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obi ls: now done in C (preparing things for R packages to read DMS) and

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switch to version 3.0.0b36
This commit is contained in:
Celine Mercier
2020-09-29 17:51:39 +02:00
parent b6648ae81e
commit 137c109f86
14 changed files with 460 additions and 59 deletions
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24
python/obitools3/commands/ls.pyx
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@ -31,27 +31,11 @@ def run(config):
input = open_uri(config['obi']['inputURI'])
if input is None:
raise Exception("Could not read input")
if input[2] == DMS and not config['ls']['longformat']:
dms = input[0]
l = []
for viewname in input[0]:
view = dms[viewname]
l.append(tostr(viewname) + "\t(Date created: " + str(bytes2str_object(view.comments["Date created"]))+")")
view.close()
l.sort()
for v in l:
print(v)
# Print representation
if config['ls']['longformat']:
print(input[1].repr_longformat())
else:
print(repr(input[1]))
if input[2] == DMS:
taxolist = ["\n### Taxonomies:"]
for t in Taxonomy.list_taxos(input[0]):
taxolist.append("\t"+tostr(t))
if len(taxolist) > 1:
for t in taxolist:
print(t)
if config['ls']['longformat'] and len(input[1].comments) > 0:
print("\n### Comments:")
print(str(input[1].comments))
input[0].close(force=True)

1
python/obitools3/dms/capi/obidms.pxd
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@ -34,6 +34,7 @@ cdef extern from "obidms.h" nogil:
int obi_close_dms(OBIDMS_p dms, bint force)
char* obi_dms_get_dms_path(OBIDMS_p dms)
char* obi_dms_get_full_path(OBIDMS_p dms, const_char_p path_name)
char* obi_dms_formatted_infos(OBIDMS_p dms, bint detailed)
void obi_close_atexit()
obiversion_t obi_import_column(const char* dms_path_1, const char* dms_path_2, const char* column_name, obiversion_t version_number)

3
python/obitools3/dms/capi/obidmscolumn.pxd
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@ -70,3 +70,6 @@ cdef extern from "obidmscolumn.h" nogil:
int obi_column_write_comments(OBIDMS_column_p column, const char* comments)
int obi_column_add_comment(OBIDMS_column_p column, const char* key, const char* value)
char* obi_column_formatted_infos(OBIDMS_column_p column, bint detailed)

8
python/obitools3/dms/capi/obiview.pxd
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@ -103,13 +103,17 @@ cdef extern from "obiview.h" nogil:
bint create)
int obi_view_delete_column(Obiview_p view, const_char_p column_name, bint delete_file)
OBIDMS_column_p obi_view_get_column(Obiview_p view, const_char_p column_name)
OBIDMS_column_p* obi_view_get_pointer_on_column_in_view(Obiview_p view, const_char_p column_name)
int obi_view_create_column_alias(Obiview_p view, const_char_p current_name, const_char_p alias)
char* obi_view_formatted_infos(Obiview_p view, bint detailed)
char* obi_view_formatted_infos_one_line(Obiview_p view)
int obi_view_write_comments(Obiview_p view, const_char_p comments)
int obi_view_add_comment(Obiview_p view, const_char_p key, const_char_p value)

27
python/obitools3/dms/column/column.pyx
View File

@ -302,15 +302,24 @@ cdef class Column(OBIWrapper) :
@OBIWrapper.checkIsActive
def __repr__(self) :
cdef bytes s
#cdef char* s_b
#cdef str s_str
#s_b = obi_column_formatted_infos(self.pointer())
#s_str = bytes2str(s_b)
#free(s_b)
s = self._alias + b", data type: " + self.data_type
#return s_str
return bytes2str(s)
cdef str s
cdef char* sc
cdef OBIDMS_column_p pointer = self.pointer()
sc = obi_column_formatted_infos(pointer, False)
s = bytes2str(sc)
free(sc)
return s
@OBIWrapper.checkIsActive
def repr_longformat(self) :
cdef str s
cdef char* sc
cdef OBIDMS_column_p pointer = self.pointer()
sc = obi_column_formatted_infos(pointer, True)
s = bytes2str(sc)
free(sc)
return s
def close(self): # TODO discuss, can't be called bc then bug when closing view that tries to close it in C

30
python/obitools3/dms/dms.pyx
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@ -10,7 +10,8 @@ from .capi.obidms cimport obi_open_dms, \
obi_dms_exists, \
obi_dms_get_full_path, \
obi_close_atexit, \
obi_dms_write_comments
obi_dms_write_comments, \
obi_dms_formatted_infos
from .capi.obitypes cimport const_char_p
@ -32,6 +33,8 @@ from .object import OBIWrapper
import json
import time
from libc.stdlib cimport free
cdef class DMS(OBIWrapper):
@ -223,13 +226,24 @@ cdef class DMS(OBIWrapper):
@OBIWrapper.checkIsActive
def __repr__(self):
cdef str s
s=""
for view_name in self.keys():
view = self.get_view(view_name)
s = s + repr(view) + "\n"
view.close()
def __repr__(self) :
cdef str s
cdef char* sc
cdef OBIDMS_p pointer = self.pointer()
sc = obi_dms_formatted_infos(pointer, False)
s = bytes2str(sc)
free(sc)
return s
@OBIWrapper.checkIsActive
def repr_longformat(self) :
cdef str s
cdef char* sc
cdef OBIDMS_p pointer = self.pointer()
sc = obi_dms_formatted_infos(pointer, True)
s = bytes2str(sc)
free(sc)
return s

31
python/obitools3/dms/view/view.pyx
View File

@ -19,7 +19,9 @@ from ..capi.obiview cimport Alias_column_pair_p, \
obi_view_delete_column, \
obi_view_create_column_alias, \
obi_view_write_comments, \
obi_delete_view
obi_delete_view, \
obi_view_formatted_infos, \
obi_view_formatted_infos_one_line
from ..capi.obidmscolumn cimport OBIDMS_column_p
from ..capi.obidms cimport OBIDMS_p
@ -59,6 +61,8 @@ import pkgutil
import json
import sys
from libc.stdlib cimport free
cdef class View(OBIWrapper) :
@ -186,15 +190,22 @@ cdef class View(OBIWrapper) :
@OBIWrapper.checkIsActive
def __repr__(self) :
cdef str s
if self.read_only: # can read date
s = "#View name:\n{name:s}\n#Date created:\n{date:s}\n#Line count:\n{line_count:d}\n#Columns:\n".format(name = bytes2str(self.name),
line_count = self.line_count,
date = str(bytes2str_object(self.comments["Date created"])))
else:
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'
cdef char* sc
cdef Obiview_p pointer = self.pointer()
sc = obi_view_formatted_infos(pointer, False)
s = bytes2str(sc)
free(sc)
return s
@OBIWrapper.checkIsActive
def repr_longformat(self) :
cdef str s
cdef char* sc
cdef Obiview_p pointer = self.pointer()
sc = obi_view_formatted_infos(pointer, True)
s = bytes2str(sc)
free(sc)
return s

2
python/obitools3/version.py
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@ -1,5 +1,5 @@
major = 3
minor = 0
serial= '0b35'
serial= '0b36'
version ="%d.%d.%s" % (major,minor,serial)