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comparison maaslin-4450aa4ecc84/src/lib/ValidateData.R @ 1:a87d5a5f2776

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Uploaded the version running on the prod server
author george-weingart
date Sun, 08 Feb 2015 23:08:38 -0500
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0:e0b5980139d9 1:a87d5a5f2776
1 #####################################################################################
2 #Copyright (C) <2012>
3 #
4 #Permission is hereby granted, free of charge, to any person obtaining a copy of
5 #this software and associated documentation files (the "Software"), to deal in the
6 #Software without restriction, including without limitation the rights to use, copy,
7 #modify, merge, publish, distribute, sublicense, and/or sell copies of the Software,
8 #and to permit persons to whom the Software is furnished to do so, subject to
9 #the following conditions:
10 #
11 #The above copyright notice and this permission notice shall be included in all copies
12 #or substantial portions of the Software.
13 #
14 #THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED,
15 #INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A
16 #PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
17 #HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
18 #OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE
19 #SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
20 #
21 # This file is a component of the MaAsLin (Multivariate Associations Using Linear Models),
22 # authored by the Huttenhower lab at the Harvard School of Public Health
23 # (contact Timothy Tickle, ttickle@hsph.harvard.edu).
24 #####################################################################################
25
26 inlinedocs <- function(
27 ##author<< Curtis Huttenhower <chuttenh@hsph.harvard.edu> and Timothy Tickle <ttickle@hsph.harvard.edu>
28 ##description<< Minor validation files to check data typing when needed.
29 ) { return( pArgs ) }
30
31 funcIsValid <- function(
32 ### Requires a data to not be NA, not be NULL
33 ### Returns True on meeting these requirements, returns false otherwise
34 ### Return boolean Indicator of not being empty (TRUE = not empty)
35 tempData = NA
36 ### Parameter tempData Is evaluated as not empty
37 ){
38 #If the data is not na or null return true
39 if(!is.null(tempData))
40 {
41 if(length(tempData)==1){ return(!is.na(tempData)) }
42 return(TRUE)
43 }
44 return(FALSE)
45 ### True (Valid) false (invalid)
46 }
47
48 funcIsValidString <- function(
49 ### Requires a data to not be NA, not be NULL, and to be of type Character
50 ### Returns True on meeting these requirements, returns false otherwise
51 ### Return boolean Indicator of identity as a string
52 tempData = NA
53 ### Parameter tempData Is evaluated as a string
54 ){
55 #If is not a valid data return false
56 if(!funcIsValid(tempData))
57 {
58 return(FALSE)
59 }
60 #If is a string return true
61 if((class(tempData)=="character")&&(length(tempData)==1))
62 {
63 return(TRUE)
64 }
65 return(FALSE)
66 ### True (Valid) false (invalid)
67 }
68
69 funcIsValidFileName <- function(
70 ### Requires a data to not be NA, not be NULL, and to be a valid string
71 ### which points to an existing file
72 ### Returns True on meeting these requirements, returns false otherwise
73 ### Return boolean Indicator of identity as a file name
74 tempData = NA,
75 ### Parameter tempData Is evaluated as a file name
76 fVerbose=FALSE
77 ### Verbose will print the file path when not valid.
78 ){
79 #If is not valid string return false
80 if(!(funcIsValidString(tempData)))
81 {
82 if(fVerbose){print(paste("FunctIsValidFileName: InvalidString. Value=",tempData,sep=""))}
83 return(FALSE)
84 }
85 #If is a valid string and points to a file
86 if(file.exists(tempData))
87 {
88 return(TRUE)
89 }
90 if(fVerbose){print(paste("FunctIsValidFileName: Path does not exist. Value=",tempData,sep=""))}
91 return(FALSE)
92 ### True (Valid) false (invalid)
93 }