From e926e73a0edd06241cfff300f480a031d5330078 Mon Sep 17 00:00:00 2001
From: Christopher Wood <cjwood@us.ibm.com>
Date: Tue, 8 Feb 2022 13:36:15 -0500
Subject: [PATCH] Fix CompositeExperiment.copy

Fix CompositeExperiment.copy to preserve any analysis object references between the original component experiment analysis classes and the composite analysis component analysis classes.
---
 .../framework/base_experiment.py              |  2 +-
 .../framework/composite/composite_analysis.py |  6 ++++
 .../composite/composite_experiment.py         |  9 ++++++
 .../fix-composite-copy-a869e9773f6a4d48.yaml  | 10 +++++++
 test/test_composite.py                        | 29 +++++++++++++++++++
 5 files changed, 55 insertions(+), 1 deletion(-)
 create mode 100644 releasenotes/notes/fix-composite-copy-a869e9773f6a4d48.yaml

diff --git a/qiskit_experiments/framework/base_experiment.py b/qiskit_experiments/framework/base_experiment.py
index 2587e365af..dfa10fd0c3 100644
--- a/qiskit_experiments/framework/base_experiment.py
+++ b/qiskit_experiments/framework/base_experiment.py
@@ -279,7 +279,7 @@ def run(
 
         # Optionally run analysis
         if analysis and experiment.analysis:
-            return self.analysis.run(experiment_data)
+            return experiment.analysis.run(experiment_data)
         else:
             return experiment_data
 
diff --git a/qiskit_experiments/framework/composite/composite_analysis.py b/qiskit_experiments/framework/composite/composite_analysis.py
index f69eb4d15d..a0c7bdf7a5 100644
--- a/qiskit_experiments/framework/composite/composite_analysis.py
+++ b/qiskit_experiments/framework/composite/composite_analysis.py
@@ -60,6 +60,12 @@ def component_analysis(self, index=None) -> Union[BaseAnalysis, List[BaseAnalysi
             return self._analyses
         return self._analyses[index]
 
+    def copy(self):
+        ret = super().copy()
+        # Recursively copy analysis
+        ret._analyses = [analysis.copy() for analysis in ret._analyses]
+        return ret
+
     def _run_analysis(self, experiment_data: ExperimentData):
         # Return list of experiment data containers for each component experiment
         # containing the marginalied data from the composite experiment
diff --git a/qiskit_experiments/framework/composite/composite_experiment.py b/qiskit_experiments/framework/composite/composite_experiment.py
index 955ef9bedd..c9dc7ec339 100644
--- a/qiskit_experiments/framework/composite/composite_experiment.py
+++ b/qiskit_experiments/framework/composite/composite_experiment.py
@@ -87,6 +87,15 @@ def copy(self) -> "BaseExperiment":
         ret = super().copy()
         # Recursively call copy of component experiments
         ret._experiments = [exp.copy() for exp in self._experiments]
+
+        # Check if the analysis in CompositeAnalysis was a reference to the
+        # original component experiment analyses and if so update the copies
+        # to preserve this relationship
+        if isinstance(self.analysis, CompositeAnalysis):
+            for i, orig_exp in enumerate(self._experiments):
+                if orig_exp.analysis is self.analysis._analyses[i]:
+                    # Update copies analysis with reference to experiment analysis
+                    ret.analysis._analyses[i] = ret._experiments[i].analysis
         return ret
 
     def _set_backend(self, backend):
diff --git a/releasenotes/notes/fix-composite-copy-a869e9773f6a4d48.yaml b/releasenotes/notes/fix-composite-copy-a869e9773f6a4d48.yaml
new file mode 100644
index 0000000000..66d844e5c9
--- /dev/null
+++ b/releasenotes/notes/fix-composite-copy-a869e9773f6a4d48.yaml
@@ -0,0 +1,10 @@
+---
+fixes:
+  - |
+    Fix :meth:`.ParallelExperiment.copy` and :meth:`.BatchExperiment.copy`
+    so that the copies preserves any references between the original
+    component experiments analysis classes and the :class:`.CompositeAnalysis`
+    classes component analysis classes.
+  - |
+    Fixes :meth:`.CompositeAnalysis.copy` to recursively make a copy of the
+    component analysis classes.
diff --git a/test/test_composite.py b/test/test_composite.py
index 8df60b2c03..881f62a36e 100644
--- a/test/test_composite.py
+++ b/test/test_composite.py
@@ -187,6 +187,35 @@ def test_composite_copy(self):
         self.check_attributes(new_instance)
         self.assertEqual(new_instance.parent_id, None)
 
+    def test_composite_copy_analysis_ref(self):
+        """Test copy of composite expeirment preserves component analysis refs"""
+
+        class Analysis(FakeAnalysis):
+            """Fake analysis class with options"""
+
+            @classmethod
+            def _default_options(cls):
+                opts = super()._default_options()
+                opts.option1 = None
+                opts.option2 = None
+                return opts
+
+        exp1 = FakeExperiment([0])
+        exp1.analysis = Analysis()
+        exp2 = FakeExperiment([1])
+        exp2.analysis = Analysis()
+
+        # Generate a copy
+        par_exp = ParallelExperiment([exp1, exp2]).copy()
+        comp_exp0 = par_exp.component_experiment(0)
+        comp_exp1 = par_exp.component_experiment(1)
+        comp_an0 = par_exp.analysis.component_analysis(0)
+        comp_an1 = par_exp.analysis.component_analysis(1)
+
+        # Check reference of analysis is preserved
+        self.assertTrue(comp_exp0.analysis is comp_an0)
+        self.assertTrue(comp_exp1.analysis is comp_an1)
+
     def test_nested_composite(self):
         """
         Test nested parallel experiments.