From 4abcfc9e2f78bb99ce678ac8e7685fb87d9e7dc4 Mon Sep 17 00:00:00 2001
From: Bryan Bartley <bryan.a.bartley@raytheon.com>
Date: Wed, 27 Apr 2022 07:56:37 -0700
Subject: [PATCH] Fix #138

---
 paml/data.py                      |  2 +-
 paml/sample_maps.py               |  4 +-
 test/test_samplemap.py            |  4 +-
 test/testfiles/sample_map_test.nt | 89 +++++++++++++------------------
 4 files changed, 42 insertions(+), 57 deletions(-)

diff --git a/paml/data.py b/paml/data.py
index 159b8f76..3990ef38 100644
--- a/paml/data.py
+++ b/paml/data.py
@@ -67,7 +67,7 @@ def is_in_mask(entry, row_col_pairs):
                             is_in_mask(coordinate_to_row_col(x), row_col_pairs)
                             for x in contents_array.data
                         ],
-                        coords={Strings.ALIQUOT: contents_array}
+                        coords=[(Strings.ALIQUOT, contents_array.data)]
                     )
     return json.dumps(mask_array.to_dict())
 SampleArray.mask = sample_array_mask
diff --git a/paml/sample_maps.py b/paml/sample_maps.py
index ef36e9ae..a150d11f 100644
--- a/paml/sample_maps.py
+++ b/paml/sample_maps.py
@@ -44,7 +44,7 @@ def many_to_one_sample_map_get_map(self):
         source_to_target_arrays = {
             source.identity : xr.DataArray([""]*len(aliquots),
                                             dims=(target.identity),
-                                            coords={target.identity: aliquots})
+                                            coords=[(target.identity, aliquots)])
             for source in sources
         }
 
@@ -68,7 +68,7 @@ def one_to_many_sample_map_get_map(self):
         source_to_target_arrays = {
             target.identity : xr.DataArray([""]*len(aliquots),
                                             dims=(source.identity),
-                                            coords={source.identity: aliquots})
+                                            coords=[(source.identity, aliquots)])
             for target in targets
         }
 
diff --git a/test/test_samplemap.py b/test/test_samplemap.py
index 19e7ee9a..9e545554 100644
--- a/test/test_samplemap.py
+++ b/test/test_samplemap.py
@@ -115,8 +115,8 @@ def test_create_protocol(self):
                                                 for reagent in reagents]
                                                 for id in aliquot_ids],
                                              dims=("aliquot", "contents"),
-                                             coords={"aliquot": aliquot_ids,
-                                                     "contents": [r.identity for r in reagents]}).to_dict()))
+                                             coords=[("aliquot", aliquot_ids),
+                                                     ("contents", [r.identity for r in reagents])]).to_dict()))
         # 3.
         sample_array_parameter = create_source.pin_parameter("sample_array")
         [old_input] = [x for x in create_source.inputs if x.name == "sample_array"]
diff --git a/test/testfiles/sample_map_test.nt b/test/testfiles/sample_map_test.nt
index a3b42d9c..5aa4a8b5 100644
--- a/test/testfiles/sample_map_test.nt
+++ b/test/testfiles/sample_map_test.nt
@@ -73,43 +73,6 @@
 <https://bbn.com/scratch/execute_1> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://sbols.org/v3#TopLevel> .
 <https://bbn.com/scratch/execute_1> <http://www.w3.org/ns/prov#endedAtTime> "2000-01-01T00:00:03"^^<http://www.w3.org/2001/XMLSchema#dateTime> .
 <https://bbn.com/scratch/execute_1> <http://www.w3.org/ns/prov#startedAtTime> "2000-01-01T00:00:02"^^<http://www.w3.org/2001/XMLSchema#dateTime> .
-<https://bbn.com/scratch/execute_2/ParameterValue1/LiteralReference1> <http://bioprotocols.org/uml#referenceValue> <https://bbn.com/scratch/test_execution/ActivityEdgeFlow3/LiteralIdentified1/SampleArray1> .
-<https://bbn.com/scratch/execute_2/ParameterValue1/LiteralReference1> <http://sbols.org/v3#displayId> "LiteralReference1" .
-<https://bbn.com/scratch/execute_2/ParameterValue1/LiteralReference1> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://bioprotocols.org/uml#LiteralReference> .
-<https://bbn.com/scratch/execute_2/ParameterValue1/LiteralReference1> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://sbols.org/v3#Identified> .
-<https://bbn.com/scratch/execute_2/ParameterValue1> <http://bioprotocols.org/paml#parameter> <https://bioprotocols.org/paml/primitives/liquid_handling/TransferByMap/OrderedPropertyValue1> .
-<https://bbn.com/scratch/execute_2/ParameterValue1> <http://bioprotocols.org/paml#parameterValue> <https://bbn.com/scratch/execute_2/ParameterValue1/LiteralReference1> .
-<https://bbn.com/scratch/execute_2/ParameterValue1> <http://sbols.org/v3#displayId> "ParameterValue1" .
-<https://bbn.com/scratch/execute_2/ParameterValue1> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://bioprotocols.org/paml#ParameterValue> .
-<https://bbn.com/scratch/execute_2/ParameterValue1> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://sbols.org/v3#Identified> .
-<https://bbn.com/scratch/execute_2/ParameterValue2/LiteralReference1> <http://bioprotocols.org/uml#referenceValue> <https://bbn.com/scratch/test_execution/ActivityEdgeFlow4/LiteralIdentified1/SampleArray1> .
-<https://bbn.com/scratch/execute_2/ParameterValue2/LiteralReference1> <http://sbols.org/v3#displayId> "LiteralReference1" .
-<https://bbn.com/scratch/execute_2/ParameterValue2/LiteralReference1> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://bioprotocols.org/uml#LiteralReference> .
-<https://bbn.com/scratch/execute_2/ParameterValue2/LiteralReference1> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://sbols.org/v3#Identified> .
-<https://bbn.com/scratch/execute_2/ParameterValue2> <http://bioprotocols.org/paml#parameter> <https://bioprotocols.org/paml/primitives/liquid_handling/TransferByMap/OrderedPropertyValue2> .
-<https://bbn.com/scratch/execute_2/ParameterValue2> <http://bioprotocols.org/paml#parameterValue> <https://bbn.com/scratch/execute_2/ParameterValue2/LiteralReference1> .
-<https://bbn.com/scratch/execute_2/ParameterValue2> <http://sbols.org/v3#displayId> "ParameterValue2" .
-<https://bbn.com/scratch/execute_2/ParameterValue2> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://bioprotocols.org/paml#ParameterValue> .
-<https://bbn.com/scratch/execute_2/ParameterValue2> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://sbols.org/v3#Identified> .
-<https://bbn.com/scratch/execute_2/ParameterValue3/LiteralReference1> <http://bioprotocols.org/uml#referenceValue> <https://bbn.com/scratch/samplemap_demo_protocol/CallBehaviorAction3/ValuePin1/LiteralIdentified1> .
-<https://bbn.com/scratch/execute_2/ParameterValue3/LiteralReference1> <http://sbols.org/v3#displayId> "LiteralReference1" .
-<https://bbn.com/scratch/execute_2/ParameterValue3/LiteralReference1> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://bioprotocols.org/uml#LiteralReference> .
-<https://bbn.com/scratch/execute_2/ParameterValue3/LiteralReference1> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://sbols.org/v3#Identified> .
-<https://bbn.com/scratch/execute_2/ParameterValue3> <http://bioprotocols.org/paml#parameter> <https://bioprotocols.org/paml/primitives/liquid_handling/TransferByMap/OrderedPropertyValue3> .
-<https://bbn.com/scratch/execute_2/ParameterValue3> <http://bioprotocols.org/paml#parameterValue> <https://bbn.com/scratch/execute_2/ParameterValue3/LiteralReference1> .
-<https://bbn.com/scratch/execute_2/ParameterValue3> <http://sbols.org/v3#displayId> "ParameterValue3" .
-<https://bbn.com/scratch/execute_2/ParameterValue3> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://bioprotocols.org/paml#ParameterValue> .
-<https://bbn.com/scratch/execute_2/ParameterValue3> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://sbols.org/v3#Identified> .
-<https://bbn.com/scratch/execute_2> <http://bioprotocols.org/paml#completedNormally> "true"^^<http://www.w3.org/2001/XMLSchema#boolean> .
-<https://bbn.com/scratch/execute_2> <http://bioprotocols.org/paml#parameterValuePair> <https://bbn.com/scratch/execute_2/ParameterValue1> .
-<https://bbn.com/scratch/execute_2> <http://bioprotocols.org/paml#parameterValuePair> <https://bbn.com/scratch/execute_2/ParameterValue2> .
-<https://bbn.com/scratch/execute_2> <http://bioprotocols.org/paml#parameterValuePair> <https://bbn.com/scratch/execute_2/ParameterValue3> .
-<https://bbn.com/scratch/execute_2> <http://sbols.org/v3#displayId> "execute_2" .
-<https://bbn.com/scratch/execute_2> <http://sbols.org/v3#hasNamespace> <https://bbn.com/scratch/> .
-<https://bbn.com/scratch/execute_2> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://bioprotocols.org/paml#BehaviorExecution> .
-<https://bbn.com/scratch/execute_2> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://sbols.org/v3#TopLevel> .
-<https://bbn.com/scratch/execute_2> <http://www.w3.org/ns/prov#endedAtTime> "2000-01-01T00:00:05"^^<http://www.w3.org/2001/XMLSchema#dateTime> .
-<https://bbn.com/scratch/execute_2> <http://www.w3.org/ns/prov#startedAtTime> "2000-01-01T00:00:04"^^<http://www.w3.org/2001/XMLSchema#dateTime> .
 <https://bbn.com/scratch/samplemap_demo_protocol/CallBehaviorAction1/OutputPin1> <http://bioprotocols.org/uml#isOrdered> "true"^^<http://www.w3.org/2001/XMLSchema#boolean> .
 <https://bbn.com/scratch/samplemap_demo_protocol/CallBehaviorAction1/OutputPin1> <http://bioprotocols.org/uml#isUnique> "true"^^<http://www.w3.org/2001/XMLSchema#boolean> .
 <https://bbn.com/scratch/samplemap_demo_protocol/CallBehaviorAction1/OutputPin1> <http://sbols.org/v3#displayId> "OutputPin1" .
@@ -215,9 +178,15 @@
 <https://bbn.com/scratch/samplemap_demo_protocol/CallBehaviorAction3/InputPin3> <http://bioprotocols.org/uml#isOrdered> "true"^^<http://www.w3.org/2001/XMLSchema#boolean> .
 <https://bbn.com/scratch/samplemap_demo_protocol/CallBehaviorAction3/InputPin3> <http://bioprotocols.org/uml#isUnique> "true"^^<http://www.w3.org/2001/XMLSchema#boolean> .
 <https://bbn.com/scratch/samplemap_demo_protocol/CallBehaviorAction3/InputPin3> <http://sbols.org/v3#displayId> "InputPin3" .
-<https://bbn.com/scratch/samplemap_demo_protocol/CallBehaviorAction3/InputPin3> <http://sbols.org/v3#name> "dispenseVelocity" .
+<https://bbn.com/scratch/samplemap_demo_protocol/CallBehaviorAction3/InputPin3> <http://sbols.org/v3#name> "amount" .
 <https://bbn.com/scratch/samplemap_demo_protocol/CallBehaviorAction3/InputPin3> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://bioprotocols.org/uml#InputPin> .
 <https://bbn.com/scratch/samplemap_demo_protocol/CallBehaviorAction3/InputPin3> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://sbols.org/v3#Identified> .
+<https://bbn.com/scratch/samplemap_demo_protocol/CallBehaviorAction3/InputPin4> <http://bioprotocols.org/uml#isOrdered> "true"^^<http://www.w3.org/2001/XMLSchema#boolean> .
+<https://bbn.com/scratch/samplemap_demo_protocol/CallBehaviorAction3/InputPin4> <http://bioprotocols.org/uml#isUnique> "true"^^<http://www.w3.org/2001/XMLSchema#boolean> .
+<https://bbn.com/scratch/samplemap_demo_protocol/CallBehaviorAction3/InputPin4> <http://sbols.org/v3#displayId> "InputPin4" .
+<https://bbn.com/scratch/samplemap_demo_protocol/CallBehaviorAction3/InputPin4> <http://sbols.org/v3#name> "dispenseVelocity" .
+<https://bbn.com/scratch/samplemap_demo_protocol/CallBehaviorAction3/InputPin4> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://bioprotocols.org/uml#InputPin> .
+<https://bbn.com/scratch/samplemap_demo_protocol/CallBehaviorAction3/InputPin4> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://sbols.org/v3#Identified> .
 <https://bbn.com/scratch/samplemap_demo_protocol/CallBehaviorAction3/ValuePin1/LiteralIdentified1/SampleMap1> <http://bioprotocols.org/paml#sampleMapSources> <https://bbn.com/scratch/samplemap_demo_protocol/CallBehaviorAction1/ValuePin2/LiteralIdentified1/SampleArray1> .
 <https://bbn.com/scratch/samplemap_demo_protocol/CallBehaviorAction3/ValuePin1/LiteralIdentified1/SampleMap1> <http://bioprotocols.org/paml#sampleMapTargets> <https://bbn.com/scratch/samplemap_demo_protocol/CallBehaviorAction2/ValuePin2/LiteralIdentified1/SampleArray1> .
 <https://bbn.com/scratch/samplemap_demo_protocol/CallBehaviorAction3/ValuePin1/LiteralIdentified1/SampleMap1> <http://bioprotocols.org/paml#sampleMapValues> "{\"dims\": [\"source_array\", \"source_aliquot\", \"target_array\", \"target_aliquot\"], \"attrs\": {}, \"data\": [[[[10.0, 10.0, 10.0, 10.0]], [[10.0, 10.0, 10.0, 10.0]], [[10.0, 10.0, 10.0, 10.0]], [[10.0, 10.0, 10.0, 10.0]]]], \"coords\": {\"source_array\": {\"dims\": [\"source_array\"], \"attrs\": {}, \"data\": [\"source\"]}, \"source_aliquot\": {\"dims\": [\"source_aliquot\"], \"attrs\": {}, \"data\": [0, 1, 2, 3]}, \"target_array\": {\"dims\": [\"target_array\"], \"attrs\": {}, \"data\": [\"target\"]}, \"target_aliquot\": {\"dims\": [\"target_aliquot\"], \"attrs\": {}, \"data\": [0, 1, 2, 3]}}, \"name\": null}" .
@@ -239,6 +208,7 @@
 <https://bbn.com/scratch/samplemap_demo_protocol/CallBehaviorAction3> <http://bioprotocols.org/uml#input> <https://bbn.com/scratch/samplemap_demo_protocol/CallBehaviorAction3/InputPin1> .
 <https://bbn.com/scratch/samplemap_demo_protocol/CallBehaviorAction3> <http://bioprotocols.org/uml#input> <https://bbn.com/scratch/samplemap_demo_protocol/CallBehaviorAction3/InputPin2> .
 <https://bbn.com/scratch/samplemap_demo_protocol/CallBehaviorAction3> <http://bioprotocols.org/uml#input> <https://bbn.com/scratch/samplemap_demo_protocol/CallBehaviorAction3/InputPin3> .
+<https://bbn.com/scratch/samplemap_demo_protocol/CallBehaviorAction3> <http://bioprotocols.org/uml#input> <https://bbn.com/scratch/samplemap_demo_protocol/CallBehaviorAction3/InputPin4> .
 <https://bbn.com/scratch/samplemap_demo_protocol/CallBehaviorAction3> <http://bioprotocols.org/uml#input> <https://bbn.com/scratch/samplemap_demo_protocol/CallBehaviorAction3/ValuePin1> .
 <https://bbn.com/scratch/samplemap_demo_protocol/CallBehaviorAction3> <http://sbols.org/v3#displayId> "CallBehaviorAction3" .
 <https://bbn.com/scratch/samplemap_demo_protocol/CallBehaviorAction3> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://bioprotocols.org/uml#CallBehaviorAction> .
@@ -307,7 +277,7 @@
 <https://bbn.com/scratch/test_execution/ActivityEdgeFlow2> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://bioprotocols.org/paml#ActivityEdgeFlow> .
 <https://bbn.com/scratch/test_execution/ActivityEdgeFlow2> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://sbols.org/v3#Identified> .
 <https://bbn.com/scratch/test_execution/ActivityEdgeFlow3/LiteralIdentified1/SampleArray1> <http://bioprotocols.org/paml#containerType> <https://bbn.com/scratch/samplemap_demo_protocol/CallBehaviorAction1/ValuePin1/LiteralIdentified1/ContainerSpec1> .
-<https://bbn.com/scratch/test_execution/ActivityEdgeFlow3/LiteralIdentified1/SampleArray1> <http://bioprotocols.org/paml#contents> "{\"dims\": [\"aliquot\"], \"attrs\": {}, \"data\": [\"A1\", \"A2\", \"A3\", \"A4\", \"A5\", \"A6\", \"A7\", \"A8\", \"A9\", \"A10\", \"A11\", \"A12\", \"B1\", \"B2\", \"B3\", \"B4\", \"B5\", \"B6\", \"B7\", \"B8\", \"B9\", \"B10\", \"B11\", \"B12\", \"C1\", \"C2\", \"C3\", \"C4\", \"C5\", \"C6\", \"C7\", \"C8\", \"C9\", \"C10\", \"C11\", \"C12\", \"D1\", \"D2\", \"D3\", \"D4\", \"D5\", \"D6\", \"D7\", \"D8\", \"D9\", \"D10\", \"D11\", \"D12\", \"E1\", \"E2\", \"E3\", \"E4\", \"E5\", \"E6\", \"E7\", \"E8\", \"E9\", \"E10\", \"E11\", \"E12\", \"F1\", \"F2\", \"F3\", \"F4\", \"F5\", \"F6\", \"F7\", \"F8\", \"F9\", \"F10\", \"F11\", \"F12\", \"G1\", \"G2\", \"G3\", \"G4\", \"G5\", \"G6\", \"G7\", \"G8\", \"G9\", \"G10\", \"G11\", \"G12\", \"H1\", \"H2\", \"H3\", \"H4\", \"H5\", \"H6\", \"H7\", \"H8\", \"H9\", \"H10\", \"H11\", \"H12\"], \"coords\": {}, \"name\": null}" .
+<https://bbn.com/scratch/test_execution/ActivityEdgeFlow3/LiteralIdentified1/SampleArray1> <http://bioprotocols.org/paml#contents> "{\"dims\": [\"aliquot\"], \"attrs\": {}, \"data\": [\"A1\", \"B1\", \"C1\", \"D1\", \"E1\", \"F1\", \"G1\", \"H1\", \"A2\", \"B2\", \"C2\", \"D2\", \"E2\", \"F2\", \"G2\", \"H2\", \"A3\", \"B3\", \"C3\", \"D3\", \"E3\", \"F3\", \"G3\", \"H3\", \"A4\", \"B4\", \"C4\", \"D4\", \"E4\", \"F4\", \"G4\", \"H4\", \"A5\", \"B5\", \"C5\", \"D5\", \"E5\", \"F5\", \"G5\", \"H5\", \"A6\", \"B6\", \"C6\", \"D6\", \"E6\", \"F6\", \"G6\", \"H6\", \"A7\", \"B7\", \"C7\", \"D7\", \"E7\", \"F7\", \"G7\", \"H7\", \"A8\", \"B8\", \"C8\", \"D8\", \"E8\", \"F8\", \"G8\", \"H8\", \"A9\", \"B9\", \"C9\", \"D9\", \"E9\", \"F9\", \"G9\", \"H9\", \"A10\", \"B10\", \"C10\", \"D10\", \"E10\", \"F10\", \"G10\", \"H10\", \"A11\", \"B11\", \"C11\", \"D11\", \"E11\", \"F11\", \"G11\", \"H11\", \"A12\", \"B12\", \"C12\", \"D12\", \"E12\", \"F12\", \"G12\", \"H12\"], \"coords\": {}, \"name\": null}" .
 <https://bbn.com/scratch/test_execution/ActivityEdgeFlow3/LiteralIdentified1/SampleArray1> <http://sbols.org/v3#displayId> "SampleArray1" .
 <https://bbn.com/scratch/test_execution/ActivityEdgeFlow3/LiteralIdentified1/SampleArray1> <http://sbols.org/v3#name> "samples" .
 <https://bbn.com/scratch/test_execution/ActivityEdgeFlow3/LiteralIdentified1/SampleArray1> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://bioprotocols.org/paml#SampleArray> .
@@ -323,7 +293,7 @@
 <https://bbn.com/scratch/test_execution/ActivityEdgeFlow3> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://bioprotocols.org/paml#ActivityEdgeFlow> .
 <https://bbn.com/scratch/test_execution/ActivityEdgeFlow3> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://sbols.org/v3#Identified> .
 <https://bbn.com/scratch/test_execution/ActivityEdgeFlow4/LiteralIdentified1/SampleArray1> <http://bioprotocols.org/paml#containerType> <https://bbn.com/scratch/samplemap_demo_protocol/CallBehaviorAction2/ValuePin1/LiteralIdentified1/ContainerSpec1> .
-<https://bbn.com/scratch/test_execution/ActivityEdgeFlow4/LiteralIdentified1/SampleArray1> <http://bioprotocols.org/paml#contents> "{\"dims\": [\"aliquot\"], \"attrs\": {}, \"data\": [\"A1\", \"A2\", \"A3\", \"A4\", \"A5\", \"A6\", \"A7\", \"A8\", \"A9\", \"A10\", \"A11\", \"A12\", \"B1\", \"B2\", \"B3\", \"B4\", \"B5\", \"B6\", \"B7\", \"B8\", \"B9\", \"B10\", \"B11\", \"B12\", \"C1\", \"C2\", \"C3\", \"C4\", \"C5\", \"C6\", \"C7\", \"C8\", \"C9\", \"C10\", \"C11\", \"C12\", \"D1\", \"D2\", \"D3\", \"D4\", \"D5\", \"D6\", \"D7\", \"D8\", \"D9\", \"D10\", \"D11\", \"D12\", \"E1\", \"E2\", \"E3\", \"E4\", \"E5\", \"E6\", \"E7\", \"E8\", \"E9\", \"E10\", \"E11\", \"E12\", \"F1\", \"F2\", \"F3\", \"F4\", \"F5\", \"F6\", \"F7\", \"F8\", \"F9\", \"F10\", \"F11\", \"F12\", \"G1\", \"G2\", \"G3\", \"G4\", \"G5\", \"G6\", \"G7\", \"G8\", \"G9\", \"G10\", \"G11\", \"G12\", \"H1\", \"H2\", \"H3\", \"H4\", \"H5\", \"H6\", \"H7\", \"H8\", \"H9\", \"H10\", \"H11\", \"H12\"], \"coords\": {}, \"name\": null}" .
+<https://bbn.com/scratch/test_execution/ActivityEdgeFlow4/LiteralIdentified1/SampleArray1> <http://bioprotocols.org/paml#contents> "{\"dims\": [\"aliquot\"], \"attrs\": {}, \"data\": [\"A1\", \"B1\", \"C1\", \"D1\", \"E1\", \"F1\", \"G1\", \"H1\", \"A2\", \"B2\", \"C2\", \"D2\", \"E2\", \"F2\", \"G2\", \"H2\", \"A3\", \"B3\", \"C3\", \"D3\", \"E3\", \"F3\", \"G3\", \"H3\", \"A4\", \"B4\", \"C4\", \"D4\", \"E4\", \"F4\", \"G4\", \"H4\", \"A5\", \"B5\", \"C5\", \"D5\", \"E5\", \"F5\", \"G5\", \"H5\", \"A6\", \"B6\", \"C6\", \"D6\", \"E6\", \"F6\", \"G6\", \"H6\", \"A7\", \"B7\", \"C7\", \"D7\", \"E7\", \"F7\", \"G7\", \"H7\", \"A8\", \"B8\", \"C8\", \"D8\", \"E8\", \"F8\", \"G8\", \"H8\", \"A9\", \"B9\", \"C9\", \"D9\", \"E9\", \"F9\", \"G9\", \"H9\", \"A10\", \"B10\", \"C10\", \"D10\", \"E10\", \"F10\", \"G10\", \"H10\", \"A11\", \"B11\", \"C11\", \"D11\", \"E11\", \"F11\", \"G11\", \"H11\", \"A12\", \"B12\", \"C12\", \"D12\", \"E12\", \"F12\", \"G12\", \"H12\"], \"coords\": {}, \"name\": null}" .
 <https://bbn.com/scratch/test_execution/ActivityEdgeFlow4/LiteralIdentified1/SampleArray1> <http://sbols.org/v3#displayId> "SampleArray1" .
 <https://bbn.com/scratch/test_execution/ActivityEdgeFlow4/LiteralIdentified1/SampleArray1> <http://sbols.org/v3#name> "samples" .
 <https://bbn.com/scratch/test_execution/ActivityEdgeFlow4/LiteralIdentified1/SampleArray1> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://bioprotocols.org/paml#SampleArray> .
@@ -397,21 +367,12 @@
 <https://bbn.com/scratch/test_execution/CallBehaviorExecution2> <http://sbols.org/v3#displayId> "CallBehaviorExecution2" .
 <https://bbn.com/scratch/test_execution/CallBehaviorExecution2> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://bioprotocols.org/paml#CallBehaviorExecution> .
 <https://bbn.com/scratch/test_execution/CallBehaviorExecution2> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://sbols.org/v3#Identified> .
-<https://bbn.com/scratch/test_execution/CallBehaviorExecution3> <http://bioprotocols.org/paml#call> <https://bbn.com/scratch/execute_2> .
-<https://bbn.com/scratch/test_execution/CallBehaviorExecution3> <http://bioprotocols.org/paml#incomingFlow> <https://bbn.com/scratch/test_execution/ActivityEdgeFlow5> .
-<https://bbn.com/scratch/test_execution/CallBehaviorExecution3> <http://bioprotocols.org/paml#incomingFlow> <https://bbn.com/scratch/test_execution/ActivityEdgeFlow6> .
-<https://bbn.com/scratch/test_execution/CallBehaviorExecution3> <http://bioprotocols.org/paml#incomingFlow> <https://bbn.com/scratch/test_execution/ActivityEdgeFlow7> .
-<https://bbn.com/scratch/test_execution/CallBehaviorExecution3> <http://bioprotocols.org/paml#node> <https://bbn.com/scratch/samplemap_demo_protocol/CallBehaviorAction3> .
-<https://bbn.com/scratch/test_execution/CallBehaviorExecution3> <http://sbols.org/v3#displayId> "CallBehaviorExecution3" .
-<https://bbn.com/scratch/test_execution/CallBehaviorExecution3> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://bioprotocols.org/paml#CallBehaviorExecution> .
-<https://bbn.com/scratch/test_execution/CallBehaviorExecution3> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://sbols.org/v3#Identified> .
 <https://bbn.com/scratch/test_execution> <http://bioprotocols.org/paml#completedNormally> "true"^^<http://www.w3.org/2001/XMLSchema#boolean> .
 <https://bbn.com/scratch/test_execution> <http://bioprotocols.org/paml#execution> <https://bbn.com/scratch/test_execution/ActivityNodeExecution1> .
 <https://bbn.com/scratch/test_execution> <http://bioprotocols.org/paml#execution> <https://bbn.com/scratch/test_execution/ActivityNodeExecution2> .
 <https://bbn.com/scratch/test_execution> <http://bioprotocols.org/paml#execution> <https://bbn.com/scratch/test_execution/ActivityNodeExecution3> .
 <https://bbn.com/scratch/test_execution> <http://bioprotocols.org/paml#execution> <https://bbn.com/scratch/test_execution/CallBehaviorExecution1> .
 <https://bbn.com/scratch/test_execution> <http://bioprotocols.org/paml#execution> <https://bbn.com/scratch/test_execution/CallBehaviorExecution2> .
-<https://bbn.com/scratch/test_execution> <http://bioprotocols.org/paml#execution> <https://bbn.com/scratch/test_execution/CallBehaviorExecution3> .
 <https://bbn.com/scratch/test_execution> <http://bioprotocols.org/paml#flow> <https://bbn.com/scratch/test_execution/ActivityEdgeFlow1> .
 <https://bbn.com/scratch/test_execution> <http://bioprotocols.org/paml#flow> <https://bbn.com/scratch/test_execution/ActivityEdgeFlow2> .
 <https://bbn.com/scratch/test_execution> <http://bioprotocols.org/paml#flow> <https://bbn.com/scratch/test_execution/ActivityEdgeFlow3> .
@@ -424,7 +385,7 @@
 <https://bbn.com/scratch/test_execution> <http://sbols.org/v3#hasNamespace> <https://bbn.com/scratch/> .
 <https://bbn.com/scratch/test_execution> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://bioprotocols.org/paml#ProtocolExecution> .
 <https://bbn.com/scratch/test_execution> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://sbols.org/v3#TopLevel> .
-<https://bbn.com/scratch/test_execution> <http://www.w3.org/ns/prov#endedAtTime> "2000-01-01T00:00:06"^^<http://www.w3.org/2001/XMLSchema#dateTime> .
+<https://bbn.com/scratch/test_execution> <http://www.w3.org/ns/prov#endedAtTime> "2000-01-01T00:00:04"^^<http://www.w3.org/2001/XMLSchema#dateTime> .
 <https://bbn.com/scratch/test_execution> <http://www.w3.org/ns/prov#qualifiedAssociation> <https://bbn.com/scratch/test_execution/Association1> .
 <https://bbn.com/scratch/test_execution> <http://www.w3.org/ns/prov#startedAtTime> "2000-01-01T00:00:00"^^<http://www.w3.org/2001/XMLSchema#dateTime> .
 <https://bioprotocols.org/paml/primitives/liquid_handling/TransferByMap/OrderedPropertyValue1/Parameter1/LiteralInteger1> <http://bioprotocols.org/uml#integerValue> "1"^^<http://www.w3.org/2001/XMLSchema#integer> .
@@ -500,7 +461,7 @@
 <https://bioprotocols.org/paml/primitives/liquid_handling/TransferByMap/OrderedPropertyValue4/Parameter1/LiteralInteger1> <http://sbols.org/v3#displayId> "LiteralInteger1" .
 <https://bioprotocols.org/paml/primitives/liquid_handling/TransferByMap/OrderedPropertyValue4/Parameter1/LiteralInteger1> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://bioprotocols.org/uml#LiteralInteger> .
 <https://bioprotocols.org/paml/primitives/liquid_handling/TransferByMap/OrderedPropertyValue4/Parameter1/LiteralInteger1> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://sbols.org/v3#Identified> .
-<https://bioprotocols.org/paml/primitives/liquid_handling/TransferByMap/OrderedPropertyValue4/Parameter1/LiteralInteger2> <http://bioprotocols.org/uml#integerValue> "0"^^<http://www.w3.org/2001/XMLSchema#integer> .
+<https://bioprotocols.org/paml/primitives/liquid_handling/TransferByMap/OrderedPropertyValue4/Parameter1/LiteralInteger2> <http://bioprotocols.org/uml#integerValue> "1"^^<http://www.w3.org/2001/XMLSchema#integer> .
 <https://bioprotocols.org/paml/primitives/liquid_handling/TransferByMap/OrderedPropertyValue4/Parameter1/LiteralInteger2> <http://sbols.org/v3#displayId> "LiteralInteger2" .
 <https://bioprotocols.org/paml/primitives/liquid_handling/TransferByMap/OrderedPropertyValue4/Parameter1/LiteralInteger2> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://bioprotocols.org/uml#LiteralInteger> .
 <https://bioprotocols.org/paml/primitives/liquid_handling/TransferByMap/OrderedPropertyValue4/Parameter1/LiteralInteger2> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://sbols.org/v3#Identified> .
@@ -511,7 +472,7 @@
 <https://bioprotocols.org/paml/primitives/liquid_handling/TransferByMap/OrderedPropertyValue4/Parameter1> <http://bioprotocols.org/uml#type> <http://www.ontology-of-units-of-measure.org/resource/om-2/Measure> .
 <https://bioprotocols.org/paml/primitives/liquid_handling/TransferByMap/OrderedPropertyValue4/Parameter1> <http://bioprotocols.org/uml#upperValue> <https://bioprotocols.org/paml/primitives/liquid_handling/TransferByMap/OrderedPropertyValue4/Parameter1/LiteralInteger1> .
 <https://bioprotocols.org/paml/primitives/liquid_handling/TransferByMap/OrderedPropertyValue4/Parameter1> <http://sbols.org/v3#displayId> "Parameter1" .
-<https://bioprotocols.org/paml/primitives/liquid_handling/TransferByMap/OrderedPropertyValue4/Parameter1> <http://sbols.org/v3#name> "dispenseVelocity" .
+<https://bioprotocols.org/paml/primitives/liquid_handling/TransferByMap/OrderedPropertyValue4/Parameter1> <http://sbols.org/v3#name> "amount" .
 <https://bioprotocols.org/paml/primitives/liquid_handling/TransferByMap/OrderedPropertyValue4/Parameter1> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://bioprotocols.org/uml#Parameter> .
 <https://bioprotocols.org/paml/primitives/liquid_handling/TransferByMap/OrderedPropertyValue4/Parameter1> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://sbols.org/v3#Identified> .
 <https://bioprotocols.org/paml/primitives/liquid_handling/TransferByMap/OrderedPropertyValue4> <http://bioprotocols.org/uml#indexValue> "3"^^<http://www.w3.org/2001/XMLSchema#integer> .
@@ -519,10 +480,34 @@
 <https://bioprotocols.org/paml/primitives/liquid_handling/TransferByMap/OrderedPropertyValue4> <http://sbols.org/v3#displayId> "OrderedPropertyValue4" .
 <https://bioprotocols.org/paml/primitives/liquid_handling/TransferByMap/OrderedPropertyValue4> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://bioprotocols.org/uml#OrderedPropertyValue> .
 <https://bioprotocols.org/paml/primitives/liquid_handling/TransferByMap/OrderedPropertyValue4> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://sbols.org/v3#Identified> .
+<https://bioprotocols.org/paml/primitives/liquid_handling/TransferByMap/OrderedPropertyValue5/Parameter1/LiteralInteger1> <http://bioprotocols.org/uml#integerValue> "1"^^<http://www.w3.org/2001/XMLSchema#integer> .
+<https://bioprotocols.org/paml/primitives/liquid_handling/TransferByMap/OrderedPropertyValue5/Parameter1/LiteralInteger1> <http://sbols.org/v3#displayId> "LiteralInteger1" .
+<https://bioprotocols.org/paml/primitives/liquid_handling/TransferByMap/OrderedPropertyValue5/Parameter1/LiteralInteger1> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://bioprotocols.org/uml#LiteralInteger> .
+<https://bioprotocols.org/paml/primitives/liquid_handling/TransferByMap/OrderedPropertyValue5/Parameter1/LiteralInteger1> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://sbols.org/v3#Identified> .
+<https://bioprotocols.org/paml/primitives/liquid_handling/TransferByMap/OrderedPropertyValue5/Parameter1/LiteralInteger2> <http://bioprotocols.org/uml#integerValue> "0"^^<http://www.w3.org/2001/XMLSchema#integer> .
+<https://bioprotocols.org/paml/primitives/liquid_handling/TransferByMap/OrderedPropertyValue5/Parameter1/LiteralInteger2> <http://sbols.org/v3#displayId> "LiteralInteger2" .
+<https://bioprotocols.org/paml/primitives/liquid_handling/TransferByMap/OrderedPropertyValue5/Parameter1/LiteralInteger2> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://bioprotocols.org/uml#LiteralInteger> .
+<https://bioprotocols.org/paml/primitives/liquid_handling/TransferByMap/OrderedPropertyValue5/Parameter1/LiteralInteger2> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://sbols.org/v3#Identified> .
+<https://bioprotocols.org/paml/primitives/liquid_handling/TransferByMap/OrderedPropertyValue5/Parameter1> <http://bioprotocols.org/uml#direction> <http://bioprotocols.org/uml#in> .
+<https://bioprotocols.org/paml/primitives/liquid_handling/TransferByMap/OrderedPropertyValue5/Parameter1> <http://bioprotocols.org/uml#isOrdered> "true"^^<http://www.w3.org/2001/XMLSchema#boolean> .
+<https://bioprotocols.org/paml/primitives/liquid_handling/TransferByMap/OrderedPropertyValue5/Parameter1> <http://bioprotocols.org/uml#isUnique> "true"^^<http://www.w3.org/2001/XMLSchema#boolean> .
+<https://bioprotocols.org/paml/primitives/liquid_handling/TransferByMap/OrderedPropertyValue5/Parameter1> <http://bioprotocols.org/uml#lowerValue> <https://bioprotocols.org/paml/primitives/liquid_handling/TransferByMap/OrderedPropertyValue5/Parameter1/LiteralInteger2> .
+<https://bioprotocols.org/paml/primitives/liquid_handling/TransferByMap/OrderedPropertyValue5/Parameter1> <http://bioprotocols.org/uml#type> <http://www.ontology-of-units-of-measure.org/resource/om-2/Measure> .
+<https://bioprotocols.org/paml/primitives/liquid_handling/TransferByMap/OrderedPropertyValue5/Parameter1> <http://bioprotocols.org/uml#upperValue> <https://bioprotocols.org/paml/primitives/liquid_handling/TransferByMap/OrderedPropertyValue5/Parameter1/LiteralInteger1> .
+<https://bioprotocols.org/paml/primitives/liquid_handling/TransferByMap/OrderedPropertyValue5/Parameter1> <http://sbols.org/v3#displayId> "Parameter1" .
+<https://bioprotocols.org/paml/primitives/liquid_handling/TransferByMap/OrderedPropertyValue5/Parameter1> <http://sbols.org/v3#name> "dispenseVelocity" .
+<https://bioprotocols.org/paml/primitives/liquid_handling/TransferByMap/OrderedPropertyValue5/Parameter1> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://bioprotocols.org/uml#Parameter> .
+<https://bioprotocols.org/paml/primitives/liquid_handling/TransferByMap/OrderedPropertyValue5/Parameter1> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://sbols.org/v3#Identified> .
+<https://bioprotocols.org/paml/primitives/liquid_handling/TransferByMap/OrderedPropertyValue5> <http://bioprotocols.org/uml#indexValue> "4"^^<http://www.w3.org/2001/XMLSchema#integer> .
+<https://bioprotocols.org/paml/primitives/liquid_handling/TransferByMap/OrderedPropertyValue5> <http://bioprotocols.org/uml#propertyValue> <https://bioprotocols.org/paml/primitives/liquid_handling/TransferByMap/OrderedPropertyValue5/Parameter1> .
+<https://bioprotocols.org/paml/primitives/liquid_handling/TransferByMap/OrderedPropertyValue5> <http://sbols.org/v3#displayId> "OrderedPropertyValue5" .
+<https://bioprotocols.org/paml/primitives/liquid_handling/TransferByMap/OrderedPropertyValue5> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://bioprotocols.org/uml#OrderedPropertyValue> .
+<https://bioprotocols.org/paml/primitives/liquid_handling/TransferByMap/OrderedPropertyValue5> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://sbols.org/v3#Identified> .
 <https://bioprotocols.org/paml/primitives/liquid_handling/TransferByMap> <http://bioprotocols.org/uml#ownedParameter> <https://bioprotocols.org/paml/primitives/liquid_handling/TransferByMap/OrderedPropertyValue1> .
 <https://bioprotocols.org/paml/primitives/liquid_handling/TransferByMap> <http://bioprotocols.org/uml#ownedParameter> <https://bioprotocols.org/paml/primitives/liquid_handling/TransferByMap/OrderedPropertyValue2> .
 <https://bioprotocols.org/paml/primitives/liquid_handling/TransferByMap> <http://bioprotocols.org/uml#ownedParameter> <https://bioprotocols.org/paml/primitives/liquid_handling/TransferByMap/OrderedPropertyValue3> .
 <https://bioprotocols.org/paml/primitives/liquid_handling/TransferByMap> <http://bioprotocols.org/uml#ownedParameter> <https://bioprotocols.org/paml/primitives/liquid_handling/TransferByMap/OrderedPropertyValue4> .
+<https://bioprotocols.org/paml/primitives/liquid_handling/TransferByMap> <http://bioprotocols.org/uml#ownedParameter> <https://bioprotocols.org/paml/primitives/liquid_handling/TransferByMap/OrderedPropertyValue5> .
 <https://bioprotocols.org/paml/primitives/liquid_handling/TransferByMap> <http://sbols.org/v3#description> "Move volumes from a collection of source samples to a collection of destination samples following a plan of value given for each location" .
 <https://bioprotocols.org/paml/primitives/liquid_handling/TransferByMap> <http://sbols.org/v3#displayId> "TransferByMap" .
 <https://bioprotocols.org/paml/primitives/liquid_handling/TransferByMap> <http://sbols.org/v3#hasNamespace> <https://bioprotocols.org/paml/primitives/liquid_handling> .