Add the possibility to create temporary objects like a temporary

directory and a temporary DMS

python/obi.py

@@ -41,7 +41,8 @@ default_config = { 'software'       : "The OBITools",
                    "nastring"       : b"NA",
                    "stripwhite"     : True,
                    "blanklineskip"  : True,
-                   "commentchar"    : b"#"
+                   "commentchar"    : b"#",
+                   "nocreatedms"    : False
                   }
 
 root_config_name='obi'

python/obitools3/apps/optiongroups/__init__.py

@@ -169,5 +169,13 @@ def __addOutputOption(optionManager):
                     metavar='OUTPUT', 
                     help='Data destination URI')
     
+    group = optionManager.add_argument_group("Management of DMS for output")
+
+    group.add_argument('--no-create-dms',
+                 action="store_true", dest="obi:nocreatedms",
+                 default=False,
+                 help="Don't create an output DMS is it is not existing")
+
+
 def addMinimalOutputOption(optionManager):
     __addOutputOption(optionManager)

python/obitools3/apps/temp.pxd

@@ -0,0 +1,10 @@
+#cython: language_level=3
+
+'''
+Created on 28 juillet 2017
+
+@author: coissac
+'''
+
+from obitools3.dms.dms cimport DMS
+from obitools3.utils cimport tobytes,tostr

python/obitools3/apps/temp.pyx

@@ -0,0 +1,96 @@
+#cython: language_level=3
+
+'''
+Created on 28 juillet 2017
+
+@author: coissac
+'''
+
+from os import environb,getpid
+from os.path import join, isdir
+from tempfile import TemporaryDirectory, _get_candidate_names
+from shutil import rmtree
+from atexit import register
+
+from obitools3.dms.dms import DMS
+
+from obitools3.apps.config import getConfiguration
+from obitools3.apps.config import logger
+
+cpdef get_temp_dir():
+    """
+    Returns a temporary directory object specific of this instance of obitools.
+    
+    This is an application function. It cannot be called out of an obi command.
+    It requires a valid configuration.
+    
+    If the function is called several time from the same obi session, the same
+    directory is returned.
+    
+    If the OBITMP environment variable exist, the temporary directory is created
+    inside this directory.
+    
+    The directory is automatically destroyed at the end of the end of the process.
+    
+        @return: a temporary python directory object.
+    """
+    cdef bytes tmpdirname
+    cdef dict config = getConfiguration()
+
+    root = config["__root_config__"]
+    
+    try:
+        return config[root]["tempdir"].name
+    except KeyError:
+        pass
+    
+    try:
+        basedir=environb[b'OBITMP']
+    except KeyError:
+        basedir=None
+    
+    tmp = TemporaryDirectory(dir=basedir)
+        
+    config[root]["tempdir"]=tmp
+    
+    return tmp.name
+ 
+cpdef get_temp_dir_name():
+    """
+    Returns the name of the  temporary directory object 
+    specific of this instance of obitools.
+    
+        @return: the name of the temporary directory.
+        
+        @see get_temp_dir
+    """
+    return get_temp_dir_name().name
+          
+               
+cpdef get_temp_dms():
+
+    cdef bytes tmpdirname                   # @DuplicatedSignature
+    cdef dict config = getConfiguration()   # @DuplicatedSignature
+    cdef DMS tmpdms
+    
+    root = config["__root_config__"]
+    
+    try:
+        return config[root]["tempdms"]
+    except KeyError:
+        pass
+
+    tmpdirname=get_temp_dir()
+        
+    tempname = join(tmpdirname,
+                    b"obi.%d.%s" % (getpid(),
+                                    tobytes(next(_get_candidate_names())))
+                   )
+        
+    tmpdms = DMS.new(tempname)
+    
+    config[root]["tempdms"]=tmpdms
+    
+    return tmpdms
+    
+    

python/obitools3/commands/import.pyx

@@ -13,6 +13,8 @@ from obitools3.dms.view.view cimport View
 from obitools3.dms.view.typed_view.view_NUC_SEQS import View_NUC_SEQS    # TODO cimport doesn't work
 from obitools3.dms.column.column cimport Column
 
+from obitools3.dms.obiseq import Nuc_Seq
+
 from obitools3.utils cimport tobytes, \
                              get_obitype, \
                              update_obitype
@@ -25,6 +27,8 @@ from obitools3.dms.capi.obierrno cimport obi_errno
 from obitools3.apps.optiongroups import addSequenceInputOption, addMinimalOutputOption
 from obitools3.uri.decode import open_uri
 
+from obitools3.apps.config import logger
+
 __title__="Imports sequences from different formats into a DMS"
  
  
@@ -78,14 +82,23 @@ def run(config):
     global             obi_errno
         
     
-    logger=config['obi']['logger']
-    
-    
-    logger.info("obi import : imports file into an DMS")
+    logger("info","obi import : imports file into an DMS")
     
     inputs = open_uri(config['obi']['inputURI'])
     
-    print(inputs)
+    if inputs[2]==Nuc_Seq:
+        v = View_NUC_SEQS
+    else:
+        v= View 
+        
+    print(v)
+    
+    output = open_uri(config['obi']['outputURI'],
+                      input=False,
+                      newviewtype=v)
+    
+    print(input)
+    print(output)
         
     sys.exit()
     

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, 
@@ -170,16 +186,23 @@ 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)