1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374
|
#cython: language_level=3
from libc.stdlib cimport free, atexit
from cpython.list cimport PyList_Size
from .capi.obidms cimport obi_open_dms, \
obi_create_dms, \
obi_close_dms, \
obi_dms_exists, \
obi_dms_get_full_path, \
obi_close_atexit, \
obi_dms_write_comments, \
obi_dms_formatted_infos
from .capi.obitypes cimport const_char_p
from obitools3.utils cimport bytes2str, \
str2bytes, \
tobytes, \
tostr, \
bytes2str_object, \
str2bytes_object, \
clean_empty_values_from_object
from .object cimport OBIDeactivatedInstanceError
from pathlib import Path
from .view import view
from .object import OBIWrapper
import json
import time
from libc.stdlib cimport free
cdef class DMS(OBIWrapper):
cdef inline OBIDMS_p pointer(self) :
return <OBIDMS_p>(self._pointer)
@staticmethod
def obi_atexit() :
atexit(obi_close_atexit)
@staticmethod
def open_or_new(object dms_name) :
cdef OBIDMS_p pointer
cdef DMS dms
cdef bytes dms_name_b = tobytes(dms_name)
if DMS.exists(dms_name_b) :
pointer = obi_open_dms(<const_char_p> dms_name_b, False)
else :
pointer = obi_create_dms(<const_char_p> dms_name_b)
if pointer == NULL :
raise Exception("Failed opening or creating an OBIDMS")
dms = OBIWrapper.new_wrapper(DMS, pointer)
return dms
@staticmethod
def exists(object dms_name) :
cdef bytes dms_name_b = tobytes(dms_name)
cdef int rep
rep = obi_dms_exists(dms_name_b)
if rep < 0 :
raise RuntimeError("Error checking if a DMS exists")
else :
return bool(rep)
@staticmethod
def new(object dms_name) :
cdef OBIDMS_p pointer
cdef DMS dms
cdef bytes dms_name_b = tobytes(dms_name)
pointer = obi_create_dms(<const_char_p> dms_name_b)
if pointer == NULL :
raise Exception("Failed creating an OBIDMS")
dms = OBIWrapper.new_wrapper(DMS, pointer)
return dms
@staticmethod
def open(object dms_name) :
cdef OBIDMS_p pointer
cdef DMS dms
cdef bytes dms_name_b = tobytes(dms_name)
pointer = obi_open_dms(<const_char_p> dms_name_b, False)
if pointer == NULL :
raise Exception("Failed opening an OBIDMS")
dms = OBIWrapper.new_wrapper(DMS, pointer)
return dms
def close(self, force=False) :
'''
Closes the DMS instance and free the associated memory (no counter, closing is final)
The `close` method is automatically called by the object destructor.
'''
cdef OBIDMS_p pointer = self.pointer()
if self.active() :
OBIWrapper.close(self)
if (obi_close_dms(pointer, force=force)) < 0 :
raise Exception("Problem closing an OBIDMS")
# name property getter
@property
def name(self) :
'''
Returns the name of the DMS instance
@rtype: bytes
'''
return <bytes> self.pointer().dms_name
# DMS full path property getter
@property
def full_path(self) :
'''
Returns the full path including the name with the extension of the DMS directory
@rtype: bytes
'''
return <bytes> self.pointer().directory_path
# DMS name with full path property getter
@property
def name_with_full_path(self) :
'''
Returns the full path with the name (meaning without the '.obidms' extension) of the DMS directory
@rtype: bytes
'''
return <bytes> self.full_path[:-7]
# command history DOT graph property getter in the form of a bytes string
@property
def dot_history_graph(self):
complete_graph = []
for view_name in self:
complete_graph.extend(self[view_name].dot_history_graph_list)
uniq_graph = []
for elt in complete_graph:
if elt not in uniq_graph:
uniq_graph.append(elt)
uniq_graph.insert(0, b"digraph \""+self.name+b"\" {\n")
uniq_graph.append(b"}")
return b"".join(uniq_graph)
@OBIWrapper.checkIsActive
def keys(self) :
cdef const_char_p path = obi_dms_get_full_path(self.pointer(), b"VIEWS")
if path == NULL:
raise RuntimeError("Cannot retrieve the view database path")
p = Path(bytes2str(path))
free(path)
for v in p.glob("*.obiview") :
yield str2bytes(v.stem)
@OBIWrapper.checkIsActive
def values(self) :
cdef bytes view_name
for view_name in self.keys():
yield self.get_view(view_name)
@OBIWrapper.checkIsActive
def items(self) :
cdef bytes view_name
for view_name in self.keys():
yield (view_name, self.get_view(view_name))
@OBIWrapper.checkIsActive
def __contains__(self, key) :
cdef str key_s = tostr(key)
cdef const_char_p path = obi_dms_get_full_path(self.pointer(), b"VIEWS")
p = Path(bytes2str(path),key_s)
free(path)
return p.with_suffix(".obiview").is_file()
cpdef int view_count(self) :
return PyList_Size(list(self.keys()))
@OBIWrapper.checkIsActive
def __len__(self) :
return self.view_count()
@OBIWrapper.checkIsActive
def __getitem__(self, object view_name):
return self.get_view(view_name)
@OBIWrapper.checkIsActive
def __iter__(self) :
return self.keys()
@OBIWrapper.checkIsActive
def get_view(self, object view_name) :
return view.View.open(self, view_name)
@OBIWrapper.checkIsActive
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
@OBIWrapper.checkIsActive
def record_command_line(self, command_line):
t = time.asctime(time.localtime(time.time()))
if "command_line_history" not in self.comments:
l = []
else:
l = self.comments["command_line_history"]
l.append({"command":command_line, "time":t})
self.comments["command_line_history"] = l
# comments property getter
@property
def comments(self):
return DMS_comments(self)
@comments.setter
def comments(self, object value):
DMS_comments(self, value)
# bash command history property getter
@property
def bash_history(self):
#s = b"#!${bash}/bin/bash\n\n"
s = b""
first = True
for command in self.command_line_history:
s+=b"#"
s+=command[b"time"]
s+=b"\nobi "
s+=command[b"command"]
s+=b"\n"
return s
# command line history property getter
@property
def command_line_history(self):
return self.comments[b"command_line_history"]
cdef class DMS_comments(dict): # Not thread safe
def __init__(self, DMS dms, value=None) :
if not dms.active() :
raise OBIDeactivatedInstanceError()
self._dms = dms
if value is not None:
self.update(value) # TODO test and discuss not overwriting (could use replace bool)
self._update_from_file()
def _update_from_file(self):
cdef bytes comments_json
cdef str comments_json_str
cdef OBIDMS_p dms_p
cdef DMS dms
if not self._dms.active() :
raise OBIDeactivatedInstanceError()
dms = self._dms
dms_p = <OBIDMS_p>(dms.pointer())
comments_json = <bytes> dms_p.infos.comments
comments_json_str = bytes2str(comments_json)
comments_dict = json.loads(comments_json_str)
str2bytes_object(comments_dict)
super(DMS_comments, self).update(comments_dict)
def __getitem__(self, object key):
if not self._dms.active() :
raise OBIDeactivatedInstanceError()
if type(key) == str:
key = str2bytes(key)
self._update_from_file()
return super(DMS_comments, self).__getitem__(key)
def __setitem__(self, object key, object value):
cdef OBIDMS_p dms_p
cdef DMS dms
if not self._dms.active() :
raise OBIDeactivatedInstanceError()
dms = self._dms
dms_p = <OBIDMS_p>(dms.pointer())
# Remove virtually empty values from the object # TODO discuss
clean_empty_values_from_object(value)
# If value is virtually empty, don't add it # TODO discuss
if value is None or len(value) == 0:
return
# Convert to bytes
if type(key) == str:
key = str2bytes(key)
value_bytes = str2bytes_object(value)
# Update dict with comments already written in file
self._update_from_file()
# Add new element # TODO don't overwrite?
super(DMS_comments, self).__setitem__(key, value_bytes)
# Convert to str because json library doens't like bytes
dict_str = {key:item for key,item in self.items()}
dict_str = bytes2str_object(dict_str)
# Convert to json string
comments_json = json.dumps(dict_str)
# Write new comments
if obi_dms_write_comments(dms_p, tobytes(comments_json)) < 0:
raise Exception("Could not write DMS comments, DMS:", dms.name, "comments:", comments_json)
def update(self, value):
for k,v in value.items():
self[k] = v
def __contains__(self, key):
return super(DMS_comments, self).__contains__(tobytes(key))
def __str__(self):
return bytes2str(self._dms.pointer().infos.comments)
|