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

Uploaded the version running on the prod server

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/maaslin-4450aa4ecc84/src/lib/ValidateData.R	Sun Feb 08 23:08:38 2015 -0500
@@ -0,0 +1,93 @@
+#####################################################################################
+#Copyright (C) <2012>
+#
+#Permission is hereby granted, free of charge, to any person obtaining a copy of
+#this software and associated documentation files (the "Software"), to deal in the
+#Software without restriction, including without limitation the rights to use, copy,
+#modify, merge, publish, distribute, sublicense, and/or sell copies of the Software,
+#and to permit persons to whom the Software is furnished to do so, subject to
+#the following conditions:
+#
+#The above copyright notice and this permission notice shall be included in all copies
+#or substantial portions of the Software.
+#
+#THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED,
+#INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A
+#PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+#HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
+#OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE
+#SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+#
+# This file is a component of the MaAsLin (Multivariate Associations Using Linear Models), 
+# authored by the Huttenhower lab at the Harvard School of Public Health
+# (contact Timothy Tickle, [e-mail]).
+#####################################################################################
+
+inlinedocs <- function(
+##author<< Curtis Huttenhower <[e-mail]> and Timothy Tickle <[e-mail]>
+##description<< Minor validation files to check data typing when needed.
+) { return( pArgs ) }
+
+funcIsValid <- function(
+### Requires a data to not be NA, not be NULL
+### Returns True on meeting these requirements, returns false otherwise
+### Return boolean Indicator of not being empty (TRUE = not empty)
+tempData = NA
+### Parameter tempData Is evaluated as not empty
+){
+  #If the data is not na or null return true
+  if(!is.null(tempData))
+  {
+    if(length(tempData)==1){ return(!is.na(tempData)) }
+    return(TRUE)
+  }
+  return(FALSE)
+  ### True (Valid) false (invalid)
+}
+
+funcIsValidString <- function(
+### Requires a data to not be NA, not be NULL, and to be of type Character
+### Returns True on meeting these requirements, returns false otherwise
+### Return boolean Indicator of identity as a string
+tempData = NA
+### Parameter tempData Is evaluated as a string
+){
+  #If is not a valid data return false
+  if(!funcIsValid(tempData))
+  {
+    return(FALSE)
+  }
+  #If is a string return true
+  if((class(tempData)=="character")&&(length(tempData)==1))
+  {
+    return(TRUE)
+  }
+  return(FALSE)
+  ### True (Valid) false (invalid)
+}
+
+funcIsValidFileName <- function(
+### Requires a data to not be NA, not be NULL, and to be a valid string
+### which points to an existing file
+### Returns True on meeting these requirements, returns false otherwise
+### Return boolean Indicator of identity as a file name
+tempData = NA,
+### Parameter tempData Is evaluated as a file name
+fVerbose=FALSE
+### Verbose will print the file path when not valid.
+){
+  #If is not valid string return false
+  if(!(funcIsValidString(tempData)))
+  {
+    if(fVerbose){print(paste("FunctIsValidFileName: InvalidString. Value=",tempData,sep=""))}
+    return(FALSE)
+  }
+  #If is a valid string and points to a file
+  if(file.exists(tempData))
+  {
+    return(TRUE)
+  }
+  if(fVerbose){print(paste("FunctIsValidFileName: Path does not exist. Value=",tempData,sep=""))}
+  return(FALSE)
+  ### True (Valid) false (invalid)
+}