Skip to content

Added similarity workflow diagram #63

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
davewalker5 merged 1 commit into from
May 12, 2026
Merged

Added similarity workflow diagram #63

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
245 changes: 245 additions & 0 deletions docs/images/similarity-analysis.bpmn
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,245 @@
<?xml version="1.0" encoding="UTF-8"?>
<bpmn:definitions xmlns:bpmn="http://www.omg.org/spec/BPMN/20100524/MODEL" xmlns:bpmndi="http://www.omg.org/spec/BPMN/20100524/DI" xmlns:dc="http://www.omg.org/spec/DD/20100524/DC" xmlns:di="http://www.omg.org/spec/DD/20100524/DI" xmlns:modeler="http://camunda.org/schema/modeler/1.0" id="Definitions_1gl9wbo" targetNamespace="http://bpmn.io/schema/bpmn" exporter="Camunda Modeler" exporterVersion="5.39.0" modeler:executionPlatform="Camunda Cloud" modeler:executionPlatformVersion="8.7.0">
<bpmn:process id="Process_1c15w5m" isExecutable="true">
<bpmn:startEvent id="StartEvent_1" name="Consensus Parameters">
<bpmn:outgoing>Flow_0hqrbhu</bpmn:outgoing>
<bpmn:messageEventDefinition id="MessageEventDefinition_1azohss" />
</bpmn:startEvent>
<bpmn:task id="Activity_0iww0ka" name="Derive Species Features">
<bpmn:incoming>Flow_0hqrbhu</bpmn:incoming>
<bpmn:outgoing>Flow_0abqfhc</bpmn:outgoing>
<bpmn:dataOutputAssociation id="DataOutputAssociation_1gh2uhe">
<bpmn:targetRef>DataObjectReference_13v9cib</bpmn:targetRef>
</bpmn:dataOutputAssociation>
</bpmn:task>
<bpmn:sequenceFlow id="Flow_0hqrbhu" sourceRef="StartEvent_1" targetRef="Activity_0iww0ka" />
<bpmn:dataObjectReference id="DataObjectReference_13v9cib" name="Species Classification Files" dataObjectRef="DataObject_1odg597" />
<bpmn:dataObject id="DataObject_1odg597" />
<bpmn:task id="Activity_0nwlk24" name="Build Feature Matrix">
<bpmn:incoming>Flow_0abqfhc</bpmn:incoming>
<bpmn:outgoing>Flow_03lflym</bpmn:outgoing>
<bpmn:property id="Property_03rgmsp" name="__targetRef_placeholder" />
<bpmn:dataInputAssociation id="DataInputAssociation_0len72j">
<bpmn:sourceRef>DataObjectReference_13v9cib</bpmn:sourceRef>
<bpmn:targetRef>Property_03rgmsp</bpmn:targetRef>
</bpmn:dataInputAssociation>
<bpmn:dataOutputAssociation id="DataOutputAssociation_0emim9g">
<bpmn:targetRef>DataObjectReference_0gd66zh</bpmn:targetRef>
</bpmn:dataOutputAssociation>
</bpmn:task>
<bpmn:sequenceFlow id="Flow_0abqfhc" sourceRef="Activity_0iww0ka" targetRef="Activity_0nwlk24" />
<bpmn:dataObjectReference id="DataObjectReference_0gd66zh" name="Species Feature Matrix" dataObjectRef="DataObject_1lsf6xl" />
<bpmn:dataObject id="DataObject_1lsf6xl" />
<bpmn:task id="Activity_1v4x4zh" name="Build Species Similarity Matrix">
<bpmn:incoming>Flow_03lflym</bpmn:incoming>
<bpmn:outgoing>Flow_1eid6sv</bpmn:outgoing>
<bpmn:property id="Property_1l4dldc" name="__targetRef_placeholder" />
<bpmn:dataInputAssociation id="DataInputAssociation_0dponsz">
<bpmn:sourceRef>DataObjectReference_0gd66zh</bpmn:sourceRef>
<bpmn:targetRef>Property_1l4dldc</bpmn:targetRef>
</bpmn:dataInputAssociation>
<bpmn:dataOutputAssociation id="DataOutputAssociation_1vvy95a">
<bpmn:targetRef>DataObjectReference_12qr9kc</bpmn:targetRef>
</bpmn:dataOutputAssociation>
</bpmn:task>
<bpmn:sequenceFlow id="Flow_03lflym" sourceRef="Activity_0nwlk24" targetRef="Activity_1v4x4zh" />
<bpmn:dataObjectReference id="DataObjectReference_12qr9kc" name="Species Similarity Matrix" dataObjectRef="DataObject_1x23lto" />
<bpmn:dataObject id="DataObject_1x23lto" />
<bpmn:task id="Activity_0snqcdu" name="Chart Species Similarity Heatmap">
<bpmn:incoming>Flow_1eid6sv</bpmn:incoming>
<bpmn:outgoing>Flow_0vd7dj3</bpmn:outgoing>
<bpmn:property id="Property_1i8ut06" name="__targetRef_placeholder" />
<bpmn:dataInputAssociation id="DataInputAssociation_0x57f43">
<bpmn:sourceRef>DataObjectReference_12qr9kc</bpmn:sourceRef>
<bpmn:targetRef>Property_1i8ut06</bpmn:targetRef>
</bpmn:dataInputAssociation>
<bpmn:dataOutputAssociation id="DataOutputAssociation_0xj5k2q">
<bpmn:targetRef>DataObjectReference_1vu1xf6</bpmn:targetRef>
</bpmn:dataOutputAssociation>
</bpmn:task>
<bpmn:sequenceFlow id="Flow_1eid6sv" sourceRef="Activity_1v4x4zh" targetRef="Activity_0snqcdu" />
<bpmn:dataObjectReference id="DataObjectReference_1vu1xf6" name="Heatmap" dataObjectRef="DataObject_1cczq4x" />
<bpmn:dataObject id="DataObject_1cczq4x" />
<bpmn:task id="Activity_0fpz6zt" name="Cluster Species by Similarity">
<bpmn:incoming>Flow_0vd7dj3</bpmn:incoming>
<bpmn:outgoing>Flow_179mxmw</bpmn:outgoing>
<bpmn:property id="Property_10s62on" name="__targetRef_placeholder" />
<bpmn:dataInputAssociation id="DataInputAssociation_1759rw8">
<bpmn:sourceRef>DataObjectReference_12qr9kc</bpmn:sourceRef>
<bpmn:targetRef>Property_10s62on</bpmn:targetRef>
</bpmn:dataInputAssociation>
<bpmn:dataOutputAssociation id="DataOutputAssociation_0c4kahx">
<bpmn:targetRef>DataObjectReference_0f7bhfh</bpmn:targetRef>
</bpmn:dataOutputAssociation>
</bpmn:task>
<bpmn:sequenceFlow id="Flow_0vd7dj3" sourceRef="Activity_0snqcdu" targetRef="Activity_0fpz6zt" />
<bpmn:dataObjectReference id="DataObjectReference_0f7bhfh" name="Species Clustering and Linkage" dataObjectRef="DataObject_04d6wpt" />
<bpmn:dataObject id="DataObject_04d6wpt" />
<bpmn:task id="Activity_16wenfg" name="Chart Species Cluster Dendogram">
<bpmn:incoming>Flow_179mxmw</bpmn:incoming>
<bpmn:outgoing>Flow_018xh3n</bpmn:outgoing>
<bpmn:property id="Property_0trulhw" name="__targetRef_placeholder" />
<bpmn:dataInputAssociation id="DataInputAssociation_0lz5fh8">
<bpmn:sourceRef>DataObjectReference_0f7bhfh</bpmn:sourceRef>
<bpmn:targetRef>Property_0trulhw</bpmn:targetRef>
</bpmn:dataInputAssociation>
<bpmn:dataOutputAssociation id="DataOutputAssociation_1f8ure4">
<bpmn:targetRef>DataObjectReference_07f49dd</bpmn:targetRef>
</bpmn:dataOutputAssociation>
</bpmn:task>
<bpmn:sequenceFlow id="Flow_179mxmw" sourceRef="Activity_0fpz6zt" targetRef="Activity_16wenfg" />
<bpmn:sequenceFlow id="Flow_018xh3n" sourceRef="Activity_16wenfg" targetRef="Event_09abwcm" />
<bpmn:endEvent id="Event_09abwcm">
<bpmn:incoming>Flow_018xh3n</bpmn:incoming>
<bpmn:terminateEventDefinition id="TerminateEventDefinition_1erei0d" />
</bpmn:endEvent>
<bpmn:dataObjectReference id="DataObjectReference_07f49dd" name="Species Cluster Dendogram" dataObjectRef="DataObject_0am19aj" />
<bpmn:dataObject id="DataObject_0am19aj" />
</bpmn:process>
<bpmndi:BPMNDiagram id="BPMNDiagram_1">
<bpmndi:BPMNPlane id="BPMNPlane_1" bpmnElement="Process_1c15w5m">
<bpmndi:BPMNShape id="Event_0vigjox_di" bpmnElement="StartEvent_1">
<dc:Bounds x="182" y="272" width="36" height="36" />
<bpmndi:BPMNLabel>
<dc:Bounds x="172" y="315" width="57" height="27" />
</bpmndi:BPMNLabel>
</bpmndi:BPMNShape>
<bpmndi:BPMNShape id="Activity_0iww0ka_di" bpmnElement="Activity_0iww0ka">
<dc:Bounds x="270" y="250" width="100" height="80" />
<bpmndi:BPMNLabel />
</bpmndi:BPMNShape>
<bpmndi:BPMNShape id="DataObjectReference_13v9cib_di" bpmnElement="DataObjectReference_13v9cib">
<dc:Bounds x="302" y="395" width="36" height="50" />
<bpmndi:BPMNLabel>
<dc:Bounds x="289" y="452" width="65" height="40" />
</bpmndi:BPMNLabel>
</bpmndi:BPMNShape>
<bpmndi:BPMNShape id="Activity_0nwlk24_di" bpmnElement="Activity_0nwlk24">
<dc:Bounds x="430" y="250" width="100" height="80" />
<bpmndi:BPMNLabel />
</bpmndi:BPMNShape>
<bpmndi:BPMNShape id="DataObjectReference_0gd66zh_di" bpmnElement="DataObjectReference_0gd66zh">
<dc:Bounds x="462" y="395" width="36" height="50" />
<bpmndi:BPMNLabel>
<dc:Bounds x="370.5" y="406" width="81" height="27" />
</bpmndi:BPMNLabel>
</bpmndi:BPMNShape>
<bpmndi:BPMNShape id="Activity_1v4x4zh_di" bpmnElement="Activity_1v4x4zh">
<dc:Bounds x="590" y="250" width="100" height="80" />
<bpmndi:BPMNLabel />
</bpmndi:BPMNShape>
<bpmndi:BPMNShape id="DataObjectReference_12qr9kc_di" bpmnElement="DataObjectReference_12qr9kc">
<dc:Bounds x="622" y="395" width="36" height="50" />
<bpmndi:BPMNLabel>
<dc:Bounds x="524.5" y="406" width="87" height="27" />
</bpmndi:BPMNLabel>
</bpmndi:BPMNShape>
<bpmndi:BPMNShape id="Activity_0snqcdu_di" bpmnElement="Activity_0snqcdu">
<dc:Bounds x="750" y="250" width="100" height="80" />
<bpmndi:BPMNLabel />
</bpmndi:BPMNShape>
<bpmndi:BPMNShape id="Activity_0fpz6zt_di" bpmnElement="Activity_0fpz6zt">
<dc:Bounds x="910" y="250" width="100" height="80" />
<bpmndi:BPMNLabel />
</bpmndi:BPMNShape>
<bpmndi:BPMNShape id="Activity_16wenfg_di" bpmnElement="Activity_16wenfg">
<dc:Bounds x="1070" y="250" width="100" height="80" />
<bpmndi:BPMNLabel />
</bpmndi:BPMNShape>
<bpmndi:BPMNShape id="Event_18p7gcb_di" bpmnElement="Event_09abwcm">
<dc:Bounds x="1232" y="272" width="36" height="36" />
</bpmndi:BPMNShape>
<bpmndi:BPMNShape id="DataObjectReference_07f49dd_di" bpmnElement="DataObjectReference_07f49dd">
<dc:Bounds x="1102" y="395" width="36" height="50" />
<bpmndi:BPMNLabel>
<dc:Bounds x="1081" y="452" width="78" height="27" />
</bpmndi:BPMNLabel>
</bpmndi:BPMNShape>
<bpmndi:BPMNShape id="DataObjectReference_0f7bhfh_di" bpmnElement="DataObjectReference_0f7bhfh">
<dc:Bounds x="942" y="135" width="36" height="50" />
<bpmndi:BPMNLabel>
<dc:Bounds x="924" y="85" width="71" height="40" />
</bpmndi:BPMNLabel>
</bpmndi:BPMNShape>
<bpmndi:BPMNShape id="DataObjectReference_1vu1xf6_di" bpmnElement="DataObjectReference_1vu1xf6">
<dc:Bounds x="782" y="135" width="36" height="50" />
<bpmndi:BPMNLabel>
<dc:Bounds x="777" y="111" width="45" height="14" />
</bpmndi:BPMNLabel>
</bpmndi:BPMNShape>
<bpmndi:BPMNEdge id="Flow_0hqrbhu_di" bpmnElement="Flow_0hqrbhu">
<di:waypoint x="218" y="290" />
<di:waypoint x="270" y="290" />
</bpmndi:BPMNEdge>
<bpmndi:BPMNEdge id="DataOutputAssociation_1gh2uhe_di" bpmnElement="DataOutputAssociation_1gh2uhe">
<di:waypoint x="319" y="330" />
<di:waypoint x="318" y="395" />
</bpmndi:BPMNEdge>
<bpmndi:BPMNEdge id="Flow_0abqfhc_di" bpmnElement="Flow_0abqfhc">
<di:waypoint x="370" y="290" />
<di:waypoint x="430" y="290" />
</bpmndi:BPMNEdge>
<bpmndi:BPMNEdge id="DataInputAssociation_0len72j_di" bpmnElement="DataInputAssociation_0len72j">
<di:waypoint x="338" y="405" />
<di:waypoint x="433" y="326" />
</bpmndi:BPMNEdge>
<bpmndi:BPMNEdge id="DataOutputAssociation_0emim9g_di" bpmnElement="DataOutputAssociation_0emim9g">
<di:waypoint x="479" y="330" />
<di:waypoint x="478" y="395" />
</bpmndi:BPMNEdge>
<bpmndi:BPMNEdge id="Flow_03lflym_di" bpmnElement="Flow_03lflym">
<di:waypoint x="530" y="290" />
<di:waypoint x="590" y="290" />
</bpmndi:BPMNEdge>
<bpmndi:BPMNEdge id="DataInputAssociation_0dponsz_di" bpmnElement="DataInputAssociation_0dponsz">
<di:waypoint x="498" y="405" />
<di:waypoint x="593" y="326" />
</bpmndi:BPMNEdge>
<bpmndi:BPMNEdge id="DataOutputAssociation_1vvy95a_di" bpmnElement="DataOutputAssociation_1vvy95a">
<di:waypoint x="639" y="330" />
<di:waypoint x="638" y="395" />
</bpmndi:BPMNEdge>
<bpmndi:BPMNEdge id="Flow_1eid6sv_di" bpmnElement="Flow_1eid6sv">
<di:waypoint x="690" y="290" />
<di:waypoint x="750" y="290" />
</bpmndi:BPMNEdge>
<bpmndi:BPMNEdge id="DataInputAssociation_0x57f43_di" bpmnElement="DataInputAssociation_0x57f43">
<di:waypoint x="658" y="405" />
<di:waypoint x="753" y="326" />
</bpmndi:BPMNEdge>
<bpmndi:BPMNEdge id="DataOutputAssociation_0xj5k2q_di" bpmnElement="DataOutputAssociation_0xj5k2q">
<di:waypoint x="800" y="250" />
<di:waypoint x="800" y="185" />
</bpmndi:BPMNEdge>
<bpmndi:BPMNEdge id="Flow_0vd7dj3_di" bpmnElement="Flow_0vd7dj3">
<di:waypoint x="850" y="290" />
<di:waypoint x="910" y="290" />
</bpmndi:BPMNEdge>
<bpmndi:BPMNEdge id="DataOutputAssociation_0c4kahx_di" bpmnElement="DataOutputAssociation_0c4kahx">
<di:waypoint x="961" y="250" />
<di:waypoint x="962" y="185" />
</bpmndi:BPMNEdge>
<bpmndi:BPMNEdge id="Flow_179mxmw_di" bpmnElement="Flow_179mxmw">
<di:waypoint x="1010" y="290" />
<di:waypoint x="1070" y="290" />
</bpmndi:BPMNEdge>
<bpmndi:BPMNEdge id="Flow_018xh3n_di" bpmnElement="Flow_018xh3n">
<di:waypoint x="1170" y="290" />
<di:waypoint x="1232" y="290" />
</bpmndi:BPMNEdge>
<bpmndi:BPMNEdge id="DataOutputAssociation_1f8ure4_di" bpmnElement="DataOutputAssociation_1f8ure4">
<di:waypoint x="1121" y="330" />
<di:waypoint x="1122" y="395" />
</bpmndi:BPMNEdge>
<bpmndi:BPMNEdge id="DataInputAssociation_0lz5fh8_di" bpmnElement="DataInputAssociation_0lz5fh8">
<di:waypoint x="978" y="175" />
<di:waypoint x="1072" y="255" />
</bpmndi:BPMNEdge>
<bpmndi:BPMNEdge id="DataInputAssociation_1759rw8_di" bpmnElement="DataInputAssociation_1759rw8">
<di:waypoint x="658" y="420" />
<di:waypoint x="960" y="420" />
<di:waypoint x="960" y="330" />
</bpmndi:BPMNEdge>
</bpmndi:BPMNPlane>
</bpmndi:BPMNDiagram>
</bpmn:definitions>
Binary file added docs/images/similarity-analysis.png
View file
Open in desktop
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Loading