Python anydbm.error() Examples

def populate_molecules_dict(self):
        # Shelve creates a file with specific database. Using a temp file requires a workaround to open it.
        t_filename = tempfile.NamedTemporaryFile(delete=True).name
        # dbm could not work: Eg. dbm.error: cannot add item.
        # Use dumbdbm for the local execution. Python 3 should fix this issue.
        dumb_dict = dbm.open(t_filename, 'n')
        shelve_out = shelve.Shelf(dict=dumb_dict)
        for uri in self.molecule_uri:
            self._logger.debug('ChEMBL getting Molecule from %s', uri)
            with URLZSource(uri).open() as f_obj:
                for line in f_obj:
                    #TODO handle malformed JSON lines better
                    mol = json.loads(line)
                    shelve_out[str(mol["molecule_chembl_id"])] = mol

        self._logger.debug('ChEMBL Molecule loading done.')
        return shelve_out 

def truncate_to_max(errors, max_errors):
    """If max_errors was specified, truncate the list of errors.

    Give the total number of times that the error was found elsewhere.
    """
    if len(errors) > max_errors:
        start1, end1, err1, msg1, replacements = errors[0]

        if len(errors) == (max_errors + 1):
            msg1 += " Found once elsewhere."
        else:
            msg1 += " Found {} times elsewhere.".format(len(errors))

        errors = errors[1:max_errors]
        errors = [(start1, end1, err1, msg1, replacements)] + errors

    return errors 

def create(self):
        """
        Create a new on-disk database.

        :raises anydbm.error: If there's a problem creating the database.
        """
        if self.filename:
            self.db = anydbm.open(self.filename, "n") #raises anydbm.error
            self.db["--Reserved--type"] = self.type
            self.db.sync()
        else:
            self.db = {} 

def open(self):
        """
        Open a pre-existing on-disk database.

        :raises anydbm.error: If there's a problem opening the database.
        :raises ValueError: If the database is not of the right type.
        """
        if not self.filename:
            raise ValueError("Can only open on-disk databases")
        self.db = anydbm.open(self.filename, "w") #raises anydbm.error
        try:
            if self.db["--Reserved--type"] != self.type:
                raise ValueError("Not a %s database" % self.type)
        except KeyError:
            raise ValueError("Not a recognized database") 

def create(self):
        """Create a new on-disk database.

        @raise anydbm.error: If there's a problem creating the database.
        """
        if self.filename:
            self.db = anydbm.open(self.filename, "n") #raises anydbm.error
            self.db["--Reserved--type"] = self.type
            self.db.sync()
        else:
            self.db = {} 

def open(self):
        """Open a pre-existing on-disk database.

        @raise anydbm.error: If there's a problem opening the database.
        @raise ValueError: If the database is not of the right type.
        """
        if not self.filename:
            raise ValueError("Can only open on-disk databases")
        self.db = anydbm.open(self.filename, "w") #raises anydbm.error
        try:
            if self.db["--Reserved--type"] != self.type:
                raise ValueError("Not a %s database" % self.type)
        except KeyError:
            raise ValueError("Not a recognized database") 

def create(self):
        """Create a new on-disk database.

        @raise anydbm.error: If there's a problem creating the database.
        """
        if self.filename:
            self.db = anydbm.open(self.filename, "n") #raises anydbm.error
            self.db["--Reserved--type"] = self.type
            self.db.sync()
        else:
            self.db = {} 

def open(self):
        """Open a pre-existing on-disk database.

        @raise anydbm.error: If there's a problem opening the database.
        @raise ValueError: If the database is not of the right type.
        """
        if not self.filename:
            raise ValueError("Can only open on-disk databases")
        self.db = anydbm.open(self.filename, "w") #raises anydbm.error
        try:
            if self.db["--Reserved--type"] != self.type:
                raise ValueError("Not a %s database" % self.type)
        except KeyError:
            raise ValueError("Not a recognized database") 

def populate_synonyms_for_molecule(self, molecule_set, molecules_syn_dict):
        def _append_to_mol2syn(m2s_dict, molecule):
            """if molecule has synonyms create a clean entry in m2s_dict with all synms for that chembl_id.
            Returns either None if goes ok or the molecule chembl id if something wrong"""
            if 'molecule_synonyms' in molecule and molecule['molecule_synonyms']:
                synonyms = []
                for syn in molecule['molecule_synonyms']:
                    synonyms.append(syn['synonyms'])
                    synonyms.append(syn['molecule_synonym'])
                synonyms = list(set(synonyms))
                m2s_dict[molecule['molecule_chembl_id']] = synonyms
                return None
            else:
                return molecule['molecule_chembl_id']

        if not molecule_set or not len(molecule_set):
            self._logger.warn("No molecules in set")
            return

        data = {'molecules':[]}
        for mol_k in molecule_set:
            if mol_k in self.molecules_dict:
                data['molecules'].append(self.molecules_dict[mol_k])
            else:
                raise ValueError('problem retrieving the molecule info from the local db', str(mol_k))

        #if the data is what we expected, process it
        if 'molecules' in data:
            map_f = functools.partial(_append_to_mol2syn, molecules_syn_dict)
            mols_without_syn = \
                list(itertools.filterfalse(lambda mol: mol is None, map(map_f, data['molecules'])))
            if mols_without_syn:
                self._logger.debug('molecule list with no synonyms %s', str(mols_without_syn))

        else:
            self._logger.error("there is no 'molecules' key in the structure")
            raise RuntimeError("unexpected chembl API response") 

def _get_cache(cachepath):
    if cachepath in _cache_shelves:
        return _cache_shelves[cachepath]

    try:
        cache = shelve.open(cachepath, protocol=2)
    except dbm.error:
        # dbm error on open - delete and retry
        print('Error (%s) opening %s - will attempt to delete and re-open.' %
              (sys.exc_info()[1], cachepath))
        try:
            os.remove(cachepath)
            cache = shelve.open(cachepath, protocol=2)
        except Exception:
            print('Error on re-open: %s' % sys.exc_info()[1])
            cache = None
    except Exception:
        # unknown error
        print('Could not open cache file %s, maybe name collision. '
              'Error: %s' % (cachepath, traceback.format_exc()))
        cache = None

    # Don't fail on bad caches
    if cache is None:
        print('Using in-memory shelf for cache file %s' % cachepath)
        cache = shelve.Shelf(dict())

    _cache_shelves[cachepath] = cache
    return cache 

def lint(input_file, debug=False):
    """Run the linter on the input file."""
    options = load_options()

    if isinstance(input_file, string_types):
        text = input_file
    else:
        text = input_file.read()

    # Get the checks.
    checks = get_checks(options)

    # Apply all the checks.
    errors = []
    for check in checks:

        result = check(text)

        for error in result:
            (start, end, check, message, replacements) = error
            (line, column) = line_and_column(text, start)
            if not is_quoted(start, text):
                errors += [(check, message, line, column, start, end,
                           end - start, "warning", replacements)]

        if len(errors) > options["max_errors"]:
            break

    # Sort the errors by line and column number.
    errors = sorted(errors[:options["max_errors"]], key=lambda e: (e[2], e[3]))

    return errors 

def assert_error(text, check, n=1):
    """Assert that text has n errors of type check."""
    assert_error.description = "No {} error for '{}'".format(check, text)
    assert(check in [error[0] for error in lint(text)])