Pipeline Object FileList Fix

CHANGELOG.md

@@ -46,10 +46,13 @@ release.
 
 - Fixed relative paths not being properly converted to absolute paths in isisVarInit.py [4274](https://github.com/USGS-Astrogeology/ISIS3/issues/4274)
 - Fixed issue where serial numbers for Kaguya TC and MI image could not be generated. [4235](https://github.com/USGS-Astrogeology/ISIS3/issues/4235)
+- Fixed hardcoded file naming in the hijitter app dealing with output from pipeline. [#4372](https://github.com/USGS-Astrogeology/ISIS3/pull/4372)
 - Fixed "About Qview" to point to website documentation. [4333](https://github.com/USGS-Astrogeology/ISIS3/issues/4333)
 
 ### Changed
 
+- Updated the FileList object to handle files that do not contain a trailing new line character. [#4372](https://github.com/USGS-Astrogeology/ISIS3/pull/4372)
+
 - Refactored Blob class to be used by classes that serialize to a Cube instead of inherited from. Impacted classes are GisBlob, History, ImagePolygon, OriginalLabel, OriginalXmlLabel, StrethBlob, StringBlob, and Table. [#4082](https://github.com/USGS-Astrogeology/ISIS3/issues/4082)
 
 - Fixed hi2isis MRO:ADC_TIMING_SETTINGS label conversion issue [4290](https://github.com/USGS-Astrogeology/ISIS3/issues/4290)

isis/src/base/apps/cubeit/cubeit.xml

@@ -94,8 +94,7 @@
         </brief>
         <description>
           Each file in this list, one per line, will be added to
-          the output cube in the order they appear. The last file
-	  in the list must followed by a blank line.
+          the output cube in the order they appear.
         </description>
         <filter>
           *.lis

isis/src/base/objs/FileList/FileList.cpp

@@ -89,9 +89,10 @@ namespace Isis {
     Isis::IString s;
     bool bHasQuotes = false;
 
-    in.getline(buf, 65536);
     bool isComment = false;
-    while (!in.eof()) {
+    do {
+      in.getline(buf, 65536);
+
       s = buf;
       string::size_type loc = s.find("\"", 0);
 
@@ -108,7 +109,6 @@ namespace Isis {
 
       isComment = false;
       if(strlen(buf) == 0) {
-        in.getline(buf, 65536);
         continue;
       }
       for (int index = 0; index < (int)strlen(buf); index++) {
@@ -125,7 +125,6 @@ namespace Isis {
         }
       }
       if (isComment) {
-        in.getline(buf, 65536);
         continue;
       }
       else {
@@ -138,9 +137,9 @@ namespace Isis {
         }
 
         this->push_back(s.ToQt());
-        in.getline(buf, 65536);
       }
-    }
+
+    } while(!in.eof());
     if (this->size() == 0) {
       string msg = "Input Stream Empty";
       throw IException(IException::User, msg, _FILEINFO_);

isis/src/base/objs/Pipeline/Pipeline.cpp

@@ -15,7 +15,7 @@ find files of those names at the top level of this repository. **/
 #include "Application.h"
 #include "Preference.h"
 #include "Progress.h"
-#include "TextFile.h"
+#include "FileList.h"
 #include "FileName.h"
 
 using namespace Isis;
@@ -236,13 +236,13 @@ namespace Isis {
 
             QStringList listData = cmd.split(" ");
             QString listFileName = listData.takeFirst();
-            TextFile listFile(listFileName, "overwrite");
+            FileList listFile;
 
             while (!listData.isEmpty()) {
-              listFile.PutLine(listData.takeFirst());
+              listFile.push_back(listData.takeFirst());
             }
 
-            listFile.Close();
+            listFile.write(listFileName);
           }
           else {
             // Nothing special is happening, just execute the program
@@ -353,21 +353,9 @@ namespace Isis {
    */
   void Pipeline::SetInputListFile(const QString &inputParam) {
     UserInterface &ui = Application::GetUserInterface();
+    FileName inputFileName = FileName(ui.GetFileName(inputParam));
 
-    TextFile filelist(FileName(ui.GetFileName(inputParam)).expanded());
-    QString filename;
-    int branch = 1;
-
-    while (filelist.GetLineNoFilter(filename)) {
-      p_originalInput.push_back(filename);
-      p_inputBranches.push_back(inputParam + toString(branch));
-      p_virtualBands.push_back("");
-      p_finalOutput.push_back(FileName(filename).name());
-
-      branch ++;
-    }
-
-    p_outputListNeedsModifiers = true;
+    SetInputListFile(inputFileName);
   }
 
 
@@ -380,15 +368,16 @@ namespace Isis {
    *                                       to p_inputBranches
    */
   void Pipeline::SetInputListFile(const FileName &inputFileName) {
-    TextFile filelist(inputFileName.expanded());
-    QString filename;
+    FileList filelist(inputFileName.expanded());
+    FileName filename;
     int branch = 1;
 
-    while (filelist.GetLineNoFilter(filename)) {
-      p_originalInput.push_back(filename);
-      p_inputBranches.push_back(FileName(inputFileName).expanded() + " " + QString(branch));
-      p_finalOutput.push_back(FileName(filename).name());
+    while (!filelist.isEmpty()) {
+      filename = filelist.takeFirst();
+      p_originalInput.push_back(filename.expanded());
+      p_inputBranches.push_back(inputFileName.name() + toString(branch));
       p_virtualBands.push_back("");
+      p_finalOutput.push_back(filename.name());
 
       branch ++;
     }
@@ -536,10 +525,11 @@ namespace Isis {
   void Pipeline::SetOutputListFile(const FileName &outputFileNameList) {
     p_finalOutput.clear();
 
-    TextFile filelist(outputFileNameList.expanded());
+    FileList filelist(outputFileNameList.expanded());
     QString filename;
 
-    while (filelist.GetLineNoFilter(filename)) {
+    while (!filelist.isEmpty()) {
+      filename = filelist.takeFirst().expanded();
       p_finalOutput.push_back(filename);
     }
 

isis/src/base/objs/Pipeline/Pipeline.h

@@ -142,6 +142,11 @@ namespace Isis {
    *                           control statements. References # 795.
    *   @history 2016-08-28 Kelvin Rodriguez - Removed useless if statement comparing
    *                           a reference variable to Null. Part of porting to OS X 10.11.
+   *   @history 2021-17-03 Adam Paquette - Update SetInputListFile to use the
+   *                           FileList object rather than the TextFile object.
+   *                           Also updated SetInputListFile isisparameter
+   *                           function to chain into the SetInputListFile FileName
+   *                           function.
    */
   class Pipeline {
     public:

isis/src/base/objs/Pipeline/Pipeline.truth

@@ -420,20 +420,20 @@ PIPELINE -------> unitTest3 <------- PIPELINE
 
 Testing listing methods
 PIPELINE -------> unitTest4 <------- PIPELINE
-cubeatt FROM="fileA" TO="./fileA.jitter.copy.FROM1.cub"
-cubeatt FROM="fileB" TO="./fileB.jitter.copy.FROM2.cub"
-cubeatt FROM="fileC" TO="./fileC.jitter.copy.FROM3.cub"
-spiceinit FROM="./fileA.jitter.copy.FROM1.cub" ATTACH="NO"
-spiceinit FROM="./fileB.jitter.copy.FROM2.cub" ATTACH="NO"
-spiceinit FROM="./fileC.jitter.copy.FROM3.cub" ATTACH="NO"
-echo -e "\n./fileA.jitter.copy.FROM1.cub\n./fileB.jitter.copy.FROM2.cub\n./fileC.jitter.copy.FROM3.cub" > ./appjit.lis
+cubeatt FROM="fileA" TO="./fileA.jitter.copy.unitTest.lis1.cub"
+cubeatt FROM="fileB" TO="./fileB.jitter.copy.unitTest.lis2.cub"
+cubeatt FROM="fileC" TO="./fileC.jitter.copy.unitTest.lis3.cub"
+spiceinit FROM="./fileA.jitter.copy.unitTest.lis1.cub" ATTACH="NO"
+spiceinit FROM="./fileB.jitter.copy.unitTest.lis2.cub" ATTACH="NO"
+spiceinit FROM="./fileC.jitter.copy.unitTest.lis3.cub" ATTACH="NO"
+echo -e "\n./fileA.jitter.copy.unitTest.lis1.cub\n./fileB.jitter.copy.unitTest.lis2.cub\n./fileC.jitter.copy.unitTest.lis3.cub" > ./appjit.lis
 appjit FROMLIST="./appjit.lis" MASTER="MASTER.cub" DEGREE="1"
-noproj FROM="./fileA.jitter.copy.FROM1.cub" TO="./fileA.jitter.cub" MATCH="MATCH.cub"
-noproj FROM="./fileB.jitter.copy.FROM2.cub" TO="./fileB.jitter.cub" MATCH="MATCH.cub"
-noproj FROM="./fileC.jitter.copy.FROM3.cub" TO="./fileC.jitter.cub" MATCH="MATCH.cub"
-rm ./fileA.jitter.copy.FROM1.cub
-rm ./fileB.jitter.copy.FROM2.cub
-rm ./fileC.jitter.copy.FROM3.cub
+noproj FROM="./fileA.jitter.copy.unitTest.lis1.cub" TO="./fileA.jitter.cub" MATCH="MATCH.cub"
+noproj FROM="./fileB.jitter.copy.unitTest.lis2.cub" TO="./fileB.jitter.cub" MATCH="MATCH.cub"
+noproj FROM="./fileC.jitter.copy.unitTest.lis3.cub" TO="./fileC.jitter.cub" MATCH="MATCH.cub"
+rm ./fileA.jitter.copy.unitTest.lis1.cub
+rm ./fileB.jitter.copy.unitTest.lis2.cub
+rm ./fileC.jitter.copy.unitTest.lis3.cub
 rm ./appjit.lis
 PIPELINE -------> unitTest4 <------- PIPELINE
 

isis/src/mro/apps/hijitter/main.cpp

@@ -196,9 +196,9 @@ void IsisMain() {
   }
 
   // the outputs from this pipeline are temporary files created by cubeatt
+  std::vector<QString> outputs = mainPipeline.OriginalBranches();
   for (int i = 0; i < g_numFiles; i++) {
-    g_tempFiles.push_back(FileName("$TEMPORARY/noproj.FROM"
-                                   + toString(i + 1) + ".cub").expanded());
+    g_tempFiles.push_back(FileName("$TEMPORARY/noproj."  + outputs[i] + ".cub").expanded());
   }
 
   // Do some calculations, delete the final outputs from the pipeline
@@ -508,6 +508,8 @@ void processNoprojFiles(Pipeline &p) {
   hijitregProg.SetMaximumSteps(1);
   hijitregProg.CheckStatus();
 
+  std::vector<QString> outputs = p.OriginalBranches();
+
   for (int i = 0; i < g_numFiles - 1; i++) {
     // If this CCD and the consecutive CCD are both in the input list,
     // use the current cubes in the pipeline to create an output flat
@@ -525,8 +527,8 @@ void processNoprojFiles(Pipeline &p) {
       QString flatFileName = tempDir + "/first" + toString(g_ccdNumbers[i])
                             + "-" + toString(g_ccdNumbers[i+1]) + ".flat";
       QString params = "";
-      params += "FROM=" + tempDir + "/noproj.FROM" + toString(i + 1) + ".cub";
-      params += " MATCH=" + tempDir + "/noproj.FROM" + toString(i + 2) + ".cub";
+      params += "FROM=" + tempDir + "/noproj." + outputs[i] + ".cub";
+      params += " MATCH=" + tempDir + "/noproj." + outputs[i + 1] + ".cub";
       params += " REGDEF=" + ui.GetFileName("REGDEF");
       params += " FLAT=" + flatFileName;
 
@@ -610,7 +612,7 @@ void processNoprojFiles(Pipeline &p) {
     throw IException(IException::Programmer, msg, _FILEINFO_);
   }
 
-  Cube cube(FileName("$TEMPORARY/noproj.FROM1.cub").expanded(), "r");
+  Cube cube(FileName("$TEMPORARY/noproj." + outputs[0] + ".cub").expanded(), "r");
   Camera *cam = CameraFactory::Create(cube);
 
   double lineRate = cam->DetectorMap()->LineRate();

isis/tests/FileListTests.cpp

@@ -45,3 +45,16 @@ TEST(FileList, FileNameConstructor)
   fl1.write(output);
   EXPECT_STREQ(expectedOutput.c_str(), output.str().c_str());
 }
+
+TEST(FileList, FileNameNoNewLine)
+{
+  std::istringstream input(
+  "/usgs/pkgs/isis3/isis/src/base/objs/FileList/FileList.cpp\n"
+  "/usgs/pkgs/isis3/isis/src/base/objs/FileList/FileList.h");
+  std::ostringstream output;
+  std::string expectedOutput = "/usgs/pkgs/isis3/isis/src/base/objs/FileList/FileList.cpp\n"
+     "/usgs/pkgs/isis3/isis/src/base/objs/FileList/FileList.h\n";
+  Isis::FileList fl1(input);
+  fl1.write(output);
+  EXPECT_STREQ(expectedOutput.c_str(), output.str().c_str());
+}