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Feat/comp/get input format #2315

Merged
merged 296 commits into from
Feb 10, 2022
Merged

Feat/comp/get input format #2315

merged 296 commits into from
Feb 10, 2022

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jdcpni
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@jdcpni jdcpni commented Feb 9, 2022

• composition.py:

  • get_input_format():
    • add form option that returns dict formatted for use as inputs arg of run() method
    • support label_dicts that specify labels for entire mech, not ports individually
    • _parse_labels(): fix bugs to support above

• utilities.py:

  • nested_depth(): returns depth of ragged lists and np arrays

• test_composition.py:

  • add test_get_input_format()

@jdcpni
-
8ed5e87
@jdcpni
Merge branch 'fix/ocm/llvm_num_estimates' into refactor/ocm/state_inp…
bcfbae9 
…ut_ports

# Conflicts:
#	psyneulink/core/llvm/builder_context.py
@jdcpni
Merge branch 'devel' of https://github.com/PrincetonUniversity/PsyNeu…
8a564aa 
…Link into refactor/ocm/state_input_ports
@jdcpni
• composition.py:
883b49d 
  - _update_controller: added
  - add_controller and _analyze_graph(): call _update_controller
@jdcpni
-
d2faa86
@jdcpni
• composition.py
a632f72 
  _update_controller:  fixed to loop through all input_ports of comp INPUT nodes
@jdcpni
• test_control.py
0e1a32e 
  - test_agent_rep_assignement_as_controller_and_replacement:
      updated to test that shadowing projections to state_input_ports
      are properly added and deleted
@jdcpni
Merge branch 'devel' of https://github.com/PrincetonUniversity/PsyNeu…
1d996fb 
…Link into refactor/ocm/state_input_ports

� Conflicts:
�	tests/composition/test_control.py
@jdcpni
Merge branch 'devel' of https://github.com/PrincetonUniversity/PsyNeu…
cbe6d24 
…Link into devel
@jdcpni
• optimizationfunctions.py:
3856bdd 
  - _function: refactored to put use aggregation_function at end
  - _grid_evaluate:  still needs to return all_samples
@jdcpni
Merge branch 'refactor/ocm/state_input_ports' of https://github.com/P…
0eb6514 
…rincetonUniversity/PsyNeuLink into refactor/ocm/state_input_ports

� Conflicts:
�	psyneulink/core/components/mechanisms/modulatory/control/optimizationcontrolmechanism.py
@jdcpni
-
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@jdcpni
• composition.py
d580849 
  - added call to _update_controller to add_node
  - moved test for projections to controller.state_input_ports to run()
@jdcpni
-
79b6ed6
@jdcpni
Merge branch 'devel' of https://github.com/PrincetonUniversity/PsyNeu…
1a5dd50 
…Link into refactor/ocm/state_input_ports
@jdcpni
• composition.py:
34b179e 
  moved calls to _update_controller to _complete_init_of_partially_initialized_nodes
  moved _update_controller to ocm._update_state_input_ports

• optimizationcontrolmechanism.py:
  added _update_state_input_ports [**still needed work**]
@jdcpni
• composition.py:
dff750a 
  moved calls to _update_controller to _complete_init_of_partially_initialized_nodes
  moved _update_controller to ocm._update_state_input_ports
  _instantiate_controller_shadow_projections [still needs to be implemented]

• optimizationcontrolmechanism.py:
  added _update_state_input_ports [**still needed work**]
@jdcpni
Merge branch 'refactor/ocm/state_input_ports' of https://github.com/P…
38e5bae 
…rincetonUniversity/PsyNeuLink into refactor/ocm/state_input_ports
@jdcpni
• composition.py
d487a4c 
  added needs_update_controller
@jdcpni
-
779add6
@jdcpni
• composition.py:
5c361e2 
  - implemented self.needs_update_controller
  - moved implementation of controlsignal projections
    from add_controller to _instantiate_control_projections
    that is called in _complete_init_of_partially_initialized_nodes

Note: still need to set  self.needs_update_controller to False
      after instantiating state_input_ports and projections to them
@jdcpni
-
0c2de6a
@jdcpni
Merge branch 'devel' of https://github.com/PrincetonUniversity/PsyNeu…
a7436db 
…Link into devel
@jdcpni
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@jdcpni
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@jdcpni
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@jdcpni
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@jdcpni
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@jdcpni
Merge branch 'refactor/ocm/state_input_ports' of https://github.com/P…
fa4e038 
…rincetonUniversity/PsyNeuLink into refactor/ocm/state_input_ports
jdcpni and others added 25 commits February 6, 2022 17:51
@jdcpni
• test_composition.py:
5302106 
  add: test_get_input_format()
@jdcpni
- Before adding trials and labels to template to Composition.get_inpu…
e2b2bb5 
…t_format()
@jdcpni
Merge branch 'devel' of https://github.com/PrincetonUniversity/PsyNeu…
7cea79e 
…Link into fix/comp_and_mech/input_variable

� Conflicts:
�	psyneulink/core/compositions/composition.py
@jdcpni
- Before adding trials and labels to template to Composition.get_inpu…
06acf06 
…t_format()
@jdcpni
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@jdcpni
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@jdcpni
- Before adding trials and labels to template to Composition.get_inpu…
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…t_format()
-
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@jdcpni
- Before adding trials and labels to template to Composition.get_inpu…
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…t_format()
@jdcpni
- Before adding trials and labels to template to Composition.get_inpu…
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…t_format()
@jdcpni
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@jdcpni
• composition.py:
5505fd0 
  - get_input_format():
    - add form option that returns dict formatted for use as **inputs** arg of run() method
    - support dict that specifies labels for entire mech, not ports individually
    - _parse_labels(): fix bugs to support above

• utilities.py:
  - nested_depth(): returns depth of ragged lists and np.ndarrays

• test_composition.py:
  - add test_get_input_format()
@jdcpni
Merge branch 'devel' of https://github.com/PrincetonUniversity/PsyNeu…
06037aa 
…Link into feat/comp/get_input_format
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This PR causes the following changes to the html docs (ubuntu-latest-3.7-x64):

diff -r docs-base/Composition.html docs-head/Composition.html
606,607c606,607
< outer Composition, are assigned <a class="reference internal" href="#id18" title="psyneulink.core.compositions.composition.NodeRole.PROBE"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">PROBE</span></code></a> in addition to their other <a class="reference internal" href="#psyneulink.core.compositions.composition.NodeRole" title="psyneulink.core.compositions.composition.NodeRole"><code class="xref any py py-class docutils literal notranslate"><span class="pre">roles</span></code></a> in the
< nested Composition.  The only difference between <a class="reference internal" href="#id18" title="psyneulink.core.compositions.composition.NodeRole.PROBE"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">PROBE</span></code></a> and <a class="reference internal" href="#psyneulink.core.compositions.composition.NodeRole.OUTPUT" title="psyneulink.core.compositions.composition.NodeRole.OUTPUT"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">OUTPUT</span></code></a> Nodes
---
> outer Composition, are assigned <a class="reference internal" href="#id22" title="psyneulink.core.compositions.composition.NodeRole.PROBE"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">PROBE</span></code></a> in addition to their other <a class="reference internal" href="#psyneulink.core.compositions.composition.NodeRole" title="psyneulink.core.compositions.composition.NodeRole"><code class="xref any py py-class docutils literal notranslate"><span class="pre">roles</span></code></a> in the
> nested Composition.  The only difference between <a class="reference internal" href="#id22" title="psyneulink.core.compositions.composition.NodeRole.PROBE"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">PROBE</span></code></a> and <a class="reference internal" href="#psyneulink.core.compositions.composition.NodeRole.OUTPUT" title="psyneulink.core.compositions.composition.NodeRole.OUTPUT"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">OUTPUT</span></code></a> Nodes
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< <a class="reference internal" href="#id18" title="psyneulink.core.compositions.composition.NodeRole.PROBE"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">PROBE</span></code></a> Nodes are <em>not</em> included in the <a class="reference internal" href="#id0" title="psyneulink.core.compositions.composition.Composition.output_values"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">output_values</span></code></a> or <a class="reference internal" href="#psyneulink.core.compositions.composition.Composition.results" title="psyneulink.core.compositions.composition.Composition.results"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">results</span></code></a> for the outermost Composition to which they project (although they <em>are</em> still included
---
> <a class="reference internal" href="#id22" title="psyneulink.core.compositions.composition.NodeRole.PROBE"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">PROBE</span></code></a> Nodes are <em>not</em> included in the <a class="reference internal" href="#id0" title="psyneulink.core.compositions.composition.Composition.output_values"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">output_values</span></code></a> or <a class="reference internal" href="#psyneulink.core.compositions.composition.Composition.results" title="psyneulink.core.compositions.composition.Composition.results"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">results</span></code></a> for the outermost Composition to which they project (although they <em>are</em> still included
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< <a class="reference internal" href="#psyneulink.core.compositions.composition.Composition.include_probes_in_output" title="psyneulink.core.compositions.composition.Composition.include_probes_in_output"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">include_probes_in_output</span></code></a> is True, then any <a class="reference internal" href="#id18" title="psyneulink.core.compositions.composition.NodeRole.PROBE"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">PROBE</span></code></a> Nodes
---
> <a class="reference internal" href="#psyneulink.core.compositions.composition.Composition.include_probes_in_output" title="psyneulink.core.compositions.composition.Composition.include_probes_in_output"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">include_probes_in_output</span></code></a> is True, then any <a class="reference internal" href="#id22" title="psyneulink.core.compositions.composition.NodeRole.PROBE"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">PROBE</span></code></a> Nodes
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< <a class="reference internal" href="#id18" title="psyneulink.core.compositions.composition.NodeRole.PROBE"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">PROBE</span></code></a> Nodes can be visualized, along with any Projections treated differently from those of
---
> <a class="reference internal" href="#id22" title="psyneulink.core.compositions.composition.NodeRole.PROBE"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">PROBE</span></code></a> Nodes can be visualized, along with any Projections treated differently from those of
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< <div><p><a class="reference internal" href="#id18" title="psyneulink.core.compositions.composition.NodeRole.PROBE"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">PROBE</span></code></a> Nodes are useful for <a class="reference internal" href="OptimizationControlMechanism.html#optimizationcontrolmechanism-model-based"><span class="std std-ref">model-based optimization using an</span></a>, in which the value of one or more Nodes in a nested Composition
---
> <div><p><a class="reference internal" href="#id22" title="psyneulink.core.compositions.composition.NodeRole.PROBE"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">PROBE</span></code></a> Nodes are useful for <a class="reference internal" href="OptimizationControlMechanism.html#optimizationcontrolmechanism-model-based"><span class="std std-ref">model-based optimization using an</span></a>, in which the value of one or more Nodes in a nested Composition
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< include the InputPorts of the nested Composition.  These can be accessed using the Composition’s <a class="reference internal" href="#id15" title="psyneulink.core.compositions.composition.Composition.external_input_ports"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">exernal_input_ports</span></code></a> attribute.</p>
---
> include the InputPorts of the nested Composition.  These can be accessed using the Composition’s <a class="reference internal" href="#id19" title="psyneulink.core.compositions.composition.Composition.external_input_ports"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">exernal_input_ports</span></code></a> attribute.</p>
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< Composition.  If the Composition has an <a class="reference internal" href="#id18" title="psyneulink.core.compositions.composition.NodeRole.PROBE"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">PROBE</span></code></a> Nodes, then they too project to the Composition’s
< output_CIM.  If the Composition is nested in another, then the <a class="reference internal" href="Mechanism.html#psyneulink.core.components.mechanisms.mechanism.Mechanism_Base.value" title="psyneulink.core.components.mechanisms.mechanism.Mechanism_Base.value"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">values</span></code></a> of the <a class="reference internal" href="#id18" title="psyneulink.core.compositions.composition.NodeRole.PROBE"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">PROBE</span></code></a> Nodes are also included in the Composition’s <a class="reference internal" href="#id0" title="psyneulink.core.compositions.composition.Composition.output_values"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">output_values</span></code></a>;  if it
---
> Composition.  If the Composition has an <a class="reference internal" href="#id22" title="psyneulink.core.compositions.composition.NodeRole.PROBE"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">PROBE</span></code></a> Nodes, then they too project to the Composition’s
> output_CIM.  If the Composition is nested in another, then the <a class="reference internal" href="Mechanism.html#psyneulink.core.components.mechanisms.mechanism.Mechanism_Base.value" title="psyneulink.core.components.mechanisms.mechanism.Mechanism_Base.value"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">values</span></code></a> of the <a class="reference internal" href="#id22" title="psyneulink.core.compositions.composition.NodeRole.PROBE"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">PROBE</span></code></a> Nodes are also included in the Composition’s <a class="reference internal" href="#id0" title="psyneulink.core.compositions.composition.Composition.output_values"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">output_values</span></code></a>;  if it
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< <a class="reference internal" href="#id18" title="psyneulink.core.compositions.composition.NodeRole.PROBE"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">PROBE</span></code></a> Nodes of a nested Composition, like <a class="reference internal" href="#psyneulink.core.compositions.composition.NodeRole.OUTPUT" title="psyneulink.core.compositions.composition.NodeRole.OUTPUT"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">OUTPUT</span></code></a> Nodes,
---
> <a class="reference internal" href="#id22" title="psyneulink.core.compositions.composition.NodeRole.PROBE"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">PROBE</span></code></a> Nodes of a nested Composition, like <a class="reference internal" href="#psyneulink.core.compositions.composition.NodeRole.OUTPUT" title="psyneulink.core.compositions.composition.NodeRole.OUTPUT"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">OUTPUT</span></code></a> Nodes,
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< The outputs of <a class="reference internal" href="#id18" title="psyneulink.core.compositions.composition.NodeRole.PROBE"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">PROBE</span></code></a> Nodes are included in the <a class="reference internal" href="#id0" title="psyneulink.core.compositions.composition.Composition.output_values"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">output_values</span></code></a> and
---
> The outputs of <a class="reference internal" href="#id22" title="psyneulink.core.compositions.composition.NodeRole.PROBE"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">PROBE</span></code></a> Nodes are included in the <a class="reference internal" href="#id0" title="psyneulink.core.compositions.composition.Composition.output_values"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">output_values</span></code></a> and
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< <figure class="align-default" id="id19">
---
> <figure class="align-default" id="id23">
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< and in italics, above each Mechanism).</span><a class="headerlink" href="#id19" title="Permalink to this image">¶</a></p>
---
> and in italics, above each Mechanism).</span><a class="headerlink" href="#id23" title="Permalink to this image">¶</a></p>
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< <figure class="align-default" id="id20">
---
> <figure class="align-default" id="id24">
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< one that projects to the ComparatorMechanism and assigned as the <a class="reference internal" href="#psyneulink.core.compositions.composition.NodeRole.OUTPUT" title="psyneulink.core.compositions.composition.NodeRole.OUTPUT"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">OUTPUT</span></code></a> Node.</span><a class="headerlink" href="#id20" title="Permalink to this image">¶</a></p>
---
> one that projects to the ComparatorMechanism and assigned as the <a class="reference internal" href="#psyneulink.core.compositions.composition.NodeRole.OUTPUT" title="psyneulink.core.compositions.composition.NodeRole.OUTPUT"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">OUTPUT</span></code></a> Node.</span><a class="headerlink" href="#id24" title="Permalink to this image">¶</a></p>
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< <figure class="align-default" id="id21">
---
> <figure class="align-default" id="id25">
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< method with the argument <code class="docutils literal notranslate"><span class="pre">animate={'show_learning':True}</span></code>.</span><a class="headerlink" href="#id21" title="Permalink to this image">¶</a></p>
---
> method with the argument <code class="docutils literal notranslate"><span class="pre">animate={'show_learning':True}</span></code>.</span><a class="headerlink" href="#id25" title="Permalink to this image">¶</a></p>
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< <a class="reference internal" href="Mechanism.html"><span class="doc">Mechanisms</span></a>, and the corresponding attribute (<a class="reference internal" href="#id15" title="psyneulink.core.compositions.composition.Composition.external_input_ports"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">external_input_ports</span></code></a>)
---
> <a class="reference internal" href="Mechanism.html"><span class="doc">Mechanisms</span></a>, and the corresponding attribute (<a class="reference internal" href="#id19" title="psyneulink.core.compositions.composition.Composition.external_input_ports"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">external_input_ports</span></code></a>)
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< that input_port.  Similar considerations extend to the <a class="reference internal" href="#id15" title="psyneulink.core.compositions.composition.Composition.external_input_ports"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">external_input_ports</span></code></a>
---
> that input_port.  Similar considerations extend to the <a class="reference internal" href="#id19" title="psyneulink.core.compositions.composition.Composition.external_input_ports"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">external_input_ports</span></code></a>
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< <figure class="align-default" id="id22">
---
> <figure class="align-default" id="id26">
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< Mechanism <code class="docutils literal notranslate"><span class="pre">c</span></code> on every <a class="reference internal" href="Time.html#psyneulink.core.scheduling.time.TimeScale.TRIAL" title="psyneulink.core.scheduling.time.TimeScale.TRIAL"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">TRIAL</span></code></a>.</span><a class="headerlink" href="#id22" title="Permalink to this image">¶</a></p>
---
> Mechanism <code class="docutils literal notranslate"><span class="pre">c</span></code> on every <a class="reference internal" href="Time.html#psyneulink.core.scheduling.time.TimeScale.TRIAL" title="psyneulink.core.scheduling.time.TimeScale.TRIAL"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">TRIAL</span></code></a>.</span><a class="headerlink" href="#id26" title="Permalink to this image">¶</a></p>
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< (<a class="reference internal" href="Mechanism.html#psyneulink.core.components.mechanisms.mechanism.Mechanism_Base.external_input_ports" title="psyneulink.core.components.mechanisms.mechanism.Mechanism_Base.external_input_ports"><code class="xref any py py-attr docutils literal n
...

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lgtm-com bot commented Feb 9, 2022

This pull request introduces 1 alert when merging 06037aa into 7332ab5 - view on LGTM.com

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Coverage Status

Coverage increased (+0.01%) to 84.337% when pulling 06037aa on feat/comp/get_input_format into 7332ab5 on devel.

@jdcpni jdcpni merged commit 82d43be into devel Feb 10, 2022
@jdcpni jdcpni deleted the feat/comp/get_input_format branch February 10, 2022 00:33
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