Unverified Commit 899ec83a authored by acpaquette's avatar acpaquette Committed by GitHub
Browse files

Pipeline Object FileList Fix (#4372) 



* Update SetInputListFile to use the FileList object rather than the TextFile object.
Also updated SetInputListFile isisparameter function to chain into the 
SetInputListFile FileName function.

* Modified filelist to handle list files with no trailing new line character

* Added a test to check that filelist retains expected new functionality

* Fixed issues with pipeline and hardcoded values in hijitter

* Removed specific mention of trailing new line necessity in cubeit.xml

* Updated changelog

Co-authored-by: default avatarJesse Mapel <jmapel@usgs.gov>
parent 2df71934

CHANGELOG.md

+3 −0
Original line number Diff line number Diff line
@@ -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

+1 −2
Original line number Diff line number Diff line
@@ -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

+5 −6
Original line number Diff line number Diff line
@@ -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

+16 −26
Original line number Diff line number Diff line
@@ -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

+5 −0
Original line number Diff line number Diff line
@@ -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: