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-# flowjo-plugin-data-dump
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+## FlowJo Data Dump Plugin
+
+Note: This plugin is to be used in conjuction with [flowjo-plugin-testbed](https://github.com/nicbarker/flowjo-plugin-testbed)
+
+### Usage
+- Download the plugin .jar from the releases page
+- Place it in your `/Applications/plugins` directory or windows equivalent
+- Start FlowJo
+- Select a sample or node then click Workspace -> Plugins -> FlowJoPluginDataDump
+- It will save files to the output folder and give you a popup window that says something like this:
+- Import [flowjo-plugin-testbed.jar](https://github.com/nicbarker/flowjo-plugin-testbed) and call the following on your plugin:
+```Java
+invokeAlgorithm(FlowJoPluginTestbed.getFcmlFromFile("/some/directory/FlowJo Plugin Data Dump/fcmlQueryElement.xml"), FlowJoPluginTestbed.createFileObject("/some/directory/FlowJo Plugin Data Dump/st_HM-1_CHECK192_001..ExtNode.csv"), FlowJoPluginTestbed.createFileObject("/some/directory/FlowJo Plugin Data Dump"));
+```
+In your plugin, create a main function and call the `invokeAlgorithm()` from the previous step
+```Java
+    public static void main(String[] args) {
+        YourPlugin plugin = new YourPlugin();
+        try {
+            plugin.invokeAlgorithm(FlowJoPluginTestbed.getFcmlFromFile("/some/directory/FlowJo Plugin Data Dump/fcmlQueryElement.xml"), FlowJoPluginTestbed.createFileObject("/some/directory/FlowJo Plugin Data Dump/st_HM-1_CHECK192_001..ExtNode.csv"), FlowJoPluginTestbed.createFileObject("/some/directory/FlowJo Plugin Data Dump"));
+        } catch (IOException e) {
+            e.printStackTrace();
+        }
+    }
+```
+
+- You'll now be able to use standard Java development and debugging practise to test if your plugin works.
+
+### Rationale
+The standard cycle for developing and debugging [FlowJo](https://www.flowjo.com/) plugins can be quite painful, and usually involves some variation of the following:
+
+- Build a fat .jar file including dependencies for your plugin
+- Copy it into your `/Applications/plugins` directory or windows equivalent
+- Start FlowJo from the command line
+- Open your workspace
+- Wait for FlowJo to finish scanning for .jar files
+- Run the plugin and check the console for errors
+
+Sometimes this process can take upwards of 5 minutes for a single round trip, which is not feasible if you're developing a plugin or have a programming style that requires a lot of back and forth debugging. By using this in combination with [flowjo-plugin-testbed](https://github.com/nicbarker/flowjo-plugin-testbed), you'll be able to get quick debugging