Plugin Examples¶
This section has a very basic example plugin and its code.
Basic Plugin¶
This plugin goes through the explog and presents a few entries in the plugin output. It produces an HTML output but does not take any parameters.
#!/usr/bin/python
# Copyright (C) 2013 Ion Torrent Systems, Inc. All Rights Reserved
#
# Samples: LogParser
# plugin demonstrating simple log parsing ability
#
import json
import os
from django.utils.functional import cached_property
from ion.plugin import *
class LogParser(IonPlugin):
# The version number for this plugin
version = "5.4.0.0"
# this plugin can run on fullchip runs, thumbnail runs, and composite (merged via project page) runs
# when this plugin is manually launched, only the 'launch' method is called
runtypes = [RunType.FULLCHIP, RunType.THUMB, RunType.COMPOSITE]
# specify when the plugin is called. For log parsing, stay simple and just get called when the run completes.
# the plugin can also be called before the run starts, at the block level, or after all other default plugins run
runlevels = [RunLevel.DEFAULT]
# a simple cached version of the start plugin property
@cached_property
def startplugin_json(self):
return self.startplugin
def read_explog(self):
"""This method reads and outputs an array of colon-delimited key/value pairs from the explog_final.txt"""
path = os.path.join(self.startplugin_json['runinfo']['raw_data_dir'], "explog_final.txt")
if not os.path.exists(path):
raise Exception("explog_final.txt missing")
# parse the log file for all of the values in a colon-delimited parameter
data = dict()
for line in open(path):
# accommodates formatting issues in explog
datum = line.split(":", 1)
if len(datum) == 2:
key, value = datum
data[key.strip()] = value.strip()
return data
def launch(self, data=None):
"""This is the primary launch method for the plugin."""
na = '<strong>NA</strong>'
# creates a results object that is written out later. This holds data that can be scrapped by a LIMS system,
and will be part of the |TS| database
exp_log_data = self.read_explog()
results_json = {
'Project': exp_log_data.get('Project', None) or na,
'Sample': exp_log_data.get('Sample', None) or na,
'Library': exp_log_data.get('Library', None) or na,
}
# open up an HTML file to dump interesting log file findings to
with open(self.startplugin_json['runinfo']['results_dir'] + '/LogParser_block.html', 'w') as html_handle:
html_handle.write('<html><body>')
html_handle.write("Project is: %s<br \>" % results_json['Project'])
html_handle.write("Sample is: %s<br \>" % results_json['Sample'])
html_handle.write("Library is: %s<br \>" % results_json['Library'])
html_handle.write('</body></hmtl>')
# write out our results json object
with open(self.startplugin_json['runinfo']['results_dir'] + '/results.json', 'w') as results_handle:
json.dump(results_json, results_handle, indent=4)
return True
# Devel use - running directly
if __name__ == "__main__":
PluginCLI()
Plugin which uses a subprocess¶
#!/usr/bin/python
# Copyright (C) 2013 Ion Torrent Systems, Inc. All Rights Reserved
#
# Samples: LogParser
# plugin demonstrating simple log parsing ability
#
import json
import os
from django.utils.functional import cached_property
from ion.plugin import *
from subprocess import check_output
class CallSubprocessExample(IonPlugin):
# The version number for this plugin
version = "5.4.0.0"
# this plugin can run on fullchip runs, thumbnail runs, and composite (merged via project page) runs
# note that when the plugin is manually launched, only the 'launch' method will be called
runtypes = [RunType.FULLCHIP, RunType.THUMB, RunType.COMPOSITE]
# specify when the plugin is called. For log parsing, stay simple and just get called when the run completes.
# but can also be called before the run starts, at the block level, or after all other default plugins run
runlevels = [RunLevel.DEFAULT]
# a simple cached version of the start plugin property
@cached_property
def startplugin_json(self):
return self.startplugin
def launch(self, data=None):
"""This is the primary launch method for the plugin."""
path_to_executable = "MyExecutable"
arg1 = 'First Argument'
arg2 = 'Second Argument'
results = check_output([path_to_executable, arg1, arg2], cwd=self.startplugin_json['runinfo']['plugin']['path'])
return True
# Devel use - running directly
if __name__ == "__main__":
PluginCLI()
Accessing Barcode Data¶
#!/usr/bin/python
# Copyright (C) 2013 Ion Torrent Systems, Inc. All Rights Reserved
#
# Samples: LogParser
# plugin demonstrating simple log parsing ability
#
import json
import os
from django.utils.functional import cached_property
from ion.plugin import *
from subprocess import check_output
class BarcodesExample(IonPlugin):
# The version number for this plugin
version = "5.4.0.0"
# this plugin can run on fullchip runs, thumbnail runs, and composite (merged via project page) runs
# note that when the plugin is manually launched, only the 'launch' method will be called
runtypes = [RunType.FULLCHIP, RunType.THUMB, RunType.COMPOSITE]
# specify when the plugin is called. For log parsing, stay simple and just get called when the run completes.
# but can also be called before the run starts, at the block level, or after all other default plugins run
runlevels = [RunLevel.DEFAULT]
# a simple cached version of the start plugin property
@cached_property
def startplugin_json(self):
return self.startplugin
@cached_property
def barcodes_json:
with open('barcodes.json', 'r') as barcodes_handle:
return json.load(barcodes_handle)
def launch(self, data=None):
"""This is the primary launch method for the plugin."""
for barcode_name, barcode_values in self.barcodes_json.iteritems():
# do you work per barcode here!
print("Barcode Name: " + barcode_name)
print("Bam File: " + barcode_values['bam_file']
return True
# Devel use - running directly
if __name__ == "__main__":
PluginCLI()
Using the REST API¶
import json
import requests
api_response = requests.get('http://HOSTNAME/APPNAME/api/v1/APIENDPOINT/?ARG1=VAL1&api_key=' + self.startplugin['runinfo']['api_key'])
api_response.raise_for_status()
api_json_response = json.loads(api_response.content)
Displaying Progress¶
When displaying progress, this needs to be manually updated by re-writing the *_block.html file intermittently during the process. Here is a simple example of how to construct a method to do this.
...
def update_progress(self, current_progress, max_progress)
with open(self.startplugin['runinfo']['results_dir'] + '/progress_block.html', 'w') as html_handle:
html_handle.write('<html><body>')
html_handle.write("The current progress is %d of %d" %(current_progress, max_progress))
html_handle.write('</body></hmtl>')
...
Rendering Templates¶
When outputting HTML files, using templates can be cleaner than assembling long stings. Below is an example of using Django templates. This example uses an HTML template named progress_block_template.html inside a templates directory inside the plugins root directory.
from django.conf import settings
from django.template.loader import render_to_string
settings.configure(TEMPLATE_DIR=self.startplugin["runinfo"]["plugin"]["path"] + '/templates')
with open(self.startplugin['runinfo']['results_dir'] + '/progress_block.html', 'w') as html_handle:
html_handle.write(render_to_string("progress_block_template.html", {"current_progress": 54}))