Cython: Columns: added support for JSON formatted comments

python/obitools3/dms/column/column.pxd

@@ -29,6 +29,9 @@ cdef class Column(OBIWrapper) :
     @staticmethod
     cdef type get_python_type(obitype_t obitype, bint multi_elts)
 
+cdef class Column_comments(dict):
+    cdef Column  _column
+
 
 cdef class Column_multi_elts(Column) :
 

python/obitools3/dms/column/column.pyx

@@ -13,7 +13,8 @@ from ..capi.obidms cimport obi_import_column
 
 from ..capi.obidmscolumn cimport OBIDMS_column_header_p, \
                                  obi_close_column, \
-                                 obi_get_elements_names
+                                 obi_get_elements_names, \
+                                 obi_column_write_comments
                                      
 from ..capi.obiutils cimport obi_format_date
  
@@ -26,7 +27,10 @@ from ..object cimport OBIDeactivatedInstanceError
 
 from obitools3.utils cimport tobytes, \
                              bytes2str, \
-                             str2bytes
+                             str2bytes, \
+                             str2bytes_object, \
+                             bytes2str_object, \
+                             clean_empty_values_from_object
  
 from obitools3.dms.column import typed_column
  
@@ -35,6 +39,8 @@ from libc.stdlib  cimport free
 import importlib
 import inspect
 import pkgutil
+import json
+
 
 cdef class Column(OBIWrapper) :
     '''
@@ -82,13 +88,13 @@ cdef class Column(OBIWrapper) :
                    bint      to_eval=False,
                    object    associated_column_name=b"",
                    int       associated_column_version=-1,
-                   object    comments=b"",
+                   object    comments={},
                    object    alias=b""):
         # TODO indexer_name?
         
         cdef bytes  column_name_b = tobytes(column_name)
         cdef bytes  alias_b = tobytes(alias)
-        cdef bytes  comments_b = tobytes(comments)
+        cdef bytes  comments_b = str2bytes(json.dumps(bytes2str_object(comments)))
         cdef bytes  associated_column_name_b = tobytes(associated_column_name)
         cdef list   elements_names_s
         cdef bytes  elements_names_b
@@ -373,13 +379,6 @@ cdef class Column(OBIWrapper) :
             raise OBIDeactivatedInstanceError()
         return self.pointer().header.to_eval
 
-    # comments property getter
-    @property
-    def comments(self):
-        if not self.active() :
-            raise OBIDeactivatedInstanceError()
-        return self.pointer().header.comments
-     
     # creation_date property getter
     @property
     def creation_date(self):
@@ -387,6 +386,96 @@ cdef class Column(OBIWrapper) :
             raise OBIDeactivatedInstanceError()
         return obi_format_date(self.pointer().header.creation_date)
 
+    # comments property getter
+    @property
+    def comments(self):
+        return Column_comments(self)
+    @comments.setter
+    def comments(self, object value):
+        Column_comments(self, value)
+
+          
+cdef class Column_comments(dict):   # Not thread safe
+    def __init__(self, Column column, value=None) :
+        if not column.active() :
+            raise OBIDeactivatedInstanceError()
+        self._column = column
+        if value is not None:
+            self.update(value)     # TODO test and discuss not overwriting (could use replace bool)
+        self._update_from_file()
+
+    def _update_from_file(self):
+        cdef bytes comments_json
+        cdef str comments_json_str
+        cdef OBIDMS_column_p column_p
+        cdef Column column
+        if not self._column.active() :
+            raise OBIDeactivatedInstanceError()
+        column = self._column
+        column_p = <OBIDMS_column_p>(column.pointer())
+        comments_json = <bytes> column_p.header.comments
+        comments_json_str = bytes2str(comments_json)
+        comments_dict = json.loads(comments_json_str)
+        str2bytes_object(comments_dict)
+        super(Column_comments, self).update(comments_dict)
+        
+    def __getitem__(self, object key):
+        if not self._column.active() :
+            raise OBIDeactivatedInstanceError()
+        if type(key) == str:
+            key = str2bytes(key)
+        self._update_from_file()
+        return super(Column_comments, self).__getitem__(key)
+
+    def __setitem__(self, object key, object value):
+        cdef OBIDMS_column_p column_p
+        cdef Column column
+
+        if not self._column.active() :
+            raise OBIDeactivatedInstanceError()
+
+        column = self._column
+        column_p = <OBIDMS_column_p>(column.pointer())
+        
+        # Remove virtually empty values from the object    # TODO discuss
+        clean_empty_values_from_object(value)
+        
+        # If value is virtually empty, don't add it    # TODO discuss
+        if value is None or len(value) == 0:
+            return
+        
+        # Convert to bytes
+        if type(key) == str:
+            key = str2bytes(key)
+        value_bytes = str2bytes_object(value)
+
+        # Update dict with comments already written in file
+        self._update_from_file()
+           
+        # Add new element  # TODO don't overwrite?
+        super(Column_comments, self).__setitem__(key, value_bytes)
+        
+        # Convert to str because json library doens't like bytes
+        dict_str = {key:item for key,item in self.items()}
+        dict_str = bytes2str_object(dict_str)
+        
+        # Convert to json string
+        comments_json = json.dumps(dict_str)        
+
+        # Write new comments
+        if obi_column_write_comments(column_p, tobytes(comments_json)) < 0:
+            raise Exception("Could not write column comments: %s", comments_json)
+
+    def update(self, value):
+        for k,v in value.items():
+            self[k] = v
+
+    def __contains__(self, key):
+        return super(Column_comments, self).__contains__(tobytes(key))
+
+    def __str__(self):
+        return bytes2str(self._column.pointer().header.comments)
+
 
 ######################################################################################################
  

python/obitools3/dms/dms.cfiles

@@ -18,6 +18,8 @@
 ../../../src/libecoPCR/ecodna.c
 ../../../src/libecoPCR/ecoError.c
 ../../../src/libecoPCR/ecoMalloc.c
+../../../src/libjson/cJSON.c
+../../../src/libjson/json_utils.c
 ../../../src/obiavl.c
 ../../../src/obiblob_indexer.c
 ../../../src/obiblob.c

python/obitools3/utils.cfiles

@@ -18,6 +18,8 @@
 ../../src/libecoPCR/ecodna.c
 ../../src/libecoPCR/ecoError.c
 ../../src/libecoPCR/ecoMalloc.c
+../../src/libjson/cJSON.c
+../../src/libjson/json_utils.c
 ../../src/obiavl.c
 ../../src/obiblob_indexer.c
 ../../src/obiblob.c