--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/LICENSE	Fri Jan 23 14:14:08 2015 +0100
@@ -0,0 +1,202 @@
+
+                                 Apache License
+                           Version 2.0, January 2004
+                        http://www.apache.org/licenses/
+
+   TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION
+
+   1. Definitions.
+
+      "License" shall mean the terms and conditions for use, reproduction,
+      and distribution as defined by Sections 1 through 9 of this document.
+
+      "Licensor" shall mean the copyright owner or entity authorized by
+      the copyright owner that is granting the License.
+
+      "Legal Entity" shall mean the union of the acting entity and all
+      other entities that control, are controlled by, or are under common
+      control with that entity. For the purposes of this definition,
+      "control" means (i) the power, direct or indirect, to cause the
+      direction or management of such entity, whether by contract or
+      otherwise, or (ii) ownership of fifty percent (50%) or more of the
+      outstanding shares, or (iii) beneficial ownership of such entity.
+
+      "You" (or "Your") shall mean an individual or Legal Entity
+      exercising permissions granted by this License.
+
+      "Source" form shall mean the preferred form for making modifications,
+      including but not limited to software source code, documentation
+      source, and configuration files.
+
+      "Object" form shall mean any form resulting from mechanical
+      transformation or translation of a Source form, including but
+      not limited to compiled object code, generated documentation,
+      and conversions to other media types.
+
+      "Work" shall mean the work of authorship, whether in Source or
+      Object form, made available under the License, as indicated by a
+      copyright notice that is included in or attached to the work
+      (an example is provided in the Appendix below).
+
+      "Derivative Works" shall mean any work, whether in Source or Object
+      form, that is based on (or derived from) the Work and for which the
+      editorial revisions, annotations, elaborations, or other modifications
+      represent, as a whole, an original work of authorship. For the purposes
+      of this License, Derivative Works shall not include works that remain
+      separable from, or merely link (or bind by name) to the interfaces of,
+      the Work and Derivative Works thereof.
+
+      "Contribution" shall mean any work of authorship, including
+      the original version of the Work and any modifications or additions
+      to that Work or Derivative Works thereof, that is intentionally
+      submitted to Licensor for inclusion in the Work by the copyright owner
+      or by an individual or Legal Entity authorized to submit on behalf of
+      the copyright owner. For the purposes of this definition, "submitted"
+      means any form of electronic, verbal, or written communication sent
+      to the Licensor or its representatives, including but not limited to
+      communication on electronic mailing lists, source code control systems,
+      and issue tracking systems that are managed by, or on behalf of, the
+      Licensor for the purpose of discussing and improving the Work, but
+      excluding communication that is conspicuously marked or otherwise
+      designated in writing by the copyright owner as "Not a Contribution."
+
+      "Contributor" shall mean Licensor and any individual or Legal Entity
+      on behalf of whom a Contribution has been received by Licensor and
+      subsequently incorporated within the Work.
+
+   2. Grant of Copyright License. Subject to the terms and conditions of
+      this License, each Contributor hereby grants to You a perpetual,
+      worldwide, non-exclusive, no-charge, royalty-free, irrevocable
+      copyright license to reproduce, prepare Derivative Works of,
+      publicly display, publicly perform, sublicense, and distribute the
+      Work and such Derivative Works in Source or Object form.
+
+   3. Grant of Patent License. Subject to the terms and conditions of
+      this License, each Contributor hereby grants to You a perpetual,
+      worldwide, non-exclusive, no-charge, royalty-free, irrevocable
+      (except as stated in this section) patent license to make, have made,
+      use, offer to sell, sell, import, and otherwise transfer the Work,
+      where such license applies only to those patent claims licensable
+      by such Contributor that are necessarily infringed by their
+      Contribution(s) alone or by combination of their Contribution(s)
+      with the Work to which such Contribution(s) was submitted. If You
+      institute patent litigation against any entity (including a
+      cross-claim or counterclaim in a lawsuit) alleging that the Work
+      or a Contribution incorporated within the Work constitutes direct
+      or contributory patent infringement, then any patent licenses
+      granted to You under this License for that Work shall terminate
+      as of the date such litigation is filed.
+
+   4. Redistribution. You may reproduce and distribute copies of the
+      Work or Derivative Works thereof in any medium, with or without
+      modifications, and in Source or Object form, provided that You
+      meet the following conditions:
+
+      (a) You must give any other recipients of the Work or
+          Derivative Works a copy of this License; and
+
+      (b) You must cause any modified files to carry prominent notices
+          stating that You changed the files; and
+
+      (c) You must retain, in the Source form of any Derivative Works
+          that You distribute, all copyright, patent, trademark, and
+          attribution notices from the Source form of the Work,
+          excluding those notices that do not pertain to any part of
+          the Derivative Works; and
+
+      (d) If the Work includes a "NOTICE" text file as part of its
+          distribution, then any Derivative Works that You distribute must
+          include a readable copy of the attribution notices contained
+          within such NOTICE file, excluding those notices that do not
+          pertain to any part of the Derivative Works, in at least one
+          of the following places: within a NOTICE text file distributed
+          as part of the Derivative Works; within the Source form or
+          documentation, if provided along with the Derivative Works; or,
+          within a display generated by the Derivative Works, if and
+          wherever such third-party notices normally appear. The contents
+          of the NOTICE file are for informational purposes only and
+          do not modify the License. You may add Your own attribution
+          notices within Derivative Works that You distribute, alongside
+          or as an addendum to the NOTICE text from the Work, provided
+          that such additional attribution notices cannot be construed
+          as modifying the License.
+
+      You may add Your own copyright statement to Your modifications and
+      may provide additional or different license terms and conditions
+      for use, reproduction, or distribution of Your modifications, or
+      for any such Derivative Works as a whole, provided Your use,
+      reproduction, and distribution of the Work otherwise complies with
+      the conditions stated in this License.
+
+   5. Submission of Contributions. Unless You explicitly state otherwise,
+      any Contribution intentionally submitted for inclusion in the Work
+      by You to the Licensor shall be under the terms and conditions of
+      this License, without any additional terms or conditions.
+      Notwithstanding the above, nothing herein shall supersede or modify
+      the terms of any separate license agreement you may have executed
+      with Licensor regarding such Contributions.
+
+   6. Trademarks. This License does not grant permission to use the trade
+      names, trademarks, service marks, or product names of the Licensor,
+      except as required for reasonable and customary use in describing the
+      origin of the Work and reproducing the content of the NOTICE file.
+
+   7. Disclaimer of Warranty. Unless required by applicable law or
+      agreed to in writing, Licensor provides the Work (and each
+      Contributor provides its Contributions) on an "AS IS" BASIS,
+      WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or
+      implied, including, without limitation, any warranties or conditions
+      of TITLE, NON-INFRINGEMENT, MERCHANTABILITY, or FITNESS FOR A
+      PARTICULAR PURPOSE. You are solely responsible for determining the
+      appropriateness of using or redistributing the Work and assume any
+      risks associated with Your exercise of permissions under this License.
+
+   8. Limitation of Liability. In no event and under no legal theory,
+      whether in tort (including negligence), contract, or otherwise,
+      unless required by applicable law (such as deliberate and grossly
+      negligent acts) or agreed to in writing, shall any Contributor be
+      liable to You for damages, including any direct, indirect, special,
+      incidental, or consequential damages of any character arising as a
+      result of this License or out of the use or inability to use the
+      Work (including but not limited to damages for loss of goodwill,
+      work stoppage, computer failure or malfunction, or any and all
+      other commercial damages or losses), even if such Contributor
+      has been advised of the possibility of such damages.
+
+   9. Accepting Warranty or Additional Liability. While redistributing
+      the Work or Derivative Works thereof, You may choose to offer,
+      and charge a fee for, acceptance of support, warranty, indemnity,
+      or other liability obligations and/or rights consistent with this
+      License. However, in accepting such obligations, You may act only
+      on Your own behalf and on Your sole responsibility, not on behalf
+      of any other Contributor, and only if You agree to indemnify,
+      defend, and hold each Contributor harmless for any liability
+      incurred by, or claims asserted against, such Contributor by reason
+      of your accepting any such warranty or additional liability.
+
+   END OF TERMS AND CONDITIONS
+
+   APPENDIX: How to apply the Apache License to your work.
+
+      To apply the Apache License to your work, attach the following
+      boilerplate notice, with the fields enclosed by brackets "[]"
+      replaced with your own identifying information. (Don't include
+      the brackets!)  The text should be enclosed in the appropriate
+      comment syntax for the file format. We also recommend that a
+      file or class name and description of purpose be included on the
+      same "printed page" as the copyright notice for easier
+      identification within third-party archives.
+
+   Copyright [yyyy] [name of copyright owner]
+
+   Licensed under the Apache License, Version 2.0 (the "License");
+   you may not use this file except in compliance with the License.
+   You may obtain a copy of the License at
+
+       http://www.apache.org/licenses/LICENSE-2.0
+
+   Unless required by applicable law or agreed to in writing, software
+   distributed under the License is distributed on an "AS IS" BASIS,
+   WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+   See the License for the specific language governing permissions and
+   limitations under the License.

--- /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