obi ls: various improvements

python/obitools3/commands/ls.pyx

@@ -3,7 +3,9 @@
 from obitools3.uri.decode import open_uri
 from obitools3.apps.config import logger
 from obitools3.dms import DMS
+from obitools3.dms.taxo.taxo cimport Taxonomy
 from obitools3.apps.optiongroups import addMinimalInputOption
+from obitools3.utils cimport tostr
 
  
 __title__="Print a preview of a DMS, view, column...."
@@ -11,6 +13,12 @@ __title__="Print a preview of a DMS, view, column...."
 
 def addOptions(parser):    
     addMinimalInputOption(parser)
+    group = parser.add_argument_group('obi ls specific options')
+
+    group.add_argument('-l',
+                     action="store_true", dest="ls:longformat",
+                     default=False,
+                     help="Detailed list in long format with all metadata.")
 
 
 def run(config):
@@ -23,6 +31,21 @@ def run(config):
     input = open_uri(config['obi']['inputURI'])
     if input is None:
         raise Exception("Could not read input")
-    
-    print(repr(input[1]))
+    if input[2] == DMS and not config['ls']['longformat']:
+        dms = input[0]
+        l = []
+        for view in input[0]:
+            l.append(tostr(view) + "\t(Date created: " + tostr(dms[view].comments["Date created"])+")")
+        l.sort()
+        for v in l:
+            print(v)
+    else:
+        print(repr(input[1]))
+    if input[2] == DMS:
+        print("\n### Taxonomies:")
+        for t in Taxonomy.list_taxos(input[0]):
+            print("\t", tostr(t))
+    if config['ls']['longformat'] and len(input[1].comments) > 0:
+        print("\n### Comments:")
+        print(str(input[1].comments))
      

python/obitools3/dms/taxo/taxo.pyx

@@ -1,6 +1,7 @@
 #cython: language_level=3
 
 from obitools3.utils cimport str2bytes, bytes2str, tobytes, tostr
+from ..capi.obidms cimport OBIDMS_p, obi_dms_get_full_path
                           
 from ..capi.obitaxonomy cimport obi_taxonomy_exists, \
                                 obi_read_taxonomy, \
@@ -17,8 +18,9 @@ from ..capi.obitaxonomy cimport obi_taxonomy_exists, \
                                 ecotx_t                
                                            
 from cpython.pycapsule cimport PyCapsule_New, PyCapsule_GetPointer
-
 import tarfile
+from pathlib import Path
+from libc.stdlib  cimport free
 
 
 cdef class Taxonomy(OBIWrapper) :
@@ -38,6 +40,24 @@ cdef class Taxonomy(OBIWrapper) :
             return e
     
     
+    @staticmethod
+    def list_taxos(DMS dms):
+        
+        cdef OBIDMS_p dms_p
+        cdef const char* path
+        
+        dms_p = dms.pointer()
+        path = obi_dms_get_full_path(dms_p, b"TAXONOMY")
+        if path == NULL:
+            raise RuntimeError("Cannot retrieve the taxonomy directory path")
+        
+        p = Path(bytes2str(path))
+        free(path)
+        
+        for tax in p.glob("*") :
+            yield str2bytes(tax.stem)
+
+
     @staticmethod
     def open(DMS dms, object name) :
         

python/obitools3/dms/view/view.pyx

@@ -177,8 +177,7 @@ cdef class View(OBIWrapper) :
     
     @OBIWrapper.checkIsActive
     def __repr__(self) :         
-        cdef str s = "#View name:\n{name:s}\n#Comments:\n{comments:s}\n#Line count:\n{line_count:d}\n#Columns:\n".format(name       = bytes2str(self.name),
-                                                                                                                         comments   = str(self.comments),
+        cdef str s = "#View name:\n{name:s}\n#Line count:\n{line_count:d}\n#Columns:\n".format(name       = bytes2str(self.name),
                                                                                                                          line_count = self.line_count)
         for column_name in self.keys() :
             s = s + repr(self[column_name]) + '\n'

src/obiview.c

@@ -1096,6 +1096,16 @@ static int finish_view(Obiview_p view)
      		 (column->header)->finished = true;
 	 }
 
+	 // Add the time in the view comments
+	 time_t t;
+	 t = time(&t);
+	 if (obi_view_add_comment(view, "Date created", strtok(ctime(&t), "\n")) < 0)
+	 {
+		obi_set_errno(OBIVIEW_ERROR);
+		obidebug(1, "\nError adding the date of creation when finishing a view");
+		return -1;
+	}
+
 	// Flag the view as finished
 	(view->infos)->finished = true;