Add the possibility to create temporary objects like a temporary

directory and a temporary DMS

python/obitools3/uri/decode.pxd

@@ -8,3 +8,4 @@ from obitools3.dms.taxo.taxo cimport Taxonomy
 from obitools3.utils cimport tobytes, tostr
 from obitools3.files.universalopener cimport uopen
 
+cdef open_dms(bytes path, bint create=?)

python/obitools3/uri/decode.pyx

@@ -11,11 +11,12 @@ from obitools3.parsers.universal import entryIteratorFactory
 
 from obitools3.dms.obiseq import Nuc_Seq
 from obitools3.apps.config import getConfiguration,logger
+from obitools3.apps.temp import get_temp_dms
 
 class MalformedURIException(RuntimeError):
     pass
 
-cdef open_dms(bytes path,create=False):
+cdef open_dms(bytes path, bint create=False):
     """
     Opens a DMS from the path part of an URI
     """
@@ -50,13 +51,15 @@ cdef open_dms(bytes path,create=False):
         pos=pos+1
     return None
 
-def open_dms_element(DMS dms, bytes path):
+def open_dms_element(DMS dms, bytes path, 
+                     bint create=False,
+                     type newviewtype=View):
     """
     """
     cdef list path_parts = path.split(b'/')
-    
+
     # The URI is only composed of a DMS
-    if not path_parts:
+    if not path:
         return (dms,dms)
     
     # The URI is target a taxonomy
@@ -74,7 +77,10 @@ def open_dms_element(DMS dms, bytes path):
     # The URI is target a view
     # dms:dmspath/viewname[/columnname|#line|*[/#line|columnname|*[/subcolumn]]]
     
-    view = View.open(dms,path_parts[0])
+    if create:
+        view = newviewtype.new(dms,path_parts[0])
+    else:
+        view = newviewtype.open(dms,path_parts[0])
     
     if len(path_parts) > 1:
         if path_parts[1]==b'*':
@@ -128,7 +134,9 @@ def open_dms_element(DMS dms, bytes path):
     return (dms,subsubpart)
                          
 
-def open_uri(uri,bint input=True):
+def open_uri(uri,
+             bint input=True,
+             type newviewtype=View):
     cdef bytes urib = tobytes(uri)
     cdef bytes scheme
     cdef tuple dms
@@ -146,19 +154,27 @@ def open_uri(uri,bint input=True):
     except KeyError:
         default_dms=None
         
+    try:
+        create=(not input) and (not config["obi"]["nocreatedms"])
+    except KeyError:
+        create=not input
+        
     scheme = urip.scheme
 
     error = None
     
-    if scheme==b"" :
-        dms = open_dms(urip.path)
+    if scheme==b"" or scheme==b"dms" :
+        dms = open_dms(urip.path,create)
         if dms is None and default_dms is not None:
             dms=(default_dms,urip.path)
            
         
         if dms is not None:
             try:
-                resource=open_dms_element(*dms)
+                resource=open_dms_element(dms[0],dms[1],
+                                          create,
+                                          newviewtype
+                                          )
                 scheme=b"dms"
                 urip = ParseResultBytes(scheme=b"dms", 
                                         netloc=urip.netloc, 
@@ -169,17 +185,24 @@ def open_uri(uri,bint input=True):
                 
                 if default_dms is None:
                     config["obi"]["defaultdms"]=resource[0]
-                    
-                return (resource[0],resource[1],urlunparse(urip))
+                 
+                return (resource[0],
+                        resource[1],
+                        type(resource[1]),
+                        urlunparse(urip))
             except Exception as e:
                 error=e
+                
+    if scheme==b"dms" :
+        logger('error','cannot open DMS: %s', uri)
+        raise FileNotFoundError('uri')
            
     if not urip.scheme:
         urib=b"file:"+urib
     
     try:
-        logger('info','Trying to open file : %s', tostr(urib))
         file = uopen(tostr(urib))
+        logger('info','Opened file : %s', tostr(urib))
     except Exception as e:
         file = None
         error=e 
@@ -366,7 +389,10 @@ def open_uri(uri,bint input=True):
                                           blanklineskip,
                                           commentchar)
             
-        return (file,iseq,objclass)
+        
+        tmpdms = get_temp_dms()
+            
+        return (file,iseq,objclass,urib)