view_name]["line_selection"] = None
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else :
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views[view_name]["line_selection"] = {}
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views[view_name]["line_selection"]["column_name"] = bytes2str((view_p.line_selection).column_name)
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views[view_name]["line_selection"]["version"] = <int> (view_p.line_selection).version
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views[view_name]["column_references"] = {}
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column_refs = view_p.column_references
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for j in range(views[view_name]["column_count"]) :
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column_name = bytes2str((column_refs[j]).column_name)
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views[view_name]["column_references"][column_name] = {}
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views[view_name]["column_references"][column_name]["version"] = column_refs[j].version
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view_infos_p = obi_view_map_file(self.pointer, str2bytes(view_name))
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view_infos_d = {}
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view_infos_d["name"] = bytes2str(view_infos_p.name)
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view_infos_d["comments"] = bytes2str(view_infos_p.comments)
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view_infos_d["view_type"] = bytes2str(view_infos_p.view_type)
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view_infos_d["column_count"] = <int> view_infos_p.column_count
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view_infos_d["line_count"] = <int> view_infos_p.line_count
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view_infos_d["created_from"] = bytes2str(view_infos_p.created_from)
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view_infos_d["creation_date"] = bytes2str(obi_format_date(view_infos_p.creation_date))
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if (view_infos_p.all_lines) :
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view_infos_d["line_selection"] = None
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else :
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view_infos_d["line_selection"] = {}
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view_infos_d["line_selection"]["column_name"] = bytes2str((view_infos_p.line_selection).column_name)
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view_infos_d["line_selection"]["version"] = <int> (view_infos_p.line_selection).version
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view_infos_d["column_references"] = {}
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column_refs = view_infos_p.column_references
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for j in range(view_infos_d["column_count"]) :
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column_name = bytes2str((column_refs[j]).column_name)
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view_infos_d["column_references"][column_name] = {}
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view_infos_d["column_references"][column_name]["version"] = column_refs[j].version
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obi_close_view_infos(all_views_p);
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obi_view_unmap_file(self.pointer, view_infos_p)
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return views
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return view_infos_d
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# 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
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#
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# cdef Obiviews_infos_all_p all_views_p
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# cdef Obiview_infos_p view_p
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# cdef Column_reference_p column_refs
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# cdef int nb_views
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# cdef int i, j
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# cdef str view_name
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# cdef str column_name
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# cdef dict views
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# cdef bytes name_b
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#
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# views = {}
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# all_views_p = obi_read_view_infos(self.pointer)
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# if all_views_p == NULL :
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# raise Exception("No views to read")
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# nb_views = <int> (all_views_p.header).view_count
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# for i in range(nb_views) :
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# view_p = (<Obiview_infos_p> (all_views_p.view_infos)) + i
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# view_name = bytes2str(view_p.name)
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# views[view_name] = {}
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# views[view_name]["comments"] = bytes2str(view_p.comments)
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# views[view_name]["view_type"] = bytes2str(view_p.view_type)
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# views[view_name]["column_count"] = <int> view_p.column_count
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# views[view_name]["line_count"] = <int> view_p.line_count
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# views[view_name]["view_number"] = <int> view_p.view_number
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# views[view_name]["created_from"] = bytes2str(view_p.created_from)
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# views[view_name]["creation_date"] = bytes2str(obi_format_date(view_p.creation_date))
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# if (view_p.all_lines) :
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# views[view_name]["line_selection"] = None
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# else :
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# views[view_name]["line_selection"] = {}
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# views[view_name]["line_selection"]["column_name"] = bytes2str((view_p.line_selection).column_name)
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# views[view_name]["line_selection"]["version"] = <int> (view_p.line_selection).version
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# views[view_name]["column_references"] = {}
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# column_refs = view_p.column_references
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# for j in range(views[view_name]["column_count"]) :
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# column_name = bytes2str((column_refs[j]).column_name)
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# views[view_name]["column_references"][column_name] = {}
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# views[view_name]["column_references"][column_name]["version"] = column_refs[j].version
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#
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# obi_close_view_infos(all_views_p);
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#
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# return views
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@ -1,7 +1,7 @@
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#cython: language_level=3
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from .capi.obitypes cimport index_t
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from ._obidms cimport OBIDMS_column #, OBIDMS_column_multi_elts
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from ._obidms cimport OBIDMS_column , OBIDMS_column_multi_elts
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cdef class OBIDMS_column_qual(OBIDMS_column):
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@ -11,7 +11,10 @@ cdef class OBIDMS_column_qual(OBIDMS_column):
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cpdef set_str_line(self, index_t line_nb, object value)
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# cdef class OBIDMS_column_multi_elts_qual(OBIDMS_column_multi_elts):
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# cpdef object get_item(self, index_t line_nb, str element_name)
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# cpdef object get_line(self, index_t line_nb)
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# cpdef set_item(self, index_t line_nb, str element_name, object value)
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cdef class OBIDMS_column_multi_elts_qual(OBIDMS_column_multi_elts):
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cpdef object get_item(self, index_t line_nb, str element_name)
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cpdef object get_str_item(self, index_t line_nb, str element_name)
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cpdef object get_line(self, index_t line_nb)
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cpdef object get_str_line(self, index_t line_nb)
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cpdef set_item(self, index_t line_nb, str element_name, object value)
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cpdef set_str_item(self, index_t line_nb, str element_name, object value)
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@ -32,7 +32,7 @@ cdef class OBIDMS_column_qual(OBIDMS_column):
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value = obi_column_get_obiqual_int_with_elt_idx_in_view(self.view.pointer, (self.pointer)[0], line_nb, 0, &value_length)
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if obi_errno > 0 :
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raise IndexError(line_nb)
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if value == NULL : # TODO
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if value == OBIQual_int_NA :
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result = None
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else :
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result = []
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@ -47,7 +47,7 @@ cdef class OBIDMS_column_qual(OBIDMS_column):
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value = obi_column_get_obiqual_char_with_elt_idx_in_view(self.view.pointer, (self.pointer)[0], line_nb, 0)
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if obi_errno > 0 :
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raise IndexError(line_nb)
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if strcmp(value, OBIQual_char_NA) == 0 :
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if value == OBIQual_char_NA :
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result = None
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else :
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result = bytes2str(value)
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@ -58,94 +58,127 @@ cdef class OBIDMS_column_qual(OBIDMS_column):
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cdef uint8_t* value_b
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cdef int value_length
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if value is None :
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value_b = NULL # TODO
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value_length = 0
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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:
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raise Exception("Problem setting a value in a column")
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else :
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value_length = len(value)
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value_b = <uint8_t*> malloc(value_length * sizeof(uint8_t))
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for i in range(value_length) :
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value_b[i] = <uint8_t>value[i]
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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:
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raise Exception("Problem setting a value in a column")
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if value is not None :
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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:
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raise Exception("Problem setting a value in a column")
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free(value_b)
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cpdef set_str_line(self, index_t line_nb, object value):
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cdef bytes value_b
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if value is None :
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value_b = OBIQual_char_NA
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if obi_column_set_obiqual_char_with_elt_idx_in_view(self.view.pointer, (self.pointer)[0], line_nb, 0, OBIQual_char_NA) < 0:
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raise Exception("Problem setting a value in a column")
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else :
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||||
value_b = str2bytes(value)
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if obi_column_set_obiqual_char_with_elt_idx_in_view(self.view.pointer, (self.pointer)[0], line_nb, 0, value_b) < 0:
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raise Exception("Problem setting a value in a column")
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if obi_column_set_obiqual_char_with_elt_idx_in_view(self.view.pointer, (self.pointer)[0], line_nb, 0, str2bytes(value)) < 0:
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raise Exception("Problem setting a value in a column")
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||||
# TODO OR NOT?
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# cdef class OBIDMS_column_multi_elts_qual(OBIDMS_column_multi_elts):
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||||
#
|
||||
#
|
||||
# cpdef object get_item(self, index_t line_nb, str element_name):
|
||||
# cdef const uint8_t* value
|
||||
# cdef int value_length
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||||
# cdef object result
|
||||
# cdef int i
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||||
# value = obi_column_get_obiqual_int_with_elt_name_in_view(self.view.pointer, (self.pointer)[0], line_nb, str2bytes(element_name), &value_length)
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||||
# if obi_errno > 0 :
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||||
# raise IndexError(line_nb, element_name)
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||||
# if value == NULL: # TODO
|
||||
# result = None
|
||||
# else :
|
||||
# result = []
|
||||
# for i in range(value_length) :
|
||||
# result.append(<int>value[i])
|
||||
# return result
|
||||
#
|
||||
# # cpdef object get_str_item(self, index_t line_nb, str element_name):
|
||||
# # pass
|
||||
# # cdef char* value
|
||||
# # cdef object result
|
||||
# # 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 :
|
||||
# # raise IndexError(line_nb, element_name)
|
||||
# # if strcmp(value, OBISeq_NA) == 0 :
|
||||
# # result = None
|
||||
# # else :
|
||||
# # result = bytes2str(value)
|
||||
# # free(value)
|
||||
# # return result
|
||||
#
|
||||
# cpdef object get_line(self, index_t line_nb) :
|
||||
# pass
|
||||
# # cdef char* value
|
||||
# # cdef object value_in_result
|
||||
# # cdef dict result
|
||||
# # cdef index_t i
|
||||
# # cdef bint all_NA
|
||||
# # result = {}
|
||||
# # all_NA = True
|
||||
# # for i in range(self.nb_elements_per_line) :
|
||||
# # value = obi_column_get_obiseq_with_elt_idx_in_view(self.view.pointer, (self.pointer)[0], line_nb, i)
|
||||
# # if obi_errno > 0 :
|
||||
# # raise IndexError(line_nb)
|
||||
# # if strcmp(value, OBISeq_NA) == 0 :
|
||||
# # 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):
|
||||
# pass
|
||||
# # cdef bytes value_b
|
||||
# # if value is None :
|
||||
# # value_b = OBISeq_NA
|
||||
# # else :
|
||||
# # value_b = str2bytes(value)
|
||||
# # if obi_column_set_obiseq_with_elt_name_in_view(self.view.pointer, (self.pointer)[0], line_nb, str2bytes(element_name), value_b) < 0:
|
||||
# # raise Exception("Problem setting a value in a column")
|
||||
# #
|
||||
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
|
||||
cdef int value_length
|
||||
cdef object result
|
||||
cdef int i
|
||||
value = obi_column_get_obiqual_int_with_elt_name_in_view(self.view.pointer, (self.pointer)[0], line_nb, str2bytes(element_name), &value_length)
|
||||
if obi_errno > 0 :
|
||||
raise IndexError(line_nb, element_name)
|
||||
if value == OBIQual_int_NA :
|
||||
result = None
|
||||
else :
|
||||
result = []
|
||||
for i in range(value_length) :
|
||||
result.append(<int>value[i])
|
||||
return result
|
||||
|
||||
cpdef object get_str_item(self, index_t line_nb, str element_name):
|
||||
cdef char* value
|
||||
cdef object result
|
||||
value = obi_column_get_obiqual_char_with_elt_name_in_view(self.view.pointer, (self.pointer)[0], line_nb, str2bytes(element_name))
|
||||
if obi_errno > 0 :
|
||||
raise IndexError(line_nb, element_name)
|
||||
if value == OBIQual_char_NA :
|
||||
result = None
|
||||
else :
|
||||
result = bytes2str(value)
|
||||
free(value)
|
||||
return result
|
||||
|
||||
cpdef object get_line(self, index_t line_nb) :
|
||||
cdef const uint8_t* value
|
||||
cdef int value_length
|
||||
cdef object value_in_result
|
||||
cdef dict result
|
||||
cdef index_t i
|
||||
cdef int j
|
||||
cdef bint all_NA
|
||||
result = {}
|
||||
all_NA = True
|
||||
for i in range(self.nb_elements_per_line) :
|
||||
value = obi_column_get_obiqual_int_with_elt_idx_in_view(self.view.pointer, (self.pointer)[0], line_nb, i, &value_length)
|
||||
if obi_errno > 0 :
|
||||
raise IndexError(line_nb)
|
||||
if value == OBIQual_int_NA :
|
||||
value_in_result = None
|
||||
else :
|
||||
value_in_result = []
|
||||
for j in range(value_length) :
|
||||
value_in_result.append(<int>value[j])
|
||||
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 object get_str_line(self, index_t line_nb) :
|
||||
cdef char* value
|
||||
cdef object value_in_result
|
||||
cdef dict result
|
||||
cdef index_t i
|
||||
cdef bint all_NA
|
||||
result = {}
|
||||
all_NA = True
|
||||
for i in range(self.nb_elements_per_line) :
|
||||
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")
|
||||
|
||||
@ -13,7 +13,6 @@ from ._obidms cimport OBIView
|
||||
from obitools3.utils cimport str2bytes, bytes2str
|
||||
|
||||
from libc.stdlib cimport free
|
||||
from libc.string cimport strcmp
|
||||
|
||||
|
||||
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)
|
||||
if obi_errno > 0 :
|
||||
raise IndexError(line_nb)
|
||||
if strcmp(value, OBISeq_NA) == 0 :
|
||||
if value == OBISeq_NA :
|
||||
result = None
|
||||
else :
|
||||
result = bytes2str(value)
|
||||
@ -32,13 +31,12 @@ cdef class OBIDMS_column_seq(OBIDMS_column):
|
||||
return result
|
||||
|
||||
cpdef set_line(self, index_t line_nb, object value):
|
||||
cdef bytes value_b
|
||||
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 :
|
||||
value_b = str2bytes(value)
|
||||
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")
|
||||
if obi_column_set_obiseq_with_elt_idx_in_view(self.view.pointer, (self.pointer)[0], line_nb, 0, str2bytes(value)) < 0:
|
||||
raise Exception("Problem setting a value in a column")
|
||||
|
||||
# TODO choose alignment type (lcs or other) with supplementary argument
|
||||
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))
|
||||
if obi_errno > 0 :
|
||||
raise IndexError(line_nb, element_name)
|
||||
if strcmp(value, OBISeq_NA) == 0 :
|
||||
if value == OBISeq_NA :
|
||||
result = None
|
||||
else :
|
||||
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)
|
||||
if obi_errno > 0 :
|
||||
raise IndexError(line_nb)
|
||||
if strcmp(value, OBISeq_NA) == 0 :
|
||||
if value == OBISeq_NA :
|
||||
value_in_result = None
|
||||
else :
|
||||
value_in_result = bytes2str(value)
|
||||
|
||||
@ -9,8 +9,6 @@ from .capi.obitypes cimport OBIStr_NA, const_char_p
|
||||
|
||||
from obitools3.utils cimport str2bytes, bytes2str
|
||||
|
||||
from libc.string cimport strcmp
|
||||
|
||||
|
||||
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)
|
||||
if obi_errno > 0 :
|
||||
raise IndexError(line_nb)
|
||||
if strcmp(value, OBIStr_NA) == 0 :
|
||||
if value == OBIStr_NA :
|
||||
result = None
|
||||
else :
|
||||
result = bytes2str(value)
|
||||
@ -28,13 +26,12 @@ cdef class OBIDMS_column_str(OBIDMS_column):
|
||||
return result
|
||||
|
||||
cpdef set_line(self, index_t line_nb, object value):
|
||||
cdef bytes value_b
|
||||
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 :
|
||||
value_b = str2bytes(value)
|
||||
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")
|
||||
if obi_column_set_obistr_with_elt_idx_in_view(self.view.pointer, (self.pointer)[0], line_nb, 0, str2bytes(value)) < 0:
|
||||
raise Exception("Problem setting a value in a column")
|
||||
|
||||
|
||||
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))
|
||||
if obi_errno > 0 :
|
||||
raise IndexError(line_nb, element_name)
|
||||
if strcmp(value, OBIStr_NA) == 0 :
|
||||
if value == OBIStr_NA :
|
||||
result = None
|
||||
else :
|
||||
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)
|
||||
if obi_errno > 0 :
|
||||
raise IndexError(line_nb)
|
||||
if strcmp(value, OBIStr_NA) == 0 :
|
||||
if value == OBIStr_NA :
|
||||
value_in_result = None
|
||||
else :
|
||||
value_in_result = bytes2str(value)
|
||||
|
||||
@ -4,35 +4,35 @@ from ._obidms cimport OBIView_line
|
||||
|
||||
|
||||
cdef class OBI_Seq(dict) :
|
||||
cdef str id
|
||||
cdef str definition
|
||||
cdef str sequence
|
||||
cdef object id
|
||||
cdef object definition
|
||||
cdef object sequence
|
||||
|
||||
cpdef set_id(self, str id)
|
||||
cpdef get_id(self)
|
||||
cpdef set_definition(self, str definition)
|
||||
cpdef get_definition(self)
|
||||
cpdef get_sequence(self)
|
||||
cpdef set_id(self, object id)
|
||||
cpdef object get_id(self)
|
||||
cpdef set_definition(self, object definition)
|
||||
cpdef object get_definition(self)
|
||||
cpdef object get_sequence(self)
|
||||
|
||||
|
||||
cdef class OBI_Nuc_Seq(OBI_Seq) :
|
||||
cdef object quality
|
||||
|
||||
#cpdef str reverse_complement(self)
|
||||
cpdef set_sequence(self, str sequence)
|
||||
#cpdef object reverse_complement(self)
|
||||
cpdef set_sequence(self, object sequence)
|
||||
cpdef set_quality(self, object quality)
|
||||
cpdef get_quality(self)
|
||||
cpdef object get_quality(self)
|
||||
|
||||
|
||||
cdef class OBI_Nuc_Seq_Stored(OBIView_line) :
|
||||
cpdef set_id(self, str id)
|
||||
cpdef get_id(self)
|
||||
cpdef set_definition(self, str definition)
|
||||
cpdef get_definition(self)
|
||||
cpdef set_sequence(self, str sequence)
|
||||
cpdef get_sequence(self)
|
||||
cpdef set_id(self, object id)
|
||||
cpdef object get_id(self)
|
||||
cpdef set_definition(self, object definition)
|
||||
cpdef object get_definition(self)
|
||||
cpdef set_sequence(self, object sequence)
|
||||
cpdef object get_sequence(self)
|
||||
cpdef set_quality(self, object quality)
|
||||
cpdef get_quality(self)
|
||||
cpdef get_str_quality(self)
|
||||
cpdef object get_quality(self)
|
||||
cpdef object get_str_quality(self)
|
||||
|
||||
# cpdef str reverse_complement(self)
|
||||
# cpdef object reverse_complement(self)
|
||||
|
||||
@ -9,20 +9,20 @@ from .capi.obiview cimport NUC_SEQUENCE_COLUMN, \
|
||||
|
||||
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_sequence(seq)
|
||||
if definition is not None :
|
||||
self.set_definition(definition)
|
||||
|
||||
cpdef set_id(self, str id) :
|
||||
cpdef set_id(self, object id) :
|
||||
self.id = id
|
||||
self[bytes2str(ID_COLUMN)] = id
|
||||
|
||||
cpdef get_id(self) :
|
||||
return self.id
|
||||
|
||||
cpdef set_definition(self, str definition) :
|
||||
cpdef set_definition(self, object definition) :
|
||||
self.definition = definition
|
||||
self[bytes2str(DEFINITION_COLUMN)] = definition
|
||||
|
||||
@ -38,7 +38,7 @@ cdef class OBI_Seq(dict) :
|
||||
|
||||
cdef class OBI_Nuc_Seq(OBI_Seq) :
|
||||
|
||||
cpdef set_sequence(self, str sequence) :
|
||||
cpdef set_sequence(self, object sequence) :
|
||||
self.sequence = 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
|
||||
|
||||
cpdef set_id(self, str id) :
|
||||
cpdef set_id(self, object id) :
|
||||
self[bytes2str(ID_COLUMN)] = id
|
||||
|
||||
cpdef get_id(self) :
|
||||
cpdef object get_id(self) :
|
||||
return self[bytes2str(ID_COLUMN)]
|
||||
|
||||
cpdef set_definition(self, str definition) :
|
||||
cpdef set_definition(self, object definition) :
|
||||
self[bytes2str(DEFINITION_COLUMN)] = definition
|
||||
|
||||
cpdef get_definition(self) :
|
||||
cpdef object get_definition(self) :
|
||||
return self[bytes2str(DEFINITION_COLUMN)]
|
||||
|
||||
cpdef set_sequence(self, str sequence) :
|
||||
cpdef set_sequence(self, object sequence) :
|
||||
self[bytes2str(NUC_SEQUENCE_COLUMN)] = sequence
|
||||
|
||||
cpdef get_sequence(self) :
|
||||
cpdef object get_sequence(self) :
|
||||
return self[bytes2str(NUC_SEQUENCE_COLUMN)]
|
||||
|
||||
cpdef set_quality(self, object quality) :
|
||||
if type(quality) == list :
|
||||
if (type(quality) == list) or (quality is None) :
|
||||
self[bytes2str(QUALITY_COLUMN)] = quality
|
||||
else : # Quality is in str form
|
||||
(((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)]
|
||||
|
||||
cpdef get_str_quality(self) :
|
||||
cpdef object get_str_quality(self) :
|
||||
return ((self.view).columns)[bytes2str(QUALITY_COLUMN)].get_str_line(self.index)
|
||||
|
||||
# def __str__(self) :
|
||||
|
||||
@ -1,7 +1,8 @@
|
||||
#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
|
||||
|
||||
|
||||
@ -47,8 +48,8 @@ cdef extern from "obitypes.h" nogil:
|
||||
extern obibool_t OBIBool_NA
|
||||
extern const_char_p OBISeq_NA
|
||||
extern const_char_p OBIStr_NA
|
||||
extern const_char_p OBIQual_int_NA
|
||||
extern const_char_p OBIQual_char_NA
|
||||
extern uint8_t* OBIQual_int_NA
|
||||
|
||||
const_char_p name_data_type(int data_type)
|
||||
|
||||
|
||||
@ -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
|
||||
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
|
||||
|
||||
ctypedef Obiviews_header_t* Obiviews_header_p
|
||||
|
||||
|
||||
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,
|
||||
@ -114,10 +98,6 @@ cdef extern from "obiview.h" nogil:
|
||||
|
||||
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,
|
||||
index_t line_nb,
|
||||
|
||||
@ -25,7 +25,7 @@
|
||||
|
||||
|
||||
// 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?
|
||||
// check NUC_SEQS and score type (int or float if normalize)
|
||||
// what's with multiple sequence/line columns?
|
||||
|
||||
256
src/obiavl.c
256
src/obiavl.c
@ -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);
|
||||
|
||||
|
||||
/**
|
||||
* @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,
|
||||
* 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 -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 header_size;
|
||||
@ -646,7 +781,6 @@ int truncate_avl_to_size_used(OBIDMS_avl_p avl) // TODO is it necessary to unmap
|
||||
file_descriptor,
|
||||
(avl->header)->header_size
|
||||
);
|
||||
|
||||
if (avl->tree == MAP_FAILED)
|
||||
{
|
||||
obi_set_errno(OBI_AVL_ERROR);
|
||||
@ -930,9 +1064,10 @@ int add_new_avl_in_group(OBIDMS_avl_group_p avl_group)
|
||||
return -1;
|
||||
}
|
||||
|
||||
// Unmap the previous AVL
|
||||
if (unmap_an_avl((avl_group->sub_avls)[avl_group->last_avl_idx]) < 0)
|
||||
return -1;
|
||||
// Unmap the previous AVL if it's not the 1st
|
||||
if (avl_group->last_avl_idx > 0)
|
||||
if (unmap_an_avl((avl_group->sub_avls)[avl_group->last_avl_idx]) < 0)
|
||||
return -1;
|
||||
|
||||
// Increment current AVL index
|
||||
(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)
|
||||
{
|
||||
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_init(&((avl->header)->bloom_filter), MAX_NODE_COUNT_PER_AVL);
|
||||
|
||||
if (avl_idx >= 0)
|
||||
free(complete_avl_name);
|
||||
free(complete_avl_name);
|
||||
|
||||
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->avl_fd = avl_file_descriptor;
|
||||
|
||||
if (avl_idx >= 0)
|
||||
free(complete_avl_name);
|
||||
free(complete_avl_name);
|
||||
|
||||
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 avl_group;
|
||||
char* avl_dir_name;
|
||||
|
||||
avl_group = (OBIDMS_avl_group_p) malloc(sizeof(OBIDMS_avl_group_t));
|
||||
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;
|
||||
}
|
||||
|
||||
// Create 1st avl
|
||||
(avl_group->sub_avls)[0] = obi_create_avl(dms, avl_name, 0);
|
||||
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;
|
||||
avl_group->last_avl_idx = -1;
|
||||
avl_group->dms = dms;
|
||||
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
|
||||
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
|
||||
new_avl_group = obi_create_avl_group(avl_group->dms, new_avl_name);
|
||||
|
||||
// Copy the data from each old AVL to the new ones
|
||||
for (i=0; i<=(avl_group->last_avl_idx); i++)
|
||||
// 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++)
|
||||
{
|
||||
if (i > 0) // Don't need to create the 1st AVL
|
||||
{
|
||||
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]);
|
||||
if (add_existing_avl_in_group(new_avl_group, avl_group, i) < 0)
|
||||
return NULL;
|
||||
}
|
||||
|
||||
// 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
|
||||
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);
|
||||
|
||||
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);
|
||||
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);
|
||||
|
||||
// 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)
|
||||
ret_val = -1;
|
||||
}
|
||||
|
||||
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;
|
||||
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))
|
||||
{
|
||||
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;
|
||||
}
|
||||
}
|
||||
|
||||
for (i=0; i < (avl_group->last_avl_idx); i++)
|
||||
{
|
||||
if (maybe_in_avl((avl_group->sub_avls)[i], value))
|
||||
|
||||
@ -73,7 +73,7 @@ typedef struct AVL_node {
|
||||
* @brief OBIDMS AVL tree data header structure.
|
||||
*/
|
||||
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.
|
||||
*/
|
||||
@ -105,7 +105,7 @@ typedef struct OBIDMS_avl_data {
|
||||
* @brief OBIDMS AVL tree header structure.
|
||||
*/
|
||||
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.
|
||||
*/
|
||||
@ -160,7 +160,7 @@ typedef struct OBIDMS_avl {
|
||||
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.
|
||||
*/
|
||||
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.
|
||||
*/
|
||||
|
||||
43
src/obidms.c
43
src/obidms.c
@ -252,7 +252,7 @@ OBIDMS_p obi_create_dms(const char* dms_path)
|
||||
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);
|
||||
if (dms_dir == NULL)
|
||||
{
|
||||
@ -280,6 +280,14 @@ OBIDMS_p obi_create_dms(const char* dms_path)
|
||||
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
|
||||
j = 0;
|
||||
for (i=0; i<strlen(dms_path); i++)
|
||||
@ -447,6 +455,30 @@ OBIDMS_p obi_open_dms(const char* dms_path)
|
||||
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
|
||||
dms->opened_columns = (Opened_columns_list_p) malloc(sizeof(Opened_columns_list_t));
|
||||
(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)
|
||||
obi_close_column(*((dms->opened_columns)->columns));
|
||||
|
||||
// Close dms and indexer directories
|
||||
// Close dms, and view and indexer directories
|
||||
if (closedir(dms->directory) < 0)
|
||||
{
|
||||
obi_set_errno(OBIDMS_MEMORY_ERROR);
|
||||
@ -501,6 +533,13 @@ int obi_close_dms(OBIDMS_p dms)
|
||||
free(dms);
|
||||
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);
|
||||
}
|
||||
|
||||
|
||||
@ -30,6 +30,8 @@
|
||||
*/
|
||||
#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 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
|
||||
* 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.
|
||||
*/
|
||||
Opened_columns_list_p opened_columns; /**< List of opened columns.
|
||||
|
||||
@ -940,8 +940,6 @@ OBIDMS_column_p obi_clone_column(OBIDMS_p dms,
|
||||
size_t line_size;
|
||||
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);
|
||||
if (column_to_clone == NULL)
|
||||
{
|
||||
|
||||
@ -33,16 +33,22 @@ int obi_column_set_obiqual_char_with_elt_idx(OBIDMS_column_p column, index_t lin
|
||||
int i;
|
||||
int ret_value;
|
||||
|
||||
int_value_length = strlen(value);
|
||||
int_value = (uint8_t*) malloc(int_value_length * sizeof(uint8_t));
|
||||
// Check NA value
|
||||
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
|
||||
for (i=0; i<int_value_length; i++)
|
||||
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);
|
||||
|
||||
free(int_value);
|
||||
// Convert in uint8_t array to index in that format
|
||||
for (i=0; i<int_value_length; i++)
|
||||
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);
|
||||
free(int_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)
|
||||
return -1;
|
||||
|
||||
// Add the value in the indexer
|
||||
idx = obi_index_uint8(column->indexer, value, value_length);
|
||||
if (idx == -1) // An error occurred
|
||||
if (value == OBIQual_int_NA)
|
||||
{
|
||||
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
|
||||
new_indexer_name = obi_build_indexer_name((column->header)->name, (column->header)->version);
|
||||
if (new_indexer_name == NULL)
|
||||
return -1;
|
||||
column->indexer = obi_clone_indexer(column->indexer, new_indexer_name); // TODO Need to lock this somehow?
|
||||
// Add the value in the new indexer
|
||||
idx = obi_index_uint8(column->indexer, value, value_length);
|
||||
if (idx == -1)
|
||||
if (obi_errno == OBI_READ_ONLY_INDEXER_ERROR)
|
||||
{
|
||||
// TODO PUT IN A COLUMN FUNCTION
|
||||
// If the error is that the indexer is read-only, clone it
|
||||
new_indexer_name = obi_build_indexer_name((column->header)->name, (column->header)->version);
|
||||
if (new_indexer_name == NULL)
|
||||
return -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;
|
||||
}
|
||||
else
|
||||
return -1;
|
||||
}
|
||||
|
||||
// Add the value's index in the column
|
||||
*(((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);
|
||||
|
||||
// Check NA
|
||||
if (int_value == OBIQual_int_NA)
|
||||
return OBIQual_char_NA;
|
||||
|
||||
value = (char*) malloc((int_value_length + 1) * sizeof(char));
|
||||
|
||||
// Encode int quality to char quality
|
||||
|
||||
@ -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.
|
||||
*
|
||||
* @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
|
||||
* @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.
|
||||
*
|
||||
* @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
|
||||
* @author Celine Mercier (celine.mercier@metabarcoding.org)
|
||||
|
||||
@ -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)
|
||||
return -1;
|
||||
|
||||
// Add the value in the indexer
|
||||
idx = obi_index_dna_seq(column->indexer, value);
|
||||
if (idx == -1) // An error occurred
|
||||
if (value == OBISeq_NA)
|
||||
{
|
||||
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
|
||||
new_indexer_name = obi_build_indexer_name((column->header)->name, (column->header)->version);
|
||||
if (new_indexer_name == NULL)
|
||||
return -1;
|
||||
column->indexer = obi_clone_indexer(column->indexer, new_indexer_name); // TODO Need to lock this somehow?
|
||||
// Add the value in the new indexer
|
||||
idx = obi_index_dna_seq(column->indexer, value);
|
||||
if (idx == -1)
|
||||
if (obi_errno == OBI_READ_ONLY_INDEXER_ERROR)
|
||||
{
|
||||
// TODO PUT IN A COLUMN FUNCTION
|
||||
// If the error is that the indexer is read-only, clone it
|
||||
new_indexer_name = obi_build_indexer_name((column->header)->name, (column->header)->version);
|
||||
if (new_indexer_name == NULL)
|
||||
return -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;
|
||||
}
|
||||
else
|
||||
return -1;
|
||||
}
|
||||
|
||||
// Add the value's index in the column
|
||||
*(((index_t*) (column->data)) + (line_nb * ((column->header)->nb_elements_per_line)) + element_idx) = idx;
|
||||
|
||||
|
||||
@ -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)
|
||||
return -1;
|
||||
|
||||
// Add the value in the indexer
|
||||
idx = obi_index_char_str(column->indexer, value);
|
||||
if (idx == -1) // An error occurred
|
||||
if (value == OBIStr_NA)
|
||||
{
|
||||
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
|
||||
new_indexer_name = obi_build_indexer_name((column->header)->name, (column->header)->version);
|
||||
if (new_indexer_name == NULL)
|
||||
return -1;
|
||||
column->indexer = obi_clone_indexer(column->indexer, new_indexer_name); // TODO Need to lock this somehow?
|
||||
// Add the value in the new indexer
|
||||
idx = obi_index_char_str(column->indexer, value);
|
||||
if (idx == -1)
|
||||
if (obi_errno == OBI_READ_ONLY_INDEXER_ERROR)
|
||||
{
|
||||
// TODO PUT IN A COLUMN FUNCTION
|
||||
// If the error is that the indexer is read-only, clone it
|
||||
new_indexer_name = obi_build_indexer_name((column->header)->name, (column->header)->version);
|
||||
if (new_indexer_name == NULL)
|
||||
return -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;
|
||||
}
|
||||
else
|
||||
return -1;
|
||||
}
|
||||
|
||||
// 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;
|
||||
|
||||
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);
|
||||
|
||||
|
||||
@ -22,10 +22,10 @@
|
||||
#define OBIIdx_NA (INT64_MIN) /**< NA value for indices */
|
||||
#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 OBISeq_NA ("\0") /**< NA value for the type OBI_SEQ */ // TODO discuss
|
||||
#define OBIStr_NA ("\0") /**< 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_int_NA (NULL) /**< NA value for the type OBI_QUAL if the quality is in integer format */ // TODO test and discuss
|
||||
#define OBISeq_NA (NULL) /**< NA value for the type OBI_SEQ */ // TODO discuss
|
||||
#define OBIStr_NA (NULL) /**< NA value for the type OBI_STR */ // TODO 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 */
|
||||
|
||||
|
||||
/**
|
||||
|
||||
862
src/obiview.c
862
src/obiview.c
File diff suppressed because it is too large
Load Diff
102
src/obiview.h
102
src/obiview.h
@ -34,8 +34,6 @@
|
||||
*/
|
||||
#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
|
||||
* 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.
|
||||
*/
|
||||
@ -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.
|
||||
*/
|
||||
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.
|
||||
*/
|
||||
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;
|
||||
|
||||
|
||||
// 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);
|
||||
|
||||
|
||||
/**
|
||||
* @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.
|
||||
*
|
||||
@ -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.
|
||||
*
|
||||
* @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
|
||||
* @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.
|
||||
*
|
||||
* @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
|
||||
* @author Celine Mercier (celine.mercier@metabarcoding.org)
|
||||
|
||||
Reference in New Issue
Block a user