# HG changeset patch
# User pieter.lukasse@wur.nl
# Date 1422018848 -3600
# Node ID 92cf554fca03f94e8928e48bfee01e9e128d95de
# Parent 251e2377399928357b4df4f37f62df70a39a698d
minor changes/improvements
diff -r 251e23773999 -r 92cf554fca03 LICENSE
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/LICENSE Fri Jan 23 14:14:08 2015 +0100
@@ -0,0 +1,202 @@
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diff -r 251e23773999 -r 92cf554fca03 NOTICE
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/NOTICE Fri Jan 23 14:14:08 2015 +0100
@@ -0,0 +1,12 @@
+NIST-wrapper
+============================================
+
+Metabolomics tool that wraps the NIST nistms tools for matching measured spectra against
+library spectra.
+
+
+Copyright (c) 2015 by Pieter Lukasse, Plant Research International (PRI),
+Wageningen, The Netherlands. All rights reserved. See the license text below.
+
+Galaxy wrappers and installation are available from the Galaxy Tool Shed at:
+http://toolshed.g2.bx.psu.edu/view/pieterlukasse/nist_wrapper
\ No newline at end of file
diff -r 251e23773999 -r 92cf554fca03 __init__.py
diff -r 251e23773999 -r 92cf554fca03 datatypes_conf.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/datatypes_conf.xml Fri Jan 23 14:14:08 2015 +0100
@@ -0,0 +1,10 @@
+
+
+
+
+
+
+
+
+
\ No newline at end of file
diff -r 251e23773999 -r 92cf554fca03 nist_wrapper.py
--- a/nist_wrapper.py Fri Jan 23 12:34:33 2015 +0100
+++ b/nist_wrapper.py Fri Jan 23 14:14:08 2015 +0100
@@ -85,7 +85,7 @@
return new_nist_home
-def _run_NIST(new_nist_home, output_file, is_wine, log_file):
+def _run_NIST(new_nist_home, output_file, is_wine, log_file, job_size):
'''
- run : (wine) new_nist_home/MSSEARCH/nistms$.exe /INSTRUMENT /PAR=2
- monitor : new_nist_home/MSSEARCH/SRCREADY.TXT for content = "1"
@@ -117,7 +117,6 @@
pro = ""
if is_wine:
utils.log_message(log_file, "calling wine with " + exec_path)
- print "calling wine with " + exec_path
cmd = ["wine "+ exec_path + " /INSTRUMENT /PAR=2"]
# The os.setsid() is passed in the argument preexec_fn so
# it's run after the fork() and before exec() to run the shell.
@@ -132,14 +131,21 @@
timeSleeping = 0
+ startUpTime = 30
# monitor process by checking state file:
utils.log_message(log_file, "monitoring SRCREADY.TXT...")
- while timeSleeping < 20:
+ # TODO2: do the controller part
+ # TODO3: do the popover part
+ while True:
# check if SRCREADY.TXT is there already:
if os.path.exists(file_to_monitor):
break
time.sleep(2)
timeSleeping = timeSleeping+2
+ if timeSleeping > (startUpTime + job_size*2):
+ # abort with timeout:
+ utils.log_message(log_file, "No results after " + timeSleeping + " seconds...")
+ raise Exception('Error: timeout waiting for NIST results.')
# kill process:
#p.terminate() - not needed, nistm$ will terminate...nistms.exe is the one that
@@ -171,16 +177,14 @@
'''
# step 1 : generate HTML via the jinja template engine
# step 1.1: make sure to link the query spectrum data to the corresponding html object for quick rendering when needed
+
+ # copy necessary .js files as well:
+ templates_folder = os.path.dirname(__file__) + '/templates/'
+ utils.copy_dir(templates_folder, output_html_report_files_path)
html_file = open(output_html_report,'w')
html_render = ReportGenerator(os.path.dirname(__file__), 'templates/main_template.html',hits_dict, spectra_dict)
html_render.render(html_file)
- # copy necessary .js files as well:
- templates_folder = os.path.dirname(__file__) + '/templates/'
- #utils.copy_file(templates_folder + 'spectrum_gen.js', output_html_report_files_path+"/spectrum_gen.js")
- #utils.copy_dir(templates_folder + 'lib', output_html_report_files_path+'/lib' )
- #utils.copy_dir(templates_folder + 'images', output_html_report_files_path+'/images' )
- utils.copy_dir(templates_folder, output_html_report_files_path)
html_file.close()
@@ -310,15 +314,16 @@
new_nist_home = _prepare_NIST(uuid_value, nist_home_dir, nist_ini_file, spectrum_file, is_wine, output_log_file)
# run NIST search command:
- _run_NIST(new_nist_home, nist_output_file, is_wine, output_log_file)
+ spectra_dict = utils.get_spectra_file_as_dict(spectrum_file)
+ job_size = len(spectra_dict)
+ _run_NIST(new_nist_home, nist_output_file, is_wine, output_log_file, job_size)
# write output tabular:
hits_dict = utils.get_nist_out_as_dict(nist_output_file)
utils.save_dict_as_tsv(hits_dict, final_output_file)
# create report:
- if len(sys.argv) > 6:
- spectra_dict = utils.get_spectra_file_as_dict(spectrum_file)
+ if len(sys.argv) > 7:
_create_html_report(output_html_report, output_html_report_files_path, hits_dict, spectra_dict)
diff -r 251e23773999 -r 92cf554fca03 nist_wrapper.xml
--- a/nist_wrapper.xml Fri Jan 23 12:34:33 2015 +0100
+++ b/nist_wrapper.xml Fri Jan 23 14:14:08 2015 +0100
@@ -832,7 +832,7 @@
-
+
diff -r 251e23773999 -r 92cf554fca03 tool_dependencies.xml
--- a/tool_dependencies.xml Fri Jan 23 12:34:33 2015 +0100
+++ b/tool_dependencies.xml Fri Jan 23 14:14:08 2015 +0100
@@ -16,4 +16,17 @@
A Python 2 virtual environment that includes the python packages jinja2, six, argparse.
+
+
+
+ http://toolshed.g2.bx.psu.edu/repos/pieterlukasse/nist_wrapper/raw-file/tip/nist_controller.py
+
+ .
+ $GALAXY_HOME/lib/galaxy/webapps/galaxy/controllers/
+
+
+
+ Ensures nist_controller file is placed
+
+
\ No newline at end of file