schrodinger.test.stu.outcomes.standard_workups module

Contains the class _PropertyCompare, and several functions to perform test workups.

The most commonly used workup is compare_ct_property

@copyright: Schrodinger, LLC. All rights reserved.

exception schrodinger.test.stu.outcomes.standard_workups.WorkupFailure(msg, *args)

Bases: schrodinger.test.stu.outcomes.failures.WorkupFailure

__init__(msg, *args)

args

failure_type = 'workup'

with_traceback()

Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.

schrodinger.test.stu.outcomes.standard_workups.lines_in_file(file_expr, num_lines_target, tolerance)

Counts the number of lines in one or more files matching a single shell expansion expression, file_expr and checks that they are within +/- tolerance of num_lines_target.

usage: lines_in_file(‘file’, num_lines_target, tolerance)

schrodinger.test.stu.outcomes.standard_workups.files_exist(*filenames)

Checks to see if all the files exist. Inputs are assumed to be filenames or shell expansion expressions representing filenames. Note that shell expansion expressions check for _any_ match (not _all_).

usage: files_exist(‘file1’, ‘file2’, …)

schrodinger.test.stu.outcomes.standard_workups.file_exists(*filenames)

Alias for backwards compatibility.

schrodinger.test.stu.outcomes.standard_workups.many_files_exist(input_file)

Checks to see if all the files exist. Input is assumed to be a file containing list of filenames or shell expansion expressions representing filenames - one filename per line.

schrodinger.test.stu.outcomes.standard_workups.files_dont_exist(*filenames)

Checks to see if all the files don’t exist. Input is assumed to be a list of filenames or shell expansion expressions representing filenames.

usage: files_dont_exist(‘file1’, ‘file2’, …)

schrodinger.test.stu.outcomes.standard_workups.cts_in_file(filename, num_cts_target, tolerance=0)

Counts the number of cts in a file and checks that its within +/- range of the expected number of cts.

usage: cts_in_file(file, num_cts_target, tolerance)

schrodinger.test.stu.outcomes.standard_workups.cts_less_than(filename, num_cts_upper_bound)

Check that filename has fewer than num_cts_upper_bound cts.

schrodinger.test.stu.outcomes.standard_workups.cts_greater_than(filename, num_cts_lower_bound)

Check that filename has greater than num_cts_lower_bound cts.

schrodinger.test.stu.outcomes.standard_workups.compare_ct_property(filename, inp_property, inp_property_target, tolerance=0)

Compare property in the first ct to a user-provided value.

example usage: compare_ct_property(‘filename’, ‘inp_property’, 7.5, tolerance=0.01) Tolerance only works for properties that start with i or r (integers or floats).

schrodinger.test.stu.outcomes.standard_workups.parse_log_file(file_expr, pattern, occurrences=1)

Search files for a string. The string must appear at least the required number of times in each file.

Parameters

• file_expr (str) – file(s) to search; treated as a glob expression

• pattern (str) – string to search; treated as a simple substring

• occurrences (int) – minimum number of times the pattern must appear in each file. As a special case, when occurrences=0, it is treated as a maximum.

Examples:

parse_log_file('job.log', 'Job succeeded!')
parse_log_file('dock.log', 'Wrote pose', occurrences=42)
parse_log_file('*.out', 'ERRROR', occurrences=0)

schrodinger.test.stu.outcomes.standard_workups.strict_evaluate_ct_properties(stdvalue_file, structure_file)

Deprecated: Please use compare_ct_properties if possible.

Compare a subset of ct level properties for cts in a file against standard values using strict evaluation.

All properties must match within the provided per-value range in order for the comparison to be a success. Also checks that all expected cts (rows) in standard file have a corresponding match in the structure file. The structure file can have additional cts though.

Use the evaluate_ct_properties workup instead to prevent a failure from being triggered when a ct in the standard file is not found in the structure file.

Parameters

• stdvalue_file (str) – Path to a PropertyCompare file (must be a csv file with specific columns; see the _PropertyCompare class for details)

• structure_file (str) – Path to a Maestro structure file

schrodinger.test.stu.outcomes.standard_workups.evaluate_ct_properties(stdvalue_file, structure_file)

Deprecated: Please use compare_ct_properties if possible.

Compare a subset of ct level properties for cts in a file against standard values.

All properties must match within the provided per-value range in order for the comparison to be a success.

Note that a failure will NOT be triggered if a ct (row) in the standard file is not located in the structure file. To ensure that all cts in the standard match an entry in the comparison file, please use the workup strict_evaluate_ct_properties.

Parameters

• stdvalue_file (str) – Path to a PropertyCompare file (must be a csv file with specific columns; see the _PropertyCompare class for details)

• structure_file (str) – Path to a Maestro structure file

schrodinger.test.stu.outcomes.standard_workups.check_for_all_expected_cts(stdvalue_file, structure_file)

Look for the existence of all expected cts.

The structure file can have additional cts. Uses PropertyCompare standard file format: https://wiki.schrodinger.com/QA/PropertyCompare

usage: check_for_all_expected_cts(‘std_file’, ‘str_file’)

schrodinger.test.stu.outcomes.standard_workups.compare_files(filea, fileb, *options)

Find the diff of two files and compare the output.

Compare script takes the following arguments.

usage: compare_files(‘filea’, ‘fileb’, ‘-option1’, ‘value1_if_any’, ‘-option2’, ‘value2_if_any’)

Options:

<cutoff>        Absolute or relative diff allowed btw numerical fields.
                Must be a positive number. The default is 0.00001.
-r|-rel         Compare relative differences btw differing fields.
                This is the default.
-a|-abs         Compare absolute differences btw differing fields.
                The default is to compare relative differences.
-m|-mag <mag>   Minimum magnitude to use for assessing relative diffs.
                Must be positive.  The default value is 1.0.
-z              Compare magnitudes only (ignore sign differences).
-s|-skip <file> File containing regexps for lines to ignore.
                By default the file './skip_lines' is used.

schrodinger.test.stu.outcomes.standard_workups.untar(tar_name, *filenames)

Extracts a file from a tar file.

The files file1, file2, etc. will be extracted from tarName. Extract all the files in tarName, if no filename is specified.

usage: untar(tar_name, file1, file2, …)

schrodinger.test.stu.outcomes.standard_workups.unzip(zip_name, *filenames)

Extracts a file from a zip file.

The files file1, file2, etc. will be extracted from zipName.

Extract all the files in zipName,if no file name is specified

usage: unzip(zip_name, file1, file2, …)

schrodinger.test.stu.outcomes.standard_workups.gunzip(filename)

Extracts a file from a gz file. The original file is untouched, and the extracted file has the same name minus the gz extension.

usage: gunzip(filename)

schrodinger.test.stu.outcomes.standard_workups.extract_ct(input_file, output_file, index)

Extract the nth structure from input_file and write it to output_file.

usage: extract_ct(input_file, output_file, index)

schrodinger.test.stu.outcomes.standard_workups.expect_job_failure()

Expect the job to have a “bad” exit status. If this workup is included, the test will FAIL if it has a successful exit status and SUCCEED if it has a bad exit status. This is opposite of the usual behavior.