Re #7778. Eliminate erroneous use of AnalysisDataService.

In general, algorithms shouldn't be dealing directly with the ADS,
the Algorithm base class takes care of these interactions.

Code/Mantid/Framework/Crystal/src/CalculateUMatrix.cpp

@@ -69,8 +69,7 @@ namespace Crystal
     OrientedLattice o(a,b,c,alpha,beta,gamma);
     Matrix<double> B=o.getB();
 
-    PeaksWorkspace_sptr ws;
-    ws = AnalysisDataService::Instance().retrieveWS<PeaksWorkspace>(this->getProperty("PeaksWorkspace") );
+    PeaksWorkspace_sptr ws = this->getProperty("PeaksWorkspace");
     if (!ws) throw std::runtime_error("Problems reading the peaks workspace");
 
     size_t nIndexedpeaks=0;

Code/Mantid/Framework/Crystal/src/FindUBUsingIndexedPeaks.cpp

@@ -52,10 +52,7 @@ namespace Crystal
    */
   void FindUBUsingIndexedPeaks::exec()
   {
-    PeaksWorkspace_sptr ws;
-    ws = boost::dynamic_pointer_cast<PeaksWorkspace>(
-         AnalysisDataService::Instance().retrieve(this->getProperty("PeaksWorkspace")) );
-
+    PeaksWorkspace_sptr ws = this->getProperty("PeaksWorkspace");
     if (!ws)
     {
       throw std::runtime_error("Could not read the peaks workspace");

Code/Mantid/Framework/Crystal/src/FindUBUsingLatticeParameters.cpp

@@ -79,10 +79,7 @@ namespace Crystal
     int    base_index         = -1;   // these "could" be properties if need be
     double degrees_per_step   = 1.5;
 
-    PeaksWorkspace_sptr ws;
-    ws = boost::dynamic_pointer_cast<PeaksWorkspace>(
-         AnalysisDataService::Instance().retrieve(this->getProperty("PeaksWorkspace")) );
-
+    PeaksWorkspace_sptr ws = this->getProperty("PeaksWorkspace");
     if (!ws) throw std::runtime_error("Could not read the peaks workspace");
 
     std::vector<Peak> &peaks = ws->getPeaks();

Code/Mantid/Framework/Crystal/src/FindUBUsingMinMaxD.cpp

@@ -93,10 +93,7 @@ namespace Crystal
     int    base_index         = -1;   // these "could" be properties if need be
     double degrees_per_step   =  1;
 
-    PeaksWorkspace_sptr ws;
-    ws = boost::dynamic_pointer_cast<PeaksWorkspace>(
-         AnalysisDataService::Instance().retrieve(this->getProperty("PeaksWorkspace")) );
-
+    PeaksWorkspace_sptr ws = this->getProperty("PeaksWorkspace");
     if (!ws) throw std::runtime_error("Could not read the peaks workspace");
 
     std::vector<Peak> &peaks = ws->getPeaks();

Code/Mantid/Framework/Crystal/src/IndexPeaks.cpp

@@ -62,11 +62,7 @@ namespace Crystal
    */
   void IndexPeaks::exec()
   {
-                                          
-    PeaksWorkspace_sptr ws;
-    ws = boost::dynamic_pointer_cast<PeaksWorkspace>(
-         AnalysisDataService::Instance().retrieve(this->getProperty("PeaksWorkspace")) );
-
+    PeaksWorkspace_sptr ws = this->getProperty("PeaksWorkspace");
     if (!ws) 
     { 
       throw std::runtime_error("Could not read the peaks workspace");

Code/Mantid/Framework/Crystal/src/IndexSXPeaks.cpp

@@ -130,8 +130,7 @@ namespace Mantid
       using namespace Mantid::DataObjects;
       std::vector<int> peakindices = getProperty("PeakIndices");
 
-      PeaksWorkspace_sptr ws = boost::dynamic_pointer_cast<PeaksWorkspace>(
-        AnalysisDataService::Instance().retrieve(this->getProperty("PeaksWorkspace")) );
+      PeaksWorkspace_sptr ws = this->getProperty("PeaksWorkspace");
 
       // Need a least two peaks
       std::size_t npeaks=peakindices.size();

Code/Mantid/Framework/Crystal/src/OptimizeCrystalPlacement.cpp

@@ -414,14 +414,12 @@ namespace Mantid
 
       //------------------ Fix up Covariance output --------------------
       declareProperty( new  WorkspaceProperty< ITableWorkspace>(
-          "OutputNormalisedCovarianceMatrixOptX" , "" ,  Direction::Output ) ,
+          "OutputNormalisedCovarianceMatrixOptX" , "CovarianceInfo" ,  Direction::Output ) ,
           "The name of the TableWorkspace in which to store the final covariance matrix" );
 
 
       ITableWorkspace_sptr NormCov = fit_alg->getProperty( "OutputNormalisedCovarianceMatrix" );
-
-      AnalysisDataService::Instance().addOrReplace( std::string( "CovarianceInfo" ) , NormCov );
-      setPropertyValue( "OutputNormalisedCovarianceMatrixOptX" , std::string( "CovarianceInfo" ) );//What if 2 instances are run
+      setProperty( "OutputNormalisedCovarianceMatrixOptX" , NormCov );//What if 2 instances are run
 
       if ( chisq < 0 || chisq != chisq )
         sigma = -1;
@@ -448,10 +446,7 @@ namespace Mantid
 
     //-----------Fix up Resultant workspace return info -------------------
 
-      std::string ResultWorkspaceName = getPropertyValue( "FitInfoTable" );
-      AnalysisDataService::Instance().addOrReplace( ResultWorkspaceName , RRes );
-
-      setPropertyValue( "FitInfoTable" , ResultWorkspaceName );
+      setProperty( "FitInfoTable" , RRes );
 
       //----------- update instrument -------------------------
 

Code/Mantid/Framework/Crystal/src/SCDCalibratePanels.cpp

@@ -845,14 +845,12 @@ namespace Mantid
 
      declareProperty(
            new API::WorkspaceProperty<API::ITableWorkspace>
-           ("OutputNormalisedCovarianceMatrix","",Kernel::Direction::Output),
+           ("OutputNormalisedCovarianceMatrix","CovarianceInfo",Kernel::Direction::Output),
            "The name of the TableWorkspace in which to store the final covariance matrix" );
 
 
      ITableWorkspace_sptr NormCov= fit_alg->getProperty("OutputNormalisedCovarianceMatrix");
-     // setProperty("OutputNormalisedCovarianceMatrix", NormCov);
-     AnalysisDataService::Instance().addOrReplace( string("CovarianceInfo"), NormCov);
-     setPropertyValue("OutputNormalisedCovarianceMatrix",   string("CovarianceInfo"));
+     setProperty("OutputNormalisedCovarianceMatrix", NormCov);
 
      //--------------------- Get and Process Results -----------------------
      double chisq = fit_alg->getProperty( "OutputChi2overDoF");

Code/Mantid/Framework/Crystal/src/SelectCellOfType.cpp

@@ -88,10 +88,7 @@ namespace Crystal
    */
   void SelectCellOfType::exec()
   {
-    PeaksWorkspace_sptr ws;
-    ws = boost::dynamic_pointer_cast<PeaksWorkspace>(
-         AnalysisDataService::Instance().retrieve(this->getProperty("PeaksWorkspace")) );
-
+    PeaksWorkspace_sptr ws = this->getProperty("PeaksWorkspace");
     if (!ws) 
     { 
       throw std::runtime_error("Could not read the peaks workspace");

Code/Mantid/Framework/Crystal/src/SelectCellWithForm.cpp

@@ -125,10 +125,7 @@ namespace Crystal
    */
   void SelectCellWithForm::exec()
   {
-    PeaksWorkspace_sptr ws;
-    ws = boost::dynamic_pointer_cast<PeaksWorkspace>(
-         AnalysisDataService::Instance().retrieve(this->getProperty("PeaksWorkspace")) );
-
+    PeaksWorkspace_sptr ws = this->getProperty("PeaksWorkspace");
     if (!ws) 
     { 
       throw std::runtime_error("Could not read the peaks workspace");

Code/Mantid/Framework/Crystal/src/ShowPeakHKLOffsets.cpp

@@ -6,7 +6,6 @@
 #include "MantidKernel/Matrix.h"
 #include "MantidDataObjects/Peak.h"
 #include "MantidKernel/V3D.h"
-#include "MantidAPI/AnalysisDataService.h"
 #include "MantidAPI/Sample.h"
 #include "MantidGeometry/Crystal/OrientedLattice.h"
 #include "../../API/inc/MantidAPI/WorkspaceFactory.h"
@@ -119,9 +118,6 @@ namespace Mantid
 
       }
 
-      std::string output= getProperty("HKLIntegerOffsets");
-      API::AnalysisDataService::Instance().addOrReplace( output, Res );
-      setPropertyValue( "HKLIntegerOffsets",output);
       setProperty("HKLIntegerOffsets", Res);
     }
 

Code/Mantid/Framework/Crystal/src/ShowPossibleCells.cpp

@@ -40,7 +40,7 @@ namespace Crystal
   void ShowPossibleCells::init()
   {
     this->declareProperty(new WorkspaceProperty<PeaksWorkspace>(
-          "PeaksWorkspace","",Direction::InOut), "Input Peaks Workspace");
+          "PeaksWorkspace","",Direction::Input), "Input Peaks Workspace");
 
     auto mustBePositive = boost::make_shared<BoundedValidator<double> >();
     mustBePositive->setLower(0.0);
@@ -64,16 +64,13 @@ namespace Crystal
    */
   void ShowPossibleCells::exec()
   {
-    PeaksWorkspace_sptr ws;
-    ws = boost::dynamic_pointer_cast<PeaksWorkspace>(
-         AnalysisDataService::Instance().retrieve(this->getProperty("PeaksWorkspace")) );
-
+    PeaksWorkspace_const_sptr ws = this->getProperty("PeaksWorkspace");
     if (!ws) 
     { 
       throw std::runtime_error("Could not read the peaks workspace");
     }
 
-    OrientedLattice o_lattice = ws->mutableSample().getOrientedLattice();
+    OrientedLattice o_lattice = ws->sample().getOrientedLattice();
     Matrix<double> UB = o_lattice.getUB();
 
     if ( ! IndexingUtils::CheckUB( UB ) )

Code/Mantid/Framework/Crystal/src/TransformHKL.cpp

@@ -91,10 +91,7 @@ namespace Crystal
    */
   void TransformHKL::exec()
   {
-    PeaksWorkspace_sptr ws;
-    ws = boost::dynamic_pointer_cast<PeaksWorkspace>(
-         AnalysisDataService::Instance().retrieve(this->getProperty("PeaksWorkspace")) );
-
+    PeaksWorkspace_sptr ws = this->getProperty("PeaksWorkspace");
     if (!ws) 
     { 
       throw std::runtime_error("Could not read the peaks workspace");