Cython API: added a Column subclass to allow direct access to indexes

for columns that store indexes referring to other data

python/obitools3/dms/column/column_idx.pxd

@@ -0,0 +1,21 @@
+# #cython: language_level=3
+ 
+
+from ..capi.obitypes cimport index_t
+
+from .column cimport Column, \
+                      Column_multi_elts
+
+
+cdef class Column_idx(Column) :
+
+    cpdef object get_line_idx(self, index_t line_nb)
+    cpdef set_line_idx(self, index_t line_nb, object value)
+
+
+cdef class Column_multi_elts_idx(Column_multi_elts) :
+
+    cpdef object get_item_idx(self, index_t line_nb, object elt_id)
+    cpdef object get_line_idx(self, index_t line_nb)
+    cpdef set_item_idx(self, index_t line_nb, object elt_id, object value)
+    cpdef set_line_idx(self, index_t line_nb, object values)

python/obitools3/dms/column/column_idx.pyx

@@ -0,0 +1,114 @@
+#cython: language_level=3
+
+from obitools3.dms.capi.obierrno cimport obi_errno
+
+from ..view.view cimport View
+
+from obitools3.utils cimport tobytes, \
+                             obi_errno_to_exception
+
+from ..capi.obiview cimport obi_get_index_with_elt_name_and_col_p_in_view, \
+                             obi_get_index_with_elt_idx_and_col_p_in_view, \
+                             obi_set_index_with_elt_name_and_col_p_in_view, \
+                             obi_set_index_with_elt_idx_and_col_p_in_view, \
+                             Obiview_p
+
+from ..capi.obidmscolumn cimport OBIDMS_column_p
+
+from ..capi.obitypes     cimport OBI_IDX, OBIIdx_NA, index_t
+
+from cpython.long cimport PyLong_FromLongLong
+
+
+# TODO overwrite other functions from Column and Column_multi_elts
+
+
+cdef class Column_idx(Column):
+
+    cpdef object get_line_idx(self, index_t line_nb):
+        global obi_errno
+        cdef   index_t value
+        cdef   object  result 
+        value = obi_get_index_with_elt_idx_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, 0)
+        obi_errno_to_exception(obi_errno, line_nb=line_nb, elt_id=None, error_message="Problem getting a value from a column")
+        if value == OBIIdx_NA :
+            result = None
+        else :
+            result = PyLong_FromLongLong(value)
+        return result
+
+    cpdef set_line_idx(self, index_t line_nb, object value):
+        global obi_errno
+        if value is None :
+            value = OBIIdx_NA
+        if obi_set_index_with_elt_idx_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, 0, <index_t> value) < 0:
+            obi_errno_to_exception(obi_errno, line_nb=line_nb, elt_id=None, error_message="Problem setting a value in a column")
+ 
+ 
+cdef class Column_multi_elts_idx(Column_multi_elts):
+ 
+    cpdef object get_item_idx(self, index_t line_nb, object elt_id) :
+        global obi_errno
+        cdef   int       value
+        cdef   object    result
+        cdef   bytes     elt_name
+        if type(elt_id) == int :
+            value = obi_get_index_with_elt_idx_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, elt_id)
+        else :
+            elt_name = tobytes(elt_id)
+            value = obi_get_index_with_elt_name_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, elt_name)
+        obi_errno_to_exception(obi_errno, line_nb=line_nb, elt_id=elt_id, error_message="Problem getting a value from a column")
+        if value == OBIIdx_NA :
+            result = None
+        else :
+            result = PyLong_FromLongLong(value)
+        return result
+    
+    cpdef object get_line_idx(self, index_t line_nb) :
+        global obi_errno
+        cdef   index_t         value
+        cdef   int             value_in_result
+        cdef   dict            result
+        cdef   index_t         i
+        cdef   bint            all_NA
+        cdef   list            elements_names
+        cdef   Obiview_p       view_p
+        cdef   OBIDMS_column_p column_p
+        result = {}
+        all_NA = True
+        view_p = self._view.pointer()
+        column_p = self.pointer()
+        elements_names = self.elements_names
+        for i in range(self.nb_elements_per_line) :
+            value = obi_get_index_with_elt_idx_and_col_p_in_view(view_p, column_p, line_nb, i)
+            obi_errno_to_exception(obi_errno, line_nb=line_nb, elt_id=i, error_message="Problem getting a value from a column")
+            if value != OBIIdx_NA :
+                value_in_result = PyLong_FromLongLong(value)
+                result[elements_names[i]] = value_in_result
+                if all_NA :
+                    all_NA = False
+        if all_NA :
+            result = None
+        return result
+    
+    cpdef set_item_idx(self, index_t line_nb, object elt_id, object value) :
+        global obi_errno
+        cdef   bytes elt_name
+        if value is None :
+            value = OBIIdx_NA
+        if type(elt_id) == int :
+            if obi_set_index_with_elt_idx_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, elt_id, <index_t> value) < 0 :
+                obi_errno_to_exception(obi_errno, line_nb=line_nb, elt_id=elt_id, error_message="Problem setting a value in a column")
+        else :
+            elt_name = tobytes(elt_id)
+            if obi_set_index_with_elt_name_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, elt_name, <index_t> value) < 0 :
+                obi_errno_to_exception(obi_errno, line_nb=line_nb, elt_id=elt_id, error_message="Problem setting a value in a column")
+
+    cpdef set_line_idx(self, index_t line_nb, object values):
+        if values is None :
+            for element_name in self.elements_names :
+                self.set_item_idx(line_nb, element_name, None)
+        else :
+            for element_name in values :
+                self.set_item_idx(line_nb, element_name, values[element_name])
+

python/obitools3/dms/column/typed_column/seq.pxd

@@ -3,17 +3,17 @@
 
 from ...capi.obitypes cimport index_t
 
-from ..column cimport Column, \
+from ..column_idx cimport Column_idx, \
-                      Column_multi_elts
+                          Column_multi_elts_idx
 
 
-cdef class Column_seq(Column) :
+cdef class Column_seq(Column_idx) :
 
     cpdef object get_line(self, index_t line_nb)
     cpdef set_line(self, index_t line_nb, object value)
 
 
-cdef class Column_multi_elts_seq(Column_multi_elts) :
+cdef class Column_multi_elts_seq(Column_multi_elts_idx) :
 
     cpdef object get_item(self, index_t line_nb, object elt_id)
     cpdef object get_line(self, index_t line_nb)

python/obitools3/dms/column/typed_column/seq.pyx

@@ -6,6 +6,8 @@ from ..column cimport register_column_class
 
 from ...view.view cimport View
 
+from ..column cimport Column
+
 from obitools3.utils cimport tobytes, \
                              obi_errno_to_exception
 
@@ -22,7 +24,7 @@ from ...capi.obitypes     cimport OBI_SEQ, OBISeq_NA
 from libc.stdlib cimport free
 
 
-cdef class Column_seq(Column):
+cdef class Column_seq(Column_idx):
 
     @staticmethod
     def new(View    view,
@@ -68,7 +70,7 @@ cdef class Column_seq(Column):
             obi_errno_to_exception(obi_errno, line_nb=line_nb, elt_id=None, error_message="Problem setting a value in a column")
  
  
-cdef class Column_multi_elts_seq(Column_multi_elts):
+cdef class Column_multi_elts_seq(Column_multi_elts_idx):
  
     cpdef object get_item(self, index_t line_nb, object elt_id) :
         global obi_errno

python/obitools3/dms/column/typed_column/str.pxd

@@ -3,17 +3,17 @@
 
 from ...capi.obitypes cimport index_t
 
-from ..column cimport Column, \
+from ..column_idx cimport Column_idx, \
-                      Column_multi_elts
+                          Column_multi_elts_idx
 
 
-cdef class Column_str(Column) :
+cdef class Column_str(Column_idx) :
 
     cpdef object get_line(self, index_t line_nb)
     cpdef set_line(self, index_t line_nb, object value)
 
 
-cdef class Column_multi_elts_str(Column_multi_elts) :
+cdef class Column_multi_elts_str(Column_multi_elts_idx) :
 
     cpdef object get_item(self, index_t line_nb, object elt_id)
     cpdef object get_line(self, index_t line_nb)

python/obitools3/dms/column/typed_column/str.pyx

@@ -6,6 +6,8 @@ from ..column cimport register_column_class
 
 from ...view.view cimport View
 
+from ..column cimport Column
+
 from obitools3.utils cimport tobytes, \
                              obi_errno_to_exception
 
@@ -20,7 +22,7 @@ from ...capi.obidmscolumn cimport OBIDMS_column_p
 from ...capi.obitypes     cimport OBI_STR, OBIStr_NA, const_char_p
 
 
-cdef class Column_str(Column):
+cdef class Column_str(Column_idx):
 
     @staticmethod
     def new(View    view,
@@ -63,7 +65,7 @@ cdef class Column_str(Column):
             obi_errno_to_exception(obi_errno, line_nb=line_nb, elt_id=None, error_message="Problem setting a value in a column")
  
  
-cdef class Column_multi_elts_str(Column_multi_elts):
+cdef class Column_multi_elts_str(Column_multi_elts_idx):
  
     cpdef object get_item(self, index_t line_nb, object elt_id) :
         global obi_errno