dot_test: Helping tests

In frankkramer-lab/RCX: R package implementing the Cytoscape Exchange (CX) format

Helping tests

Description

Tests for validating RCX objects and its aspects.

Usage

.test_RequiredColumnsPresent(aspect, columns, verbose = FALSE)

.test_ListRequiredColumnsPresent(aspect, columns, verbose = FALSE)

.test_AllowedColumnsPresent(aspect, columns, verbose = FALSE)

.test_ListAllowedColumnsPresent(aspect, columns, verbose = FALSE)

.test_NoMergeColumn(aspect, column, verbose = FALSE)

.test_AtLeastOneColumnPresent(aspect, columns, verbose = FALSE)

.test_AtLeastOneElementPresent(aspect, element, verbose = FALSE)

.test_OneNodePresent(nodesAspect, column, verbose = FALSE)

.test_IsUnique(aspect, column, verbose = FALSE)

.test_ListAllUnique(aspect, column, verbose = FALSE)

.test_IsUniqueInLists(aspect, column, verbose = FALSE)

.test_ListAllUniqueInLists(aspect, column, verbose = FALSE)

.test_IsLogical(aspect, column, verbose = FALSE)

.test_IsNumeric(aspect, column, verbose = FALSE)

.test_ElementIsNumeric(aspect, element, verbose = FALSE)

.test_IsCharacter(aspect, column, verbose = FALSE)

.test_ListAllCharacter(aspect, element, verbose = FALSE)

.test_IsList(aspect, column, verbose = FALSE)

.test_ElementIsList(aspect, element, verbose = FALSE)

.test_IsPos(aspect, column, verbose = FALSE)

.test_IsClass(x, cls, verbose = FALSE)

.test_IsNamedList(aspect, names, verbose = FALSE)

.test_IsCVPclass(x, cls, verbose = FALSE)

.test_ListOfCVPclass(x, cls, verbose = FALSE)

.test_ContainsNA(aspect, column, verbose = FALSE)

.test_ListAllContainsNA(aspect, element, verbose = FALSE)

.test_ListAllNumeric(aspect, column, verbose = FALSE)

.test_ListAllNumericOrInDict(aspect, column, dic, verbose = FALSE)

.test_ListAllOfClass(aspect, cls, verbose = FALSE)

.test_AspectExist(rcx, aspect, verbose = FALSE)

.test_IdsInAspect(ids, aspect, column, info = "", verbose = FALSE)

.test_ValuesInSet(aspect, column, set, ignoreNA = TRUE, verbose = FALSE)

.test_DataTypeColumn(aspect, column, verbose = FALSE)

Arguments

aspect	one RCX aspect
columns	character; list of columns
verbose	logical (default=FALSE); also log the results
column	character; column name
cls	character; class name in .CLS or .CLSvp
names	character; names of list
dic	character; key in .DICT
rcx	RCX object
ids	numeric; ids
info	character (default=""); additional message for verbose
ignoreNA	logical (default=TRUE); ignore NA values

Value

logical; pass or fail the test

Functions

• .test_RequiredColumnsPresent: checks if aspect has all required columns

• .test_ListRequiredColumnsPresent: checks if all list elements have all required columns

• .test_AllowedColumnsPresent: checks if only allowed columns are set

• .test_ListAllowedColumnsPresent: checks if all list elements have only allowed columns

• .test_NoMergeColumn: checks if column with old ids is not present (would be a merge artefact)

• .test_AtLeastOneColumnPresent: checks if at least one specified column is present

• .test_AtLeastOneElementPresent: checks if at least one specified element is present

• .test_OneNodePresent: checks if at least one element (node) is present in the specified column

• .test_IsUnique: checks if all elements in specified column are unique

• .test_ListAllUnique: checks for all list elements if all elements in specified column are unique

• .test_IsUniqueInLists: checks if all elements in specified column are unique

• .test_ListAllUniqueInLists: checks if all elements in specified column are unique

• .test_IsLogical: checks if the specified column is of type logical

• .test_IsNumeric: checks if the specified column is of type numeric

• .test_ElementIsNumeric: checks if the specified column is of type numeric

• .test_IsCharacter: checks if the specified column is of type character

• .test_ListAllCharacter: checks if the specified list element are all of type character

• .test_IsList: checks if the specified column is of type list

• .test_ElementIsList: checks if the specified column is of type list

• .test_IsPos: checks if the specified column are positive integers

• .test_IsClass: checks if the specified column is of the specified class in .CLS

• .test_IsNamedList: checks if the aspect is a list with specified names

• .test_IsCVPclass: checks if the specified column is of the specified class in .CLSvp

• .test_ListOfCVPclass: checks if the all elements in the list are of class in .CLSvp

• .test_ContainsNA: checks if the specified column contains any NA values

• .test_ListAllContainsNA: checks if the specified list element contains any NA values

• .test_ListAllNumeric: checks if the specified column is a list with only numeric values (NAs and NULLs are not considered)

• .test_ListAllNumericOrInDict: checks if the specified column is a list with only numeric values (NAs and NULLs are not considered) or in .DICT

• .test_ListAllOfClass: checks if the specified column is a list with only numeric values (NAs and NULLs are not considered) or in .DICT

• .test_AspectExist: checks if the rcx object contains the specified apsect

• .test_IdsInAspect: checks if all provided ids are present in the specified column of an aspect

• .test_ValuesInSet: checks if the specified column of an aspect only contains values of the provided set

• .test_DataTypeColumn: checks if the dataType column of an aspect only contains JSON data types.

Note

Internal function only for convenience

frankkramer-lab/RCX documentation built on Feb. 4, 2023, 5:12 p.m.