lib.errors

Source Code for Module lib.errors

1 ############################################################################### 2 # # 3 # Copyright (C) 2003-2013,2019 Edward d'Auvergne # 4 # Copyright (C) 2006 Chris MacRaild # 5 # # 6 # This file is part of the program relax (http://www.nmr-relax.com). # 7 # # 8 # This program is free software: you can redistribute it and/or modify # 9 # it under the terms of the GNU General Public License as published by # 10 # the Free Software Foundation, either version 3 of the License, or # 11 # (at your option) any later version. # 12 # # 13 # This program is distributed in the hope that it will be useful, # 14 # but WITHOUT ANY WARRANTY; without even the implied warranty of # 15 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the # 16 # GNU General Public License for more details. # 17 # # 18 # You should have received a copy of the GNU General Public License # 19 # along with this program. If not, see <http://www.gnu.org/licenses/>. # 20 # # 21 ############################################################################### 22 23 # Module docstring. 24 """Module containing all of the RelaxError objects.""" 25 26 27 # Python module imports. 28 try: 29 from bz2 import BZ2File 30 bz2 = True 31 except ImportError: 32 bz2 = False 33 from re import match, search 34 import sys 35 import time 36 37 # relax module imports. 38 from lib import ansi 39 from lib.compat import pickle 40 from lib.text.string import human_readable_list 41 42 43 # Module variables for changing the behaviour of the warning system. 44 SAVE_ERROR_STATE = False # If True, then a pickled state file will be saved when a RelaxError occurs. 45 46 # Text variables. 47 ARRAY = 'a list or numpy array' 48 ARRAY_FLOAT = 'a list or numpy array of floats' 49 ARRAY_INT = 'a list or numpy array of integers' 50 ARRAY_NUM = 'a list or numpy array of numbers' 51 BIN = 'a binary number (0 or 1)' 52 BOOL = 'a Boolean (True or False)' 53 INT = 'an integer' 54 FILE = 'a file object' 55 FLOAT = 'a floating point number' 56 FUNC = 'a function' 57 LIST = 'a list' 58 LIST_BOOL = 'a list of Booleans' 59 LIST_FLOAT = 'a list of floating point numbers' 60 LIST_INT = 'a list of integers' 61 LIST_NUM = 'a list of numbers' 62 LIST_STR = 'a list of strings' 63 LIST_VAL = 'a list of values' 64 MATRIX_FLOAT = 'a matrix of floating point numbers' 65 NONE = 'None' 66 NUMPY_FLOAT = 'a numpy array of floats' 67 NUMPY_INT = 'a numpy array of integers' 68 NUMPY_NUM = 'a numpy array of numbers' 69 NUM = 'a number' 70 TUPLE = 'a tuple' 71 TUPLE_FLOAT = 'a tuple of floating point numbers' 72 TUPLE_INT = 'a tuple of integers' 73 TUPLE_NUM = 'a tuple of numbers' 74 TUPLE_STR = 'a tuple of strings' 75 STR = 'a string' 76 VAL = 'a value' 77 78

79 -def save_state():

80 """Save the program state, for debugging purposes.""" 81 82 # relax data store singleton import. Must be done here! 83 try: 84 from data_store import Relax_data_store; ds = Relax_data_store() 85 86 # Ok, this is not relax so don't do anything! 87 except ImportError: 88 return 89 90 # Append the date and time to the save file. 91 now = time.localtime() 92 file_name = "relax_state_%i%02i%02i_%02i%02i%02i" % (now[0], now[1], now[2], now[3], now[4], now[5]) 93 94 # Open the file for writing. 95 if bz2: 96 sys.stderr.write("\nStoring the relax state in the file '%s.bz2'.\n\n" % file_name) 97 file = BZ2File(file_name+'.bz2', 'w') 98 else: 99 sys.stderr.write("\nStoring the relax state in the file '%s'.\n\n" % file_name) 100 file = open(file_name, 'w') 101 102 # Pickle the data class and write it to file 103 pickle.dump(ds, file, 1) 104 105 # Close the file. 106 file.close()

107 108

109 -def list_to_text(data):

110 """Convert the given Python list to a text representation. 111 112 @param data: The list of Python objects. 113 @type data: list 114 @return: The English text version of the list. 115 @rtype: str 116 """ 117 118 # Initialise. 119 text = '' 120 121 # Loop over the elements, adding the to the list. 122 for i in range(len(data)): 123 # Add the text. 124 text += repr(data[i]) 125 126 # Comma separators. 127 if i < len(data) - 2: 128 text += ', ' 129 130 # Last separator. 131 if i == len(data) - 2: 132 text += ' and ' 133 134 # Return the text. 135 return text

136 137 138 # Base class for all errors. 139 ############################ 140

141 -class BaseError(Exception):

142 """The base class for all RelaxErrors.""" 143

144 - def __str__(self):

145 """Modify the behaviour of the error system.""" 146 147 # Save the state if the escalate flag is turned on. 148 if SAVE_ERROR_STATE: 149 save_state() 150 151 # Modify the error message to include 'RelaxError' at the start (using coloured text if a TTY). 152 if ansi.enable_control_chars(stream=2): 153 return ("%sRelaxError: %s%s\n" % (ansi.relax_error, self.text, ansi.end)) 154 else: 155 return ("RelaxError: %s\n" % self.text)

156 157

158 -class BaseArgError(BaseError):

159 """The base class for all the argument related RelaxErrors.""" 160 161 # The allowed simple types. 162 simple_types = [] 163 164 # The allowed list types (anything with a size). 165 list_types = [] 166 167

168 - def __init__(self, name, value, size=None, dim=None, rank=None, can_be_none=False):

169 """A default initialisation and error message formatting method. 170 171 @param name: The name of the argument. 172 @type name: str 173 @param value: The argument's value. 174 @type value: anything 175 @keyword size: The fixed size for list types. 176 @type size: int or None 177 @keyword dim: The expected dimensionality of the argument. 178 @type dim: tuple of (int or None) 179 @keyword rank: The rank for list or array types. 180 @type rank: int or None 181 @keyword can_be_none: A flag specifying if the argument can be None. This will tag the text ', or None' to the end of the RelaxError. 182 @type can_be_none: bool 183 """ 184 185 # Single line string representation of the argument. 186 value_str = repr(value) 187 if search("^array", value_str): 188 value_str = value_str.replace("\n", "") 189 value_str = ''.join(value_str.split()) 190 191 # The initial part of the message. 192 self.text = "The %s argument %s must be " % (name, value_str) 193 194 # Collect all elements, avoiding any class variable modifications. 195 all_types = [] 196 197 # The basic data types. 198 for i in range(len(self.simple_types)): 199 all_types.append(self.simple_types[i]) 200 201 # The list/array types. 202 for i in range(len(self.list_types)): 203 # Supplementary text. 204 supp_list = [] 205 if size != None: 206 supp_list.append("size %s" % repr(size)) 207 if rank != None: 208 supp_list.append("rank %i" % rank) 209 if dim != None: 210 supp_list.append("dimensionality %s" % repr(dim)) 211 212 # Add the type with any supplementary text. 213 if len(supp_list): 214 all_types.append("%s of %s" % (self.list_types[i], human_readable_list(supp_list, conjunction="or"))) 215 else: 216 all_types.append("%s" % self.list_types[i]) 217 218 # None is allowed. 219 if can_be_none: 220 all_types.append('None') 221 222 # Multiple elements. 223 if len(all_types) > 1: 224 self.text = self.text + "either " 225 226 # Generate the list string. 227 self.text += human_readable_list(all_types, conjunction="or") 228 229 # The end. 230 self.text = self.text + "."

231 232 233 # Standard errors. 234 ################## 235

236 -class RelaxError(BaseError):

237 - def __init__(self, text):

238 self.text = text

239 240 241 # Module import errors. 242 ####################### 243

244 -class RelaxNoModuleInstallError(BaseError):

245 - def __init__(self, desc, name):

246 self.text = "The %s module '%s' cannot be found. Please check that it is installed." % (desc, name)

247 248 249 # Fault. 250 ######## 251

252 -class RelaxFault(BaseError):

253 - def __init__(self):

254 self.text = "Impossible to be here, please re-run relax with the '--debug' flag and summit a bug report at https://web.archive.org/web/https://gna.org/projects/relax/."

255

256 - def __str__(self):

257 # Save the program state, no matter what. 258 save_state() 259 260 # Modify the error message to include 'RelaxError' at the start. 261 return ("RelaxError: " + self.text + "\n")

262 263 264 # Code implementation errors. 265 ############################# 266 267 # Not implemented yet.

268 -class RelaxImplementError(BaseError):

269 - def __init__(self, fn_name=None):

270 if fn_name: 271 self.text = "The %s function has not yet been implemented for the current data pipe." % fn_name 272 else: 273 self.text = "This has not yet been implemented for the current data pipe."

274 275 276 # Program errors. 277 ################# 278 279 # Cannot locate the program.

280 -class RelaxProgError(BaseError):

281 - def __init__(self, name):

282 self.text = "The program " + repr(name) + " cannot be found."

283 284 285 # The binary executable file does not exist (full path has been given!).

286 -class RelaxMissingBinaryError(BaseError):

287 - def __init__(self, name):

288 self.text = "The binary executable file " + repr(name) + " does not exist."

289 290 291 # The binary executable file is not executable.

292 -class RelaxNonExecError(BaseError):

293 - def __init__(self, name):

294 self.text = "The binary executable file " + repr(name) + " is not executable."

295 296 297 # The binary executable file is not located within the system path.

298 -class RelaxNoInPathError(BaseError):

299 - def __init__(self, name):

300 self.text = "The binary executable file " + repr(name) + " is not located within the system path."

301 302 303 # Program execution failure.

304 -class RelaxProgFailError(BaseError):

305 - def __init__(self, name):

306 self.text = "Execution of the program " + name + " has failed."

307 308 309 # PDB errors. 310 ############# 311 312 # PDB data corresponding to the data pipe already exists.

313 -class RelaxPdbError(BaseError):

314 - def __init__(self, pipe=None):

315 if pipe != None: 316 self.text = "PDB data corresponding to the data pipe " + repr(pipe) + " already exists." 317 else: 318 self.text = "PDB data already exists."

319 320 # No PDB loaded.

321 -class RelaxNoPdbError(BaseError):

322 - def __init__(self, pipe=None):

323 if pipe != None: 324 self.text = "No PDB file has been loaded for the data pipe " + repr(pipe) + "." 325 else: 326 self.text = "No PDB file has been loaded."

327 328 # Loading error.

329 -class RelaxPdbLoadError(BaseError):

330 - def __init__(self, name):

331 self.text = "The PDB file " + repr(name) + " could not be loaded properly, no molecular chains could be extracted."

332 333 # Multiple unit vectors.

334 -class RelaxMultiVectorError(BaseError):

335 - def __init__(self, spin_id=None):

336 if spin_id != None: 337 self.text = "The multiple unit XH bond vectors for the spin '%s' - this is not supported by the current data pipe type." % spin_id 338 else: 339 self.text = "The multiple unit XH bond vectors per spin - this is not supported by the current data pipe type."

340 341 # No unit vectors.

342 -class RelaxNoVectorsError(BaseError):

343 - def __init__(self, pipe=None):

344 if pipe: 345 self.text = "No unit vectors have been calculated for the data pipe '%s'" % pipe 346 else: 347 self.text = "No unit vectors have been calculated."

348 349 # No chains within the PDB file.

350 -class RelaxNoPdbChainError(BaseError):

351 - def __init__(self):

352 self.text = "No peptide or nucleotide chains can be found within the PDB file."

353 354 355 # Nuclear errors. 356 ################# 357 358 # Nucleus not set.

359 -class RelaxNucleusError(BaseError):

360 - def __init__(self, spin_id=None):

361 if spin_id != None: 362 self.text = "The type of nucleus for the spin '%s' has not yet been set." % spin_id 363 else: 364 self.text = "The type of nucleus has not yet been set."

365 366 # Spin type not set.

367 -class RelaxSpinTypeError(BaseError):

368 - def __init__(self, spin_id=None):

369 if spin_id != None: 370 self.text = "The nuclear isotope type for the spin '%s' has not yet been set. Please use the spin.isotope user function to set the type." % spin_id 371 else: 372 self.text = "The nuclear isotope type has not yet been set. Please use the spin.isotope user function to set the type."

373 374 375 # Argument errors. 376 ################## 377 378 379 # Misc. 380 #~~~~~~ 381 382 # Invalid argument.

383 -class RelaxInvalidError(BaseArgError):

384 - def __init__(self, name, value):

385 self.text = "The " + name + " argument " + repr(value) + " is invalid."

386 387 # Argument not in the list.

388 -class RelaxArgNotInListError(BaseArgError):

389 - def __init__(self, name, value, list):

390 self.text = "The " + name + " argument " + repr(value) + " is neither " 391 for i in range(len(list)-1): 392 self.text = self.text + repr(list[i]) + ', ' 393 self.text = self.text + 'nor ' + repr(list[-1]) + "."

394 395 # Length of the list.

396 -class RelaxLenError(BaseArgError):

397 - def __init__(self, name, len):

398 self.text = "The " + name + " argument must be of length " + repr(len) + "."

399 400 # None.

401 -class RelaxNoneError(BaseArgError):

402 - def __init__(self, name):

403 self.text = "The " + name + " argument has not been supplied."

404 405 # Not None.

406 -class RelaxArgNotNoneError(BaseArgError):

407 - def __init__(self, name, value):

408 self.text = "The %s argument of '%s' must be None."

409 410 411 # Simple types. 412 #~~~~~~~~~~~~~~ 413 414 # Boolean - the values True and False.

415 -class RelaxBoolError(BaseArgError):

416 simple_types = [BOOL]

417

418 -class RelaxNoneBoolError(BaseArgError):

419 simple_types = [NONE, BOOL]

420 421 # Binary - integers 0 and 1.

422 -class RelaxBinError(BaseArgError):

423 simple_types = [BIN]

424 425 # Float.

426 -class RelaxFloatError(BaseArgError):

427 simple_types = [FLOAT]

428

429 -class RelaxNoneFloatError(BaseArgError):

430 simple_types = [NONE, FLOAT]

431 432 # Number.

433 -class RelaxNumError(BaseArgError):

434 simple_types = [NUM]

435

436 -class RelaxNoneNumError(BaseArgError):

437 simple_types = [NONE, NUM]

438 439 # Function.

440 -class RelaxFunctionError(BaseArgError):

441 simple_types = [FUNC]

442

443 -class RelaxNoneFunctionError(BaseArgError):

444 simple_types = [NONE, FUNC]

445 446 # Integer.

447 -class RelaxIntError(BaseArgError):

448 simple_types = [INT]

449

450 -class RelaxNoneIntError(BaseArgError):

451 simple_types = [NONE, INT]

452 453 # String.

454 -class RelaxStrError(BaseArgError):

455 simple_types = [STR]

456

457 -class RelaxNoneStrError(BaseArgError):

458 simple_types = [NONE, STR]

459 460 461 # Simple mixes. 462 #~~~~~~~~~~~~~~ 463 464 # Integer or string.

465 -class RelaxIntStrError(BaseArgError):

466 simple_types = [INT, STR]

467

468 -class RelaxNoneIntStrError(BaseArgError):

469 simple_types = [NONE, INT, STR]

470 471 # String or file descriptor.

472 -class RelaxStrFileError(BaseArgError):

473 simple_types = [STR, FILE]

474

475 -class RelaxNoneStrFileError(BaseArgError):

476 simple_types = [NONE, STR, FILE]

477 478 479 # List types. 480 #~~~~~~~~~~~~ 481 482 483 # List or numpy array.

484 -class RelaxArrayError(BaseArgError):

485 list_types = [ARRAY]

486 487 # List or numpy array of floats.

488 -class RelaxArrayFloatError(BaseArgError):

489 list_types = [ARRAY_FLOAT]

490 491 # List or numpy array of ints.

492 -class RelaxArrayIntError(BaseArgError):

493 list_types = [ARRAY_INT]

494 495 # List or numpy array of numbers.

496 -class RelaxArrayNumError(BaseArgError):

497 list_types = [ARRAY_NUM]

498 499 # List.

500 -class RelaxListError(BaseArgError):

501 list_types = [LIST]

502

503 -class RelaxNoneListError(BaseArgError):

504 simple_types = [NONE] 505 list_types = [LIST]

506 507 # List of Booleans.

508 -class RelaxListBoolError(BaseArgError):

509 list_types = [LIST_BOOL]

510

511 -class RelaxNoneListBoolError(BaseArgError):

512 simple_types = [NONE] 513 list_types = [LIST_BOOL]

514 515 # List of floating point numbers.

516 -class RelaxListFloatError(BaseArgError):

517 list_types = [LIST_FLOAT]

518

519 -class RelaxNoneListFloatError(BaseArgError):

520 list_types = [LIST_FLOAT]

521 522 # List of floating point numbers or strings.

523 -class RelaxListFloatStrError(BaseArgError):

524 list_types = [LIST_FLOAT, LIST_STR]

525 526 # List of integers.

527 -class RelaxListIntError(BaseArgError):

528 list_types = [LIST_INT]

529 530 # List of integers.

531 -class RelaxNoneListIntError(BaseArgError):

532 simple_types = [NONE] 533 list_types = [LIST_INT]

534 535 # List of numbers.

536 -class RelaxListNumError(BaseArgError):

537 list_types = [LIST_NUM]

538

539 -class RelaxNoneListNumError(BaseArgError):

540 simple_types = [NONE] 541 list_types = [LIST_NUM]

542 543 # List of strings.

544 -class RelaxListStrError(BaseArgError):

545 list_types = [LIST_STR]

546

547 -class RelaxNoneListStrError(BaseArgError):

548 simple_types = [NONE] 549 list_types = [LIST_STR]

550 551 # Numpy array of floats.

552 -class RelaxNumpyFloatError(BaseArgError):

553 list_types = [NUMPY_FLOAT]

554 555 # Numpy array of ints.

556 -class RelaxNumpyIntError(BaseArgError):

557 list_types = [NUMPY_INT]

558 559 # Numpy array of numbers.

560 -class RelaxNumpyNumError(BaseArgError):

561 list_types = [NUMPY_NUM]

562 563 564 # Simple or list types. 565 #~~~~~~~~~~~~~~~~~~~~~~ 566 567 # Float or list.

568 -class RelaxNoneFloatListError(BaseArgError):

569 simple_types = [NONE, FLOAT] 570 list_types = [LIST]

571 572 # Float, str, or list.

573 -class RelaxNoneFloatStrListError(BaseArgError):

574 simple_types = [NONE, FLOAT, STR] 575 list_types = [LIST]

576 577 # Boolean or list of Booleans.

578 -class RelaxBoolListBoolError(BaseArgError):

579 simple_types = [BOOL] 580 list_types = [LIST_BOOL]

581

582 -class RelaxNoneBoolListBoolError(BaseArgError):

583 simple_types = [NONE, BOOL] 584 list_types = [LIST_BOOL]

585 586 # Integer or list of integers.

587 -class RelaxIntListIntError(BaseArgError):

588 simple_types = [INT] 589 list_types = [LIST_INT]

590

591 -class RelaxNoneIntListIntError(BaseArgError):

592 simple_types = [NONE, INT] 593 list_types = [LIST_INT]

594 595 # Number, string, or list of numbers or strings.

596 -class RelaxNumStrListNumStrError(BaseArgError):

597 simple_types = [NUM, STR] 598 list_types = [LIST_NUM, LIST_STR]

599

600 -class RelaxNoneNumStrListNumStrError(BaseArgError):

601 simple_types = [NONE, NUM, STR] 602 list_types = [LIST_NUM, LIST_STR]

603 604 # String, file object, or list of strings or file objects.

605 -class RelaxStrFileListStrFileError(BaseArgError):

606 simple_types = [STR, FILE] 607 list_types = [LIST]

608 609 # String or list.

610 -class RelaxStrListError(BaseArgError):

611 simple_types = [STR] 612 list_types = [LIST]

613

614 -class RelaxNoneStrListError(BaseArgError):

615 simple_types = [NONE, STR] 616 list_types = [LIST]

617 618 # String or list of numbers.

619 -class RelaxStrListNumError(BaseArgError):

620 simple_types = [STR] 621 list_types = [LIST_NUM]

622

623 -class RelaxNoneStrListNumError(BaseArgError):

624 simple_types = [NONE, STR] 625 list_types = [LIST_NUM]

626 627 # String or list of strings.

628 -class RelaxStrListStrError(BaseArgError):

629 simple_types = [STR] 630 list_types = [LIST_STR]

631

632 -class RelaxNoneStrListStrError(BaseArgError):

633 simple_types = [NONE, STR] 634 list_types = [LIST_STR]

635 636 # Value or list of values.

637 -class RelaxValListValError(BaseArgError):

638 simple_types = [VAL] 639 list_types = [LIST_VAL]

640

641 -class RelaxNoneValListValError(BaseArgError):

642 simple_types = [NONE, VAL] 643 list_types = [LIST_VAL]

644 645 646 # Tuple types. 647 #~~~~~~~~~~~~~ 648 649 # Tuple.

650 -class RelaxTupleError(BaseArgError):

651 list_types = [TUPLE]

652

653 -class RelaxNoneTupleError(BaseArgError):

654 simple_types = [NONE] 655 list_types = [TUPLE]

656 657 # Tuple of numbers.

658 -class RelaxTupleNumError(BaseArgError):

659 list_types = [TUPLE_NUM]

660

661 -class RelaxNoneTupleNumError(BaseArgError):

662 simple_types = [NONE] 663 list_types = [TUPLE_NUM]

664 665 666 # Simple or tuple types. 667 #~~~~~~~~~~~~~~~~~~~~~~~ 668 669 # Number or tuple.

670 -class RelaxNumTupleError(BaseArgError):

671 simple_types = [NUM] 672 list_types = [TUPLE]

673 674 # Number or tuple of numbers.

675 -class RelaxNumTupleNumError(BaseArgError):

676 simple_types = [NUM] 677 list_types = [TUPLE_NUM]

678

679 -class RelaxNoneNumTupleNumError(BaseArgError):

680 simple_types = [NONE, NUM] 681 list_types = [TUPLE_NUM]

682 683 684 # Matrix types. 685 #~~~~~~~~~~~~~~ 686 687 # Matrix of floating point numbers.

688 -class RelaxMatrixFloatError(BaseArgError):

689 list_types = [MATRIX_FLOAT]

690

691 -class RelaxNoneMatrixFloatError(BaseArgError):

692 list_types = [MATRIX_FLOAT]

693 694 695 696 # Sequence errors. 697 ################## 698 699 # No sequence loaded.

700 -class RelaxNoSequenceError(BaseError):

701 - def __init__(self, pipe=None):

702 if pipe == None: 703 self.text = "The sequence data does not exist." 704 else: 705 self.text = "The sequence data for the data pipe " + repr(pipe) + " does not exist."

706 707 # The sequence already exists.

708 -class RelaxSequenceError(BaseError):

709 - def __init__(self, pipe=None):

710 if pipe == None: 711 self.text = "The sequence data already exists." 712 else: 713 self.text = "The sequence data for the data pipe " + repr(pipe) + " already exists."

714 715 # The two sequences are different.

716 -class RelaxDiffSeqError(BaseError):

717 - def __init__(self, pipe1, pipe2):

718 self.text = "The sequences for the data pipes " + repr(pipe1) + " and " + repr(pipe2) + " are not the same."

719 720 # The number of molecules are different.

721 -class RelaxDiffMolNumError(BaseError):

722 - def __init__(self, pipe1, pipe2):

723 self.text = "The number of molecules do not match between pipes '%s' and '%s'." % (pipe1, pipe2)

724 725 # The number of residues are different.

726 -class RelaxDiffResNumError(BaseError):

727 - def __init__(self, pipe1, pipe2):

728 self.text = "The number of residues do not match between pipes '%s' and '%s'." % (pipe1, pipe2)

729 730 # The number of spins are different.

731 -class RelaxDiffSpinNumError(BaseError):

732 - def __init__(self, pipe1, pipe2):

733 self.text = "The number of spins do not match between pipes '%s' and '%s'." % (pipe1, pipe2)

734 735 # Multiple spins matching the ID.

736 -class RelaxMultiMolIDError(BaseError):

737 - def __init__(self, id):

738 if id == '': 739 self.text = "The empty molecule ID corresponds to more than a single molecule in the current data pipe." 740 else: 741 self.text = "The molecule ID '%s' corresponds to more than a single molecule in the current data pipe." % id

742 743 # Multiple spins matching the ID.

744 -class RelaxMultiResIDError(BaseError):

745 - def __init__(self, id):

746 if id == '': 747 self.text = "The empty residue ID corresponds to more than a single residue in the current data pipe." 748 else: 749 self.text = "The residue ID '%s' corresponds to more than a single residue in the current data pipe." % id

750 751 # Multiple spins matching the ID.

752 -class RelaxMultiSpinIDError(BaseError):

753 - def __init__(self, id, id_list=None):

754 if id_list != None and id == '': 755 self.text = "The empty spin ID corresponds to multiple spins, including %s." % list_to_text(id_list) 756 elif id_list == None and id == '': 757 self.text = "The empty spin ID corresponds to more than a single spin in the current data pipe." 758 elif id_list != None: 759 self.text = "The spin ID '%s' corresponds to multiple spins, including %s." % (id, list_to_text(id_list)) 760 else: 761 self.text = "The spin ID '%s' corresponds to more than a single spin in the current data pipe." % id

762 763 # Cannot find the residue in the sequence.

764 -class RelaxNoResError(BaseError):

765 - def __init__(self, number, name=None):

766 if name == None: 767 self.text = "The residue '" + repr(number) + "' cannot be found in the sequence." 768 else: 769 self.text = "The residue '" + repr(number) + " " + name + "' cannot be found in the sequence."

770 771 # Cannot find the spin in the sequence.

772 -class RelaxNoSpinError(BaseError):

773 - def __init__(self, id, pipe=None):

774 if pipe == None: 775 self.text = "The spin '%s' does not exist." % id 776 else: 777 self.text = "The spin '%s' does not exist in the '%s' data pipe." % (id, pipe)

778 779 # The sequence data is not valid.

780 -class RelaxInvalidSeqError(BaseError):

781 - def __init__(self, line, problem=None):

782 if problem == None: 783 self.text = "The sequence data in the line %s is invalid." % line 784 else: 785 self.text = "The sequence data in the line %s is invalid, %s." % (line, problem)

786 787 # The spins have not been loaded

788 -class RelaxSpinsNotLoadedError(BaseError):

789 - def __init__(self, spin_id):

790 self.text = "The spin information for the spin " + repr(spin_id) + " has not yet been loaded, please use the structure.load_spins user function."

791 792 793 # Interatomic data errors. 794 ########################## 795 796 # No interatomic data.

797 -class RelaxNoInteratomError(BaseError):

798 - def __init__(self, spin_id1=None, spin_id2=None, pipe=None):

799 if spin_id1 and pipe: 800 self.text = "The interatomic data between the spins '%s' and '%s' for the data pipe '%s' does not exist." % (spin_id1, spin_id2, pipe) 801 elif spin_id1: 802 self.text = "The interatomic data between the spins '%s' and '%s' does not exist." % (spin_id1, spin_id2) 803 elif pipe: 804 self.text = "The interatomic data for the data pipe '%s' does not exist." % pipe 805 else: 806 self.text = "The interatomic data does not exist."

807 808 # The interatomic data already exists.

809 -class RelaxInteratomError(BaseError):

810 - def __init__(self, pipe=None):

811 if pipe == None: 812 self.text = "The interatomic data already exists." 813 else: 814 self.text = "The interatomic data for the data pipe " + repr(pipe) + " already exists."

815 816 # Inconsistency in the interatomic data.

817 -class RelaxInteratomInconsistentError(BaseError):

818 - def __init__(self, pipe1, pipe2):

819 self.text = "The interatomic data is inconsistent between the data pipes '%s' and '%s'." % (pipe1, pipe2)

820 821 822 823 # Domain errors. 824 ################ 825 826 # No domain defined.

827 -class RelaxNoDomainError(BaseError):

828 - def __init__(self, id=None):

829 if id == None: 830 self.text = "No domains are defined." 831 else: 832 self.text = "The domain '%s' is not defined." % id

833 834 835 836 # Spectrometer information errors. 837 ################################## 838 839 # No frequency information.

840 -class RelaxNoFrqError(BaseError):

841 - def __init__(self, pipe_name=None, id=None):

842 self.text = "No spectrometer frequency information" 843 if id != None: 844 self.text += " for the '%s' experiment ID" % id 845 self.text += " is present" 846 if pipe_name != None: 847 self.text += " in the '%s' data pipe" % pipe_name 848 self.text += "."

849 850 851 852 # Spectral data errors. 853 ####################### 854 855 # No peak intensity data.

856 -class RelaxNoPeakIntensityError(BaseError):

857 - def __init__(self, spectrum_id=None):

858 if spectrum_id == None: 859 self.text = "No peak intensity data has been loaded." 860 else: 861 self.text = "Peak intensity data for the '%s' spectrum ID does not exist."

862 863 # No spectral data.

864 -class RelaxNoSpectraError(BaseError):

865 - def __init__(self, spectrum_id):

866 self.text = "Spectral data corresponding to the ID string '%s' does not exist." % spectrum_id

867 868 # Spectral data already exists.

869 -class RelaxSpectraError(BaseError):

870 - def __init__(self, spectrum_id):

871 self.text = "Spectral data corresponding to the ID string '%s' already exists." % spectrum_id

872 873 874 # Relaxation data errors. 875 ######################### 876 877 # No relaxation data.

878 -class RelaxNoRiError(BaseError):

879 - def __init__(self, ri_id):

880 self.text = "Relaxation data corresponding to the ID string '%s' does not exist." % ri_id

881 882 # Relaxation data already exists.

883 -class RelaxRiError(BaseError):

884 - def __init__(self, ri_id):

885 self.text = "Relaxation data corresponding to the ID string '%s' already exists." % ri_id

886 887 888 # J coupling errors. 889 #################### 890 891 # No J data.

892 -class RelaxNoJError(BaseError):

893 - def __init__(self):

894 self.text = "No J coupling data exists."

895 896 # J data already exists.

897 -class RelaxJError(BaseError):

898 - def __init__(self):

899 self.text = "J coupling data already exists."

900 901 902 # RDC and PCS data errors. 903 ########################## 904 905 # No alignment data.

906 -class RelaxNoAlignError(BaseError):

907 - def __init__(self, align_id, pipe=None):

908 if pipe != None: 909 self.text = "The alignment ID string '%s' is missing from the data pipe '%s'." % (align_id, pipe) 910 else: 911 self.text = "The alignment ID string '%s' is missing." % align_id

912 913 # Alignment data already exists.

914 -class RelaxAlignError(BaseError):

915 - def __init__(self, align_id):

916 self.text = "Alignment data corresponding to the ID string '%s' already exists." % align_id

917 918 # No RDC data.

919 -class RelaxNoRDCError(BaseError):

920 - def __init__(self, id=None):

921 if id: 922 self.text = "RDC data corresponding to the identification string " + repr(id) + " does not exist." 923 else: 924 self.text = "No RDC data exists."

925 926 # RDC data already exists.

927 -class RelaxRDCError(BaseError):

928 - def __init__(self, id):

929 self.text = "RDC data corresponding to the identification string " + repr(id) + " already exists."

930 931 # No PCS data.

932 -class RelaxNoPCSError(BaseError):

933 - def __init__(self, id=None):

934 if id: 935 self.text = "PCS data corresponding to the identification string " + repr(id) + " does not exist." 936 else: 937 self.text = "No PCS data exists."

938 939 # PCS data already exists.

940 -class RelaxPCSError(BaseError):

941 - def __init__(self, id):

942 self.text = "PCS data corresponding to the identification string " + repr(id) + " already exists."

943 944 945 # Model-free errors. 946 #################### 947 948 # Model-free data already exists.

949 -class RelaxMfError(BaseError):

950 - def __init__(self, pipe):

951 self.text = "Model-free data corresponding to the data pipe " + repr(pipe) + " already exists."

952 953 954 # Tensor errors. 955 ################ 956 957 # Tensor data corresponding to the data pipe already exists.

958 -class RelaxTensorError(BaseError):

959 - def __init__(self, tensor_type):

960 self.text = "The " + tensor_type + " tensor data already exists."

961 962 # No tensor data exists.

963 -class RelaxNoTensorError(BaseError):

964 - def __init__(self, tensor_type, tensor_label=None):

965 if not tensor_label: 966 self.text = "No " + tensor_type + " tensor data exists." 967 else: 968 self.text = "No " + tensor_type + " tensor data exists for the tensor " + repr(tensor_label) + "."

969 970 971 # File errors. 972 ############## 973 974 # No directory.

975 -class RelaxDirError(BaseError):

976 - def __init__(self, name, dir):

977 if name == None: 978 self.text = "The directory " + repr(dir) + " does not exist." 979 else: 980 self.text = "The " + name + " directory " + repr(dir) + " does not exist."

981 982 # No file.

983 -class RelaxFileError(BaseError):

984 - def __init__(self, name, file_name=None):

985 if file_name == None: 986 self.text = "The file " + repr(name) + " does not exist." 987 else: 988 self.text = "The " + name + " file " + repr(file_name) + " does not exist."

989 990 # No data in file.

991 -class RelaxFileEmptyError(BaseError):

992 - def __init__(self):

993 self.text = "The file contains no data."

994 995 # Overwrite file.

996 -class RelaxFileOverwriteError(BaseError):

997 - def __init__(self, file_name, flag):

998 self.text = "The file " + repr(file_name) + " already exists. Set the " + flag + " to True to overwrite."

999 1000 # Invalid data format.

1001 -class RelaxInvalidDataError(BaseError):

1002 - def __init__(self):

1003 self.text = "The format of the data is invalid."

1004 1005 1006 # Data pipe errors. 1007 ################### 1008 1009 # The data pipe bundle already exists.

1010 -class RelaxBundleError(BaseError):

1011 - def __init__(self, bundle):

1012 self.text = "The data pipe bundle '%s' already exists." % bundle

1013 1014 # No data pipe bundles exist.

1015 -class RelaxNoBundleError(BaseError):

1016 - def __init__(self, bundle=None):

1017 if bundle != None: 1018 self.text = "The data pipe bundle '%s' has not been created yet." % bundle 1019 else: 1020 self.text = "No data pipe bundles currently exist. Please use the pipe.bundle user function first."

1021 1022 # The data pipe already exists.

1023 -class RelaxPipeError(BaseError):

1024 - def __init__(self, pipe):

1025 self.text = "The data pipe " + repr(pipe) + " already exists."

1026 1027 # No data pipe exists.

1028 -class RelaxNoPipeError(BaseError):

1029 - def __init__(self, pipe=None):

1030 if pipe != None: 1031 self.text = "The data pipe " + repr(pipe) + " has not been created yet." 1032 else: 1033 self.text = "No data pipes currently exist. Please use the pipe.create user function first."

1034 1035 1036 # Spin-Residue-Molecule errors. 1037 ############################### 1038 1039 # Disallow molecule selection.

1040 -class RelaxMolSelectDisallowError(BaseError):

1041 - def __init__(self):

1042 self.text = "The selection of molecules is not allowed."

1043 1044 # Disallow residue selection.

1045 -class RelaxResSelectDisallowError(BaseError):

1046 - def __init__(self):

1047 self.text = "The selection of residues is not allowed."

1048 1049 # Disallow spin selection.

1050 -class RelaxSpinSelectDisallowError(BaseError):

1051 - def __init__(self):

1052 self.text = "The selection of spin systems is not allowed."

1053 1054 # The spin must be specified.

1055 -class RelaxNoSpinSpecError(BaseError):

1056 - def __init__(self):

1057 self.text = "The spin system must be specified."

1058 1059 1060 1061 # Setup errors. 1062 ############### 1063 1064 # Cannot setup the functions.

1065 -class RelaxFuncSetupError(BaseError):

1066 - def __init__(self, string):

1067 self.text = "This function is not available for " + string + "."

1068 1069 # The model already exists.

1070 -class RelaxModelError(BaseError):

1071 - def __init__(self, name=None):

1072 if name != None: 1073 self.text = "The " + name + " model already exists." 1074 else: 1075 self.text = "The model already exists."

1076 1077 1078 # The model has not been setup.

1079 -class RelaxNoModelError(BaseError):

1080 - def __init__(self, name=None):

1081 if name != None: 1082 self.text = "The specific " + name + " model has not been selected or set up." 1083 else: 1084 self.text = "The specific model has not been selected or set up."

1085 1086 1087 # Regular expression errors. 1088 ############################ 1089 1090 # Bad regular expression.

1091 -class RelaxRegExpError(BaseError):

1092 - def __init__(self, name, value):

1093 self.text = "The " + name + " argument " + repr(value) + " is not valid regular expression."

1094 1095 1096 # Data type errors. 1097 ################### 1098 1099 # Parameter cannot be set.

1100 -class RelaxParamSetError(BaseError):

1101 - def __init__(self, name, param_type=None):

1102 if param_type != None: 1103 self.text = "The " + name + " parameter, " + repr(param_type) + ", cannot be set." 1104 else: 1105 self.text = "The " + name + " parameter cannot be set."

1106 1107 # Value already exists.

1108 -class RelaxValueError(BaseError):

1109 - def __init__(self, data_type, pipe=None):

1110 if pipe != None: 1111 self.text = "The data type " + repr(data_type) + " already exists for the data pipe " + repr(pipe) + "." 1112 else: 1113 self.text = "The data type " + repr(data_type) + " already exists."

1114 1115 # No data value.

1116 -class RelaxNoValueError(BaseError):

1117 - def __init__(self, name, spin_id=None, spin_id2=None):

1118 if spin_id2 != None: 1119 self.text = "The %s value has not yet been set for spins '%s' and '%s'." % (name, spin_id, spin_id2) 1120 elif spin_id != None: 1121 self.text = "The %s value has not yet been set for spin '%s'." % (name, spin_id) 1122 else: 1123 self.text = "The " + repr(name) + " value has not yet been set."

1124 1125 # Unknown data type.

1126 -class RelaxUnknownDataTypeError(BaseError):

1127 - def __init__(self, name):

1128 self.text = "The data type " + repr(name) + " is unknown."

1129 1130 # Unknown parameter.

1131 -class RelaxUnknownParamError(BaseError):

1132 - def __init__(self, name, param_type=None):

1133 if param_type != None: 1134 self.text = "The " + name + " parameter, " + repr(param_type) + ", is unknown." 1135 else: 1136 self.text = "The " + name + " parameter is unknown."

1137 1138 # Unknown parameter combination.

1139 -class RelaxUnknownParamCombError(BaseError):

1140 - def __init__(self, name, data):

1141 self.text = "The " + repr(name) + " argument " + repr(data) + " represents an unknown parameter combination."

1142 1143 1144 # Simulation errors. 1145 #################### 1146 1147 # No simulations.

1148 -class RelaxNoSimError(BaseError):

1149 - def __init__(self, pipe=None):

1150 if pipe: 1151 self.text = "Simulations for the data pipe " + repr(pipe) + " have not been setup." 1152 else: 1153 self.text = "Simulations have not been setup."

1154 1155 1156 # Style errors. 1157 ############### 1158 1159 # Unknown style.

1160 -class RelaxStyleError(BaseError):

1161 - def __init__(self, style):

1162 self.text = "The style " + repr(style) + " is unknown."

1163 1164 1165 # Colour errors. 1166 ################ 1167 1168 # Invalid colour.

1169 -class RelaxInvalidColourError(BaseError):

1170 - def __init__(self, colour):

1171 self.text = "The colour " + repr(colour) + " is invalid."

1172 1173 1174 # Value errors. 1175 ############### 1176 1177 # Infinity.

1178 -class RelaxInfError(BaseError):

1179 - def __init__(self, name):

1180 self.text = "The invalid " + name + " floating point value of infinity has occurred."

1181 1182 # NaN (Not a Number).

1183 -class RelaxNaNError(BaseError):

1184 - def __init__(self, name):

1185 self.text = "The invalid " + name + " floating point value of NaN (Not a Number) has occurred."

1186 1187 1188 # XML errors. 1189 ############# 1190 1191 # Cannot recreate from the XML - the structure is not empty.

1192 -class RelaxFromXMLNotEmptyError(BaseError):

1193 - def __init__(self, name):

1194 self.text = "The " + name + " data structure cannot be recreated from the XML elements as the structure is not empty."

1195 1196 1197 1198 # An object of all the RelaxErrors. 1199 ################################### 1200 1201 # Function for setting up the AllRelaxErrors object.

1202 -def all_errors(names):

1203 """Function for returning all the RelaxErrors to allow the AllRelaxError object to be created.""" 1204 1205 # Empty list. 1206 list = [] 1207 1208 # Loop over all objects of this module. 1209 for name in names: 1210 # Get the object. 1211 object = globals()[name] 1212 1213 # Skip over all non error class objects. 1214 if not (isinstance(object, type(RelaxError)) or isinstance(object, type(type))) or not match('Relax', name): 1215 continue 1216 1217 # Append to the list. 1218 list.append(object) 1219 1220 # Return the list of RelaxErrors 1221 return list

1222 1223 # Initialise the AllRelaxErrors structure, as a tuple for the except statements, so it can be imported. 1224 AllRelaxErrors = tuple(all_errors(dir())) 1225