Commit 8f9f2a2d by Celine Mercier

obi ls: various improvements

parent 045a751b
......@@ -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))
#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, \
obi_read_taxdump, \
......@@ -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) :
......@@ -36,7 +38,25 @@ cdef class Taxonomy(OBIWrapper) :
% tostr(name))
else:
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) :
......
......@@ -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'
......
......@@ -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;
......
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