Repository consolidation, part 3

signalData/.gitattributes

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+* text=auto

signalData/.gitignore

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+*.class
+
+# Mobile Tools for Java (J2ME)
+.mtj.tmp/
+
+# Package Files #
+*.jar
+*.war
+*.ear
+
+# virtual machine crash logs, see http://www.java.com/en/download/help/error_hotspot.xml
+hs_err_pid*

signalData/LICENSE.txt

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signalData/README.md

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+# SignalData
+
+## Basic Setup ##
+
+1. Create a LabKey Assay Project/Folder
+  1. Hover over the Project or Folder menu, and click **Create Project** or **Create Subfolder**.
+  1. Provide a Name and select type **Assay**.
+  1. Click **Next**.
+  1. Set permissions (optional) and click **Next**.
+  1. Click **Finish**.
+1. Create a Signal Data Assay Design
+  1.  In the **Assay List** web part, click **New Assay Design**.
+  1.  On the New Assay Design page, select **Signal Data** as the assay type.
+  1.  Click **Next**.
+  1.  Name is the only required field. (Design default values should work fine.)
+  1.  Click the **Save & Close** button.
+
+## Manual Import of Signal Data Results ##
+
+Importing data is a two step process:
+
+1. Upload the metadata file. (An example metadata file is available at: https://github.com/LabKey/signalData/blob/develop/test/sampledata/signaldata/RunsMetadata/datafiles.tsv)
+1. Drag and drop the data files (Example data files are available at: https://github.com/LabKey/signalData/tree/develop/test/sampledata/signaldata/SignalDataAssayData/TestRun001)
+
+### Metadata Upload
+
+1. Go to the folder where you wish to upload results.
+1. Add the **Signal Data Upload** webpart.
+1. Confirm that **File** is selected, and click **Upload TXT, TSV, XLS, XLSX**.
+
+![Drag-and-drop to upload a run](https://github.com/LabKey/docs/blob/master/images/signal1.png?raw=true)
+
+1. Specify a Run Identifier (required).
+
+![Drag-and-drop to upload a run](https://github.com/LabKey/docs/blob/master/images/signal2.png?raw=true)
+
+### Data Upload
+
+1. Drag-and-drop any result files you want to import onto the dropzone.
+
+![Drag-and-drop to upload a run](https://github.com/LabKey/docs/blob/master/images/signal3.png?raw=true)
+
+1. Click the **Save Run** button.
+
+![Name and save a run](https://github.com/LabKey/docs/blob/master/images/signal4.png?raw=true)
+
+## View Results ##
+
+To view chromatograms for the results, follow these instructions:
+
+1. Go to the folder where your results reside.
+1. On the **Assay List** webpart, click the name of the Signal Data assay you created.
+1. Select the run(s) you want to look at, using the checkboxes.
+1. Click **View Selected Runs**.
+
+![View runs](https://github.com/LabKey/docs/blob/master/images/hplc3.png?raw=true) 
+
+1. Select the data run(s) you wish to view from the left.
+1. Click the `Overlay Selected` button.
+
+![View runs](https://github.com/LabKey/docs/blob/master/images/hplc4.png?raw=true) 
+
+1. The left selection pane will close, and the overlayed results will be displayed in the center pane.
+
+![View runs](https://github.com/LabKey/docs/blob/master/images/hplc5.png?raw=true) 
+
+1. You can zoom into the graph by entering values in the **Time** and **mV Range** text boxes, or by drawing a new area inside the graph using the mouse.
+
+![View runs](https://github.com/LabKey/docs/blob/master/images/hplc6.png?raw=true) 
+
+Enter values in the right pane to calculate areas under the curves. Select in the name column to highlight different graph lines.
+
+![View runs](https://github.com/LabKey/docs/blob/master/images/hplc7.png?raw=true) 
+
+## Installing the Signal Data Module ##
+
+[Contact us](https://www.labkey.com/company/contact-us) for details on installing the Signal Data module.
+
+

signalData/build.gradle

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+plugins {
+    id 'org.labkey.build.module'
+}

signalData/module.properties

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+ModuleClass: org.labkey.signaldata.SignalDataModule
+Label: signaldata
+Description: A module defining general X/Y plottable assays and tools for working with those assays.
+URL: https://github.com/LabKey/signalData
+License: Apache 2.0
+LicenseURL: http://www.apache.org/licenses/LICENSE-2.0
+ManageVersion: true

signalData/resources/assay/signalData/config.xml

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+<ap:provider xmlns:ap="http://labkey.org/study/assay/xml">
+    <ap:name>Signal Data</ap:name>
+    <ap:description>X/Y plottable Signal Data</ap:description>
+    <ap:requiredModules>
+        <ap:moduleName>SignalData</ap:moduleName>
+    </ap:requiredModules>
+</ap:provider>

signalData/resources/assay/signalData/domains/batch.xml

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+<ap:domain xmlns:exp="http://cpas.fhcrc.org/exp/xml" xmlns:ap="http://labkey.org/study/assay/xml">
+    <exp:Description>Signal Data Assay Batch fields</exp:Description>
+    <exp:PropertyDescriptor>
+        <exp:Name>XAxis</exp:Name>
+        <exp:Hidden>true</exp:Hidden>
+        <exp:RangeURI>http://www.w3.org/2001/XMLSchema#string</exp:RangeURI>
+        <exp:Label>X-Axis Label</exp:Label>
+        <exp:DefaultType>FixedValue</exp:DefaultType>
+        <exp:DefaultValue>Time (m)</exp:DefaultValue>
+    </exp:PropertyDescriptor>
+    <exp:PropertyDescriptor>
+        <exp:Name>YAxis</exp:Name>
+        <exp:Hidden>true</exp:Hidden>
+        <exp:RangeURI>http://www.w3.org/2001/XMLSchema#string</exp:RangeURI>
+        <exp:Label>Y-Axis Label</exp:Label>
+        <exp:DefaultType>FixedValue</exp:DefaultType>
+        <exp:DefaultValue>mV</exp:DefaultValue>
+    </exp:PropertyDescriptor>
+</ap:domain>

signalData/resources/assay/signalData/domains/result.xml

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+<ap:domain xmlns:exp="http://cpas.fhcrc.org/exp/xml" xmlns:ap="http://labkey.org/study/assay/xml">
+    <exp:Description>Signal Data Assay Results</exp:Description>
+    <exp:PropertyDescriptor>
+        <exp:Name>Name</exp:Name>
+        <exp:Required>true</exp:Required>
+        <exp:RangeURI>http://www.w3.org/2001/XMLSchema#string</exp:RangeURI>
+    </exp:PropertyDescriptor>
+    <exp:PropertyDescriptor>
+        <exp:Name>DataFile</exp:Name>
+        <exp:Required>true</exp:Required>
+        <exp:RangeURI>http://cpas.fhcrc.org/exp/xml#fileLink</exp:RangeURI>
+        <exp:Label>Data File</exp:Label>
+    </exp:PropertyDescriptor>
+</ap:domain>

signalData/resources/assay/signalData/domains/run.xml

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+<ap:domain xmlns:exp="http://cpas.fhcrc.org/exp/xml" xmlns:ap="http://labkey.org/study/assay/xml">
+    <exp:PropertyDescriptor>
+        <exp:Name>RunIdentifier</exp:Name>
+        <exp:Required>true</exp:Required>
+        <exp:RangeURI>http://www.w3.org/2001/XMLSchema#string</exp:RangeURI>
+        <exp:Label>Run Identifier</exp:Label>
+    </exp:PropertyDescriptor>
+</ap:domain>