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changeset 14:92cf554fca03

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minor changes/improvements
author pieter.lukasse@wur.nl
date Fri, 23 Jan 2015 14:14:08 +0100
parents 251e23773999
children 76d6d8a5fa29
files LICENSE NOTICE __init__.py datatypes_conf.xml nist_wrapper.py nist_wrapper.xml tool_dependencies.xml
diffstat 6 files changed, 255 insertions(+), 13 deletions(-) [+]
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+++ b/LICENSE	Fri Jan 23 14:14:08 2015 +0100
@@ -0,0 +1,202 @@
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--- /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
--- /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 @@
+<?xml version="1.0"?>
+<datatypes>
+  <datatype_files>
+  </datatype_files>
+  <registration display_path="display_applications">
+        <datatype extension="nist.tsv" type="galaxy.datatypes.tabular:Tabular" mimetype="text/csv" 
+        	display_in_upload="true" subclass="true">
+        </datatype>   
+  </registration>
+</datatypes>
\ No newline at end of file
--- 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)
 
 
--- 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 @@
 
 <outputs>
 	<data name="outputFile" format="tabular" label="${tool.name} on ${on_string} - NIST library matches (TSV)"/>
-	<data name="outputFileFinal" format="tabular" label="${tool.name} on ${on_string} - NIST library matches (TSV)"/>
+	<data name="outputFileFinal" format="nist.tsv" label="${tool.name} on ${on_string} - NIST library matches (TSV)"/>
 	<data name="outputLog" format="txt" label="${tool.name} on ${on_string} - LOG" hidden="True"/>
 	<data name="htmlReportFile" format="html" label="${tool.name} on ${on_string} - NIST matches report (HTML)"/>
 </outputs>
--- 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 @@
     <readme>A Python 2 virtual environment that includes the python packages  jinja2, six, argparse.</readme>
   </package>
 
+  <package name="nist_controller" version="0.2">
+      <install version="1.0">
+          <actions>
+              <action type="download_by_url">http://toolshed.g2.bx.psu.edu/repos/pieterlukasse/nist_wrapper/raw-file/tip/nist_controller.py</action>
+              <action type="move_directory_files">
+			<source_directory>.</source_directory>
+			<destination_directory>$GALAXY_HOME/lib/galaxy/webapps/galaxy/controllers/</destination_directory>
+		</action>
+          </actions>
+      </install>
+      <readme>Ensures nist_controller file is placed</readme>
+  </package>
+
 </tool_dependency>
\ No newline at end of file