Collaboration diagram for common.ErrorHandler.CErrorHandler:
Public Member Functions | |
| def | __init__ (s) |
| Ctor. More... | |
| def | SetOutputFile (s, ffn, mode="w") |
Set an output file instead of default sys.stderr. More... | |
| def | Write (s, errorText) |
| Emit an error message. More... | |
| def | Emit (s, token) |
| Standard way of reporting an error. More... | |
Static Public Attributes | |
| string | ERR_CANNOT_OPEN_FILE = "Cannot open file ``{0}''."; |
| string | ERR_INVALID_FILE_FORMAT = "``{0}'': Invalid file format."; |
| string | ERR_MULTIPLE_STDIN_INPUT = "Cannot read from more than one standard input."; |
| string | ERR_CANNOT_MAP_WO_ENSG = "Either input or output format must be from human."; |
| string | ERR_INVALID_COLUMN_NR = "Invalid column number: ``{0}''."; |
| string | ERR_TOO_MANY_COLUMNS = "Too many columns supplied."; |
| string | ERR_VARYING_NR_COLUMNS = "Varying number of columns in input."; |
| string | ERR_VARYING_NR_COLUMNS2 = "Varying number of columns in input: previous" +\ |
| string | ERR_INVALID_COLUMN_FOR_OPTION = "Invalid column selection '{0}' for " +\ |
| string | ERR_CANNOT_MAP_IDENTITY = "Cannot perform identity mapping."; |
| string | ERR_MUST_BE_ON_SAME_CHROM = "Pair must be on same chromosome ({0}-{1})."; |
| string | ERR_OVERLAPPING_LD_BLOCKS = "LD block overlap."; |
| string | ERR_UNKNOWN_CHROM = "Unknown chromosome: ``{0}''."; |
| string | ERR_INVALID_GENOMIC_COORDINATE = "Invalid genomic coordinate: ``{0}''."; |
| string | ERR_INVALID_STARTEND_POS = "The end position ({0}) of a genomic "+\ |
| string | ERR_INCORRECT_GENOME_BUILD = "Incompatible genome build: ``{0}''."; |
| string | ERR_COULD_NOT_CONVERT_DATA_TYPE = "Could not convert ``{0}'' to <{1}>."; |
| string | ERR_INVALID_GENOTYPE = "``{0}'': Invalid or missing genotype."; |
| string | ERR_ONLY_POSITIVE_NUMBERS = "Only positive numbers are allowed. "+\ |
| string | ERR_OPTION_MISSING = "Option(s) missing: ``{0}''."; |
| string | ERR_MUTEX_OPTIONS = "Options mutually exclude: ``{0}''."; |
| string | ERR_INVALID_COMBINATION_OF_PENETRANCE_AND_DETECTANCE |
| string | ERR_DB_DOES_NOT_EXIST_IS_EMPTY = "Database does not exist or does not " +\ |
| string | ERR_DB_NOT_INITIALIZED = "Database connector has not been initialized." |
| string | ERR_INVALID_CONFIG = "Dint configuration missing." |
| string | ERR_DB_MISSING_PY_MODULE = "Missing database interface module ``{0}''." |
| string | ERR_DB_CONNECTION_ALREADY_OPEN = "Database connection already " +\ |
| string | ERR_DB_CONNECTION_CLOSED = "Database connection to the server {0} " +\ |
| string | ERR_DB_NO_CONNECTION = "Cannot establish database connection. " +\ |
| string | ERR_DB_CONNECTION = "Database connection to the server {0} " +\ |
| string | ERR_DB_UNSUPPORTED_DB = "Unsupported database selected, we " +\ |
| string | ERR_DB_SQL_STATEMENT_WRONG = "SQL error, please insult the guy " +\ |
| string | ERR_DB_EXECUTION = "The SQL query cannot be executed for the " +\ |
| string | ERR_UNSUPPORTED_IDENTIFIER = "The identifier system {0} is unknown, " +\ |
| string | ERR_INVALID_CMD_PARAMETER = "Invalid command line parameter: ``{0}''."; |
| string | ERR_INVALID_PARAMETER = "The function parameter {0} contains the invalid "+\ |
| string | ERR_INVALID_DISEASE_SET = "{0} is not a supported disease set, valid " +\ |
| string | ERR_NO_EXACT_MATCH = "Matching of exact reference and variant allele is " +\ |
| string | ERR_INVALID_NR_WEIGHTS = "Invalid number of weights."; |
| string | ERR_INVALID_SORT_ORDER = "Invalid sort order: ``{0}''."; |
| string | ERR_NR_WEIGHTS_MISMATCH = "Number of weights does not match number of "+\ |
| string | ERR_WEIGHTS_POSITIVE = "Weights must be non-negative."; |
| string | ERR_INVALID_FILTER_ITEM = "Invalid filter item(s) ``{0}''."; |
| string | ERR_EMPTY_PANEL = "Panel file does not contain valid entries." |
| string | ERR_PVAL_NOT_COMPUTABLE = "P-value cannot be computed if no panel is "+\ |
| string | ERR_MIN_MAX = "The number {0} has to be greater or equal to {1}. " |
| string | ERR_EMPTY_FILE = "The input file/stream is empty." |
| string | ERR_EMPTY_HEADER = "The input file/stream does not contain a header."; |
| string | ERR_AC_NE_GO = "Annotation corpus does not match ontology."; |
| string | ERR_INCORRECT_AC = "Incorrect annotation corpus type ``{0}''."; |
| string | ERR_NO_GRAPH_LIB = "No suitable graph library found."; |
| string | ERR_MISSING_SAMPLE = "Sample {0} is missing from the VCF file."; |
| string | ERR_BOTH_ADD_EXTRACT = "Cannot use both args ``-a'' and ``-e''."; |
| string | ERR_RET_IC_ONLY = "Selected input type returns only information content "+\ |
| string | ERR_FUNSIM_IMPOSSIBLE = "Impossible to compute functional similarity "+\ |
| string | ERR_COLLCNT_PANEL = "Collapse and count options are applicable only "+\ |
| string | ERR_PANEL_INPTYPE_CONFLICT = "Wrong input type option for panel file."; |
| string | ERR_ONLY_SINGLE_MEASURE_POSSIBLE = "Only a single semantic and "+\ |
| string | WRN_INSUFF_COLS = "Warning: Insufficient number of columns to index "+\ |
| string | WRN_MISSING_GENOME_BUILD = "Warning: Genome build missing in ``{0}''."; |
| string | WRN_MISSING_BUILD_ASSUME_DEFAULT = "Warning: " + \ |
| string | WRN_UNEQUAL_GENOME_BUILD = "Warning: Default genome build {0} of the "+\ |
| string | WRN_OPT_NOT_EFFECTIVE = "Warning: Option ``{0}'' does not become "+\ |
| string | WRN_DET_SET |
| string | WRN_PEN_SET |
| string | WRN_MULTIPLE_VALUES_FOR_KEY = "Warning: Multiple values for key ``{0}''. "+\ |
| string | WRN_NON_BP_CHARACTERS = "Warning: {0}: Detected non-basepair characters."; |
| string | WRN_INDEL_CHARACTER = "Warning: {0}: {1} should be indicated by a"+\ |
| string | WRN_NR_BP_MISMATCH = "Warning: {0}: Number of basepairs mismatch."; |
| string | WRN_MULTIPLE_TAXIDS = "Warning: {0}: More than one taxon ID in MITAB "+\ |
| string | WRN_COV = "Warning: Genotype call for sample {0} in variant {1} was "+\ |
Detailed Description
The error handler by default writes to \c sys.stderr. This can be changed by supplying an output file for writing. This class contains all available tokens, ie. messages that may appear in many different contexts.
Constructor & Destructor Documentation
◆ __init__()
| def common.ErrorHandler.CErrorHandler.__init__ | ( | s | ) |
Ctor.
Member Function Documentation
◆ Emit()
| def common.ErrorHandler.CErrorHandler.Emit | ( | s, | |
| token | |||
| ) |
Standard way of reporting an error.
Emit an error message using one of the supported tokens.
@param token Token @c String defined in this class.
◆ SetOutputFile()
| def common.ErrorHandler.CErrorHandler.SetOutputFile | ( | s, | |
| ffn, | |||
mode = "w" |
|||
| ) |
Set an output file instead of default sys.stderr.
@param ffn Full file name of new output file.
@param mode Mode for opening the file.
@return \c True if all went ok, \c False on file opening error, an
error message has already been emitted.
◆ Write()
| def common.ErrorHandler.CErrorHandler.Write | ( | s, | |
| errorText | |||
| ) |
Emit an error message.
This function may only be used in case there is no token available,
and is the most generic form of error output.
@param errorText Error or warning message.
Member Data Documentation
◆ ERR_AC_NE_GO
|
static |
◆ ERR_BOTH_ADD_EXTRACT
|
static |
◆ ERR_CANNOT_MAP_IDENTITY
|
static |
◆ ERR_CANNOT_MAP_WO_ENSG
|
static |
◆ ERR_CANNOT_OPEN_FILE
|
static |
◆ ERR_COLLCNT_PANEL
|
static |
◆ ERR_COULD_NOT_CONVERT_DATA_TYPE
|
static |
◆ ERR_DB_CONNECTION
|
static |
◆ ERR_DB_CONNECTION_ALREADY_OPEN
|
static |
◆ ERR_DB_CONNECTION_CLOSED
|
static |
◆ ERR_DB_DOES_NOT_EXIST_IS_EMPTY
|
static |
◆ ERR_DB_EXECUTION
|
static |
◆ ERR_DB_MISSING_PY_MODULE
|
static |
◆ ERR_DB_NO_CONNECTION
|
static |
◆ ERR_DB_NOT_INITIALIZED
|
static |
◆ ERR_DB_SQL_STATEMENT_WRONG
|
static |
◆ ERR_DB_UNSUPPORTED_DB
|
static |
◆ ERR_EMPTY_FILE
|
static |
◆ ERR_EMPTY_HEADER
|
static |
◆ ERR_EMPTY_PANEL
|
static |
◆ ERR_FUNSIM_IMPOSSIBLE
|
static |
◆ ERR_INCORRECT_AC
|
static |
◆ ERR_INCORRECT_GENOME_BUILD
|
static |
◆ ERR_INVALID_CMD_PARAMETER
|
static |
◆ ERR_INVALID_COLUMN_FOR_OPTION
|
static |
◆ ERR_INVALID_COLUMN_NR
|
static |
◆ ERR_INVALID_COMBINATION_OF_PENETRANCE_AND_DETECTANCE
|
static |
Initial value:
= """
You cannot specify penetrance = {0} and detectance = {1},
because these values contradict each other.
Please change at least one of the values.
If you would like to keep detectance = {1},
change the penetrance to a value between {2} and 1.0.
If you would like to keep penetrance = {0},
change the detectance to a value between 0.0 and {3}."""
◆ ERR_INVALID_CONFIG
|
static |
◆ ERR_INVALID_DISEASE_SET
|
static |
◆ ERR_INVALID_FILE_FORMAT
|
static |
◆ ERR_INVALID_FILTER_ITEM
|
static |
◆ ERR_INVALID_GENOMIC_COORDINATE
|
static |
◆ ERR_INVALID_GENOTYPE
|
static |
◆ ERR_INVALID_NR_WEIGHTS
|
static |
◆ ERR_INVALID_PARAMETER
|
static |
◆ ERR_INVALID_SORT_ORDER
|
static |
◆ ERR_INVALID_STARTEND_POS
|
static |
◆ ERR_MIN_MAX
|
static |
◆ ERR_MISSING_SAMPLE
|
static |
◆ ERR_MULTIPLE_STDIN_INPUT
|
static |
◆ ERR_MUST_BE_ON_SAME_CHROM
|
static |
◆ ERR_MUTEX_OPTIONS
|
static |
◆ ERR_NO_EXACT_MATCH
|
static |
◆ ERR_NO_GRAPH_LIB
|
static |
◆ ERR_NR_WEIGHTS_MISMATCH
|
static |
◆ ERR_ONLY_POSITIVE_NUMBERS
|
static |
◆ ERR_ONLY_SINGLE_MEASURE_POSSIBLE
|
static |
◆ ERR_OPTION_MISSING
|
static |
◆ ERR_OVERLAPPING_LD_BLOCKS
|
static |
◆ ERR_PANEL_INPTYPE_CONFLICT
|
static |
◆ ERR_PVAL_NOT_COMPUTABLE
|
static |
◆ ERR_RET_IC_ONLY
|
static |
◆ ERR_TOO_MANY_COLUMNS
|
static |
◆ ERR_UNKNOWN_CHROM
|
static |
◆ ERR_UNSUPPORTED_IDENTIFIER
|
static |
◆ ERR_VARYING_NR_COLUMNS
|
static |
◆ ERR_VARYING_NR_COLUMNS2
|
static |
◆ ERR_WEIGHTS_POSITIVE
|
static |
◆ WRN_COV
|
static |
◆ WRN_DET_SET
|
static |
Initial value:
= """
Warning: You only selected penetrance = {0}. The detectance was set to {1},
which corresponds to the maximial value and will result in the most strict
filtering regarding detectance.
"""
◆ WRN_INDEL_CHARACTER
|
static |
◆ WRN_INSUFF_COLS
|
static |
◆ WRN_MISSING_BUILD_ASSUME_DEFAULT
|
static |
◆ WRN_MISSING_GENOME_BUILD
|
static |
◆ WRN_MULTIPLE_TAXIDS
|
static |
◆ WRN_MULTIPLE_VALUES_FOR_KEY
|
static |
◆ WRN_NON_BP_CHARACTERS
|
static |
◆ WRN_NR_BP_MISMATCH
|
static |
◆ WRN_OPT_NOT_EFFECTIVE
|
static |
◆ WRN_PEN_SET
|
static |
Initial value:
= """
Warning: You only selected detectance = {0}. The penetrance was set to {1},
which corresponds to the maximal value and will result in the most strict
filtering regarding penetrance.
"""
◆ WRN_UNEQUAL_GENOME_BUILD
|
static |
The documentation for this class was generated from the following file:
- common/ErrorHandler.py
