Run msInspect feature finding from Proteios

[Fredrik Levander]

It should be possible to run an external binary ​msInspect on a mzML or mzXML file in Proteios: java -jar -Xmx512M viewerApp.jar --findpeptides file_name.mzML and the generated peptides.tsv file should be uploaded to Proteios. To accomplish this: 1) Generate a new temporary directory in the temp folder. 2) File copied to new temporary directory. 3) Command run in the temp directory. 4) Resulting .peptides file uploaded and saved in database. 5) Other files generated and the temp dir are deleted.

• It should be possible to kill the job, and then the temp dir should be deleted.
• A release or nightly build of msInspect newer than March 2010 should be used for full mzML functionality.

[olle]

Ticket accepted.

[olle]

Design discussion.

• The design will be based on that for running an OMSSA search from Proteios SE, as the default for OMSSA is use of a locally installed search engine.
• Basic parameters will be stored in a properties file msinspect.properties, based on a template file msinspect.properties.in stored in directory client/servlet/conf/. Initially the file will only contain three parameters, the path of the directory the program is installed in, the name of the program, and the number of Megabytes of memory to use for the program.
• Results will normally be stored in a file with a name constructed from the base filename of the input spectrum file (filename without file extension) + time stamp in _YYYY_MM_DD_hh_mm_ss format + ".peptides.tsv". e.g. results for spectrum file "sample.mzXML" analyzed 2010-12-14 17:05:56 are stored in result file "sample_2010_12_14_17_05_56.peptides.tsv". The time stamp is the time the job was created, not when it was executed. This has the effect that result files for jobs created in the same batch will share the same time stamp in the filenames. In cases where msInspect keeps the original file extension as part of the result file name, the file extension will also be part of the Proteios SE result filename, e.g. "sample.mzml" gets result file "sample_2010_12_14_17_05_56.mzml.peptides.tsv".
• The desired result filename will be obtained using a temporary spectrum input file that also has a time stamp added to the filename. This will allow a simpler solution for temporary file storage than that laid out in the ticket description, as no new temporary directory needs to be created in the temp folder, as there is low risk that a file with the same name should already exist. Temporary files will therefore be stored directly in the temp folder in the first version of the routine. A cost for this simplification is that the routine needs to be aware of what temporary files the msInspect program itself creates, in order to delete these too.
• A file context extension will be created, allowing the user to select appropriate spectrum files by checking their check boxes in the file table, and then applying the new extension. The first version of the routine will not have any user parameters, so a single instruction text will be displayed together with a button coupled to an action that will create one job for each selected spectrum file.
• The action preparing the jobs will among other parameters set a time stamp for the job plug-in to use for the msInspect result files. This ensures that the same time stamp will be used for all jobs created in one batch.
• The plug-in for the msInspect feature finding will copy the spectrum file to a temporary file with a time stamp in the filename to the temp folder. The first version of the routine will then call the msInspect program with the "--findpeptides" option for the temporary file. If an active project exists, the result file will be uploaded to the project directory of the active project.
• After finished analysis, all created temporary files will be deleted if the result file was uploaded successfully, otherwise the latter is kept for manual upload. The plug-in should implement interface AbortablePluginInterface. If the plug-in receives an abort command, all created temporary files should be deleted before terminating.

[olle]

(In [4071]) Refs #668. Support for msInspect properties file added:

1. New msInspect properties template file conf/msinspect.properties.in in client/servlet/ added.

2. New class/file MsInspectPropertiesFile.java in client/servlet/ added. It gives access to settings in msInspect properties file msinspect.properties.

[olle]

(In [4072]) Refs #668. New directory action/msInspect/ in client/servlet/ added.

[olle]

(In [4073]) Refs #668. Refs #287. First version of support for running msInspect feature finding from Proteios SE:

1. New class/file action/file/UseSpectrumFileForMsInspectSearchExtension.java in client/servlet/ added. It implements interface ContextEnabled through class FileContext. List of id values for selected spectrum files are added as hidden fields to the form, and a button is displayed that is coupled to an action link to new class RunMsInspect.

2. New class/file action/msInspect/RunMsInspect.java in client/servlet/ added. It retrieves a list of id values for spectrum files from valid parameter VInteger VSPECTRUMFILEID and settings from msInspect properties file msinspect.properties, after which it creates one job for each spectrum file managed by new plug-in class RunMsInspectPlugin.

3. New class/file plugins/RunMsInspectPlugin.java in plugin/ added. It copies the spectrum input file to a temporary file with a time stamp in the file name to the temp folder, and then ruins the msInspect program on the latter file. It attempts to upload the result file, after which it deletes the created temporary files (if uploading the result file was unsuccessful, this file is kept for manual upload).

4. English dictionary file locale/en/dictionary in client/servlet/ updated with new string keys.

[olle]

(In [4074]) Refs #668. Support for running msInspect feature finding from Proteios SE updated by cleaning up code (removal of unused code sections and methods, except those that might be expected to be of use in future updates):

1. Class/file action/file/UseSpectrumFileForMsInspectSearchExtension.java in client/servlet/ updated by cleaning up code.

2. Class/file action/msInspect/RunMsInspect.java in client/servlet/ updated by cleaning up code.

3. Class/file plugins/RunMsInspectPlugin.java in plugin/ updated by cleaning up code.

[olle]

Design update:

• To work directly with existing extensions/plug-ins for analysis of msInspect result files, the uploaded result file should not contain an added time stamp (this restriction does not include the name of temporary files).

[olle]

(In [4076]) Refs #668. Class/file plugins/RunMsInspectPlugin.java in plugin/ updated by not including a time stamp in the uploaded msInspect result file:

1. Private method void msInspectSearchLocal(Request request, Response response, ...) updated by not including a time stamp in the uploaded msInspect result file.

[olle]

(In [4077]) Refs #668. Class/file action/file/UseSpectrumFileForMsInspectSearchExtension.java in client/servlet/ updated in displayed instruction text, as the uploaded msInspect result file now does not include an extra time stamp in the filename:

1. Protected method void runMe() updated in the displayed instruction text.

[olle]

Design update:

• Current version deletes a found msInspect result file in the temp folder, even if uploading it to Proteios SE fails, e.g. when a file with the same name already exists in the Proteios SE directory the file should be uploaded to. The latter is much more likely to occur when no extra time stamp is included in the name of the uploaded file. The result file in the temp folder should only be deleted if uploading it to Proteios SE is successful.

[olle]

(In [4078]) Refs #668. Class/file plugins/RunMsInspectPlugin.java in plugin/ updated to only delete an msInspect result file in the temp folder if uploading it to Proteios SE was successful:

1. Private method void msInspectSearchLocal(Request request, Response response, ...) updated to only delete an msInspect result file in the temp folder if uploading it to Proteios SE was successful. An instruction to upload the result file manually is now also added to the job message if uploading the file to Proteios SE failed.

[olle]

Design update:

• It was decided to add a new Proteios SE FileType for msInspect features.
• When running msInspect from Proteios SE, the uploaded result file should be set to the new FileType for msInspect features.

[olle]

(In [4079]) Refs #668. Addition of a new FileType constant for msInspect features:

1, Class/file core/FileType,java in api/core/ updated with new public static final String MSINSPECT_FEATURES.

2. Class/file core/Install.java in api/core/ updated in public static synchronized method void initDatabase(ProgressReporter progress, String rootPassword) to call private static method FileTypeData createFileType(String systemId, String name, String description) for new file type constant FileType.MSINSPECT_FEATURES.

[olle]

(In [4080]) Refs #668. Class/file plugins/RunMsInspectPlugin.java in plugin/ updated to set file type of uploaded msInspect result file to new file type constant FileType.MSINSPECT_FEATURES:

1. Private method void uploadMsInspectOutputFile(String directoryPath, String outputFileName, String filenameOfUploadedFile, Integer dirId, String descr) updated to set file type of uploaded msInspect result file to new file type constant FileType.MSINSPECT_FEATURES.

[olle]

Design discussion regarding implementation of progress report:

• Inspection of debug output for running msInspect on a 300 MB mzML spectrum file revealed that the time consuming step is the msInspect analysis step (prior to that msInspect builds an index file to use during the analysis).
• During the time-consuming analysis step msInspect outputs progress information in the error output stream of the type "16 Dec 2010 11:02:02,965 INFO ApplicationContext: 12.043658% complete.". The sub-string "complete" is unique to the output during this step, and can be used to parse error output for the progress information string. The integer part of the percentage number will be extracted from this string, and used as input to the Proteios SE progress reporter.
• Since some operations are performed after the msInspect analysis step, if the percentage number for the analysis step is > 99%, input to the Proteios SE progress reporter should be set to 99% (the percentage value will automatically be set to 100%, when the job is completed).

[olle]

(In [4081]) Refs #668. Class/file plugins/RunMsInspectPlugin.java in plugin/ updated with progress information during msInspect feature finding:

1. Private inner class StreamGobbler updated with new instance variable ProgressReporter myProgress, initially set to null. New constructor StreamGobbler(InputStream is, String type, OutputStream redirect, ProgressReporter progress) added, that takes a ProgressReporter argument and sets the value of instance variable myProgress to this. Public method void run() updated to call new private method void updateProgressInformation(ProgressReporter progress, String line) with the value of instance variable myProgress and the string read from the input stream.

2. Private method void msInspectSearchLocal(Request request, Response response, ProgressReporter progress, ...) updated to call new StreamGobbler constructor for the error input stream, and setting the ProgressReporter argument to the value of local variable progress.

3. New private method void updateProgressInformation(ProgressReporter progress, String line) added. It updates the progress reporter information with data parsed from the input string.

[olle]

Design update:

• It was decided to refer to processing with msInspect program as "feature detection" in displayed text. Names of classes and methods will not be changed at this stage.

[olle]

(In [4082]) Refs #668. Refs #287. the following classes/files were updated to refer to processing with msInspect program as "feature detection" in displayed text:

1. action/file/UseSpectrumFileForMsInspectSearchExtension.java in client/servlet/.

2. action/msInspect/RunMsInspect.java in client/servlet/.

3. plugins/RunMsInspectPlugin.java in plugin/.

4. locale/en/dictionary in client/servlet/.

[olle]

Design update:

• In order to work with space characters in file and directory paths, Proteios SE should use the java.lang.Runtime.getRuntime().exec(String[] cmdarray) version of the exec() call, instead of exec(String cmd).
• In order to simplify future use of a variable number of options, a string list will be used to compose the command components, which is then converted to a string array for use in the exec() call. This also simplifies debug output of the full command, as the list toString() method outputs the list contents.

[olle]

(In [4083]) Refs #668. Class/file plugins/RunMsInspectPlugin.java in plugin/ updated to use the java.lang.Runtime.getRuntime().exec(String[] cmdarray) version of the exec() call, instead of exec(String cmd), in order to work with space characters in file and directory paths.

1. Private method void msInspectSearchLocal(Request request, Response response, ...) updated to use the java.lang.Runtime.getRuntime().exec(String[] cmdarray) version of the exec() call, instead of exec(String cmd).

[olle]

(In [4084]) Refs #668. Initialization script www/WEB-INF/init.sh in client/servlet/ updated to create msinspect.properties file if not existing.

[olle]

(In [4085]) Refs #668. Proteios SE installation and update bat-files for MS Windows updated to support msInspect properties file msinspect.properties:

1. Proteios SE installation bat-file install-win.bat in misc/install/ updated to create msinspect.properties file if not existing.

2. Proteios SE update bat-file update_proteios-win.bat in misc/install/ updated to support msInspect properties file msinspect.properties.

[olle]

(In [4086]) Refs #668. Class/file plugins/RunMsInspectPlugin.java in plugin/ updated to improve job progress message and percentage information:

1. New private instance variable long inputFileSizeInBytes added, with public accessor methods. It is used to store the size of the input spectrum file in bytes for estimation of fraction of time spent in different process phases. This data is used for progress information.

2. Private method void msInspectSearchLocal(Request request, Response response, ProgressReporter progress, ...) updated to obtain the size of the input spectrum file in bytes and store it in new instance variable inputFileSizeInBytes.

3. Private method void updateProgressInformation(ProgressReporter progress, String line) updated to parse the input string for progress information in the indexing and analysis phases. Calls new private method int EstimatedTotalPercentage(int percentage, boolean isAnalysisPhase) to get the estimated total percentage from percentage values for the two different phases.

4. New private method int EstimatedTotalPercentage(int percentage, boolean isAnalysisPhase) added. It estimates total percentage of time to completion. Assumes two phases, an indexing phase and an analysis phase. Estimates the fraction of time spent in the indexing phase and analysis phase from the size of the input file, based on test runs with input files of different sizes.

[olle]

(In [4087]) Refs #668. Class/file plugins/RunMsInspectPlugin.java in plugin/ updated by removing detailed debug output from private method int EstimatedTotalPercentage(int percentage, boolean isAnalysisPhase):

1. Private method int EstimatedTotalPercentage(int percentage, boolean isAnalysisPhase) updated by commenting out line for detailed debug output.

[olle]

(In [4088]) Refs #668. Class/file plugins/RunMsInspectPlugin.java in plugin/ updated by adding job progress message during local file copying phase:

1. Private method void msInspectSearchLocal(Request request, Response response, ProgressReporter progress, ...) updated to display job progress message "Making local file copy" during local file copying phase. The percent complete number is set to 0, since this is this initial phase, before the msInspect program has been started.

[olle]

Design update:

• The user should be able to select what strategy algorithm to use for the msInspect feature detection.
• The strategies should be available in a menu select box.
• The default strategy option should be labeled "default". This option means that the msInspect command line does not include a "--strategy" option.
• The first set of supported strategy alternatives should be the classes in package org.fhcrc.cpl.viewer.feature.extraction.strategy in jar file viewerApp_2010_12_08_0006.jar, the nightly build of msInspect for 2010-12-08.
• The strategy select box should be provided with a cautionary text, noting that the installed version of msInspect might not support all strategy options.

[olle]

(In [4089]) Refs #668. Refs #287. Support for running msInspect feature detection from Proteios SE updated to allow user selected strategy option:

1. Class/file action/file/UseSpectrumFileForMsInspectSearchExtension.java in client/servlet/ updated by adding a menu select box for selecting a strategy option. The option string parameter is coupled to new valid parameter VString RunMsInspect.VMSINSPECTSTRATEGY. The default option is marked "default", and corresponds to no strategy option being used.

2. Class/file action/msInspect/RunMsInspect.java in client/servlet/ updated to retrieve the string from new valid parameter VString VMSINSPECTSTRATEGY and transferring it as a job parameter to plug-in class RunMsInspectPlugin.

3. Class/file plugins/RunMsInspectPlugin.java in plugin/ updated to retrieve the strategy string from the job parameter. If the string is null or an empty string (corresponding to the default option), no changes are made to the msInspect command line. Otherwise, the retrieved string is used as value for an extra option --strategy=value in the msInspect command line.

4. English dictionary file locale/en/dictionary in client/servlet/ updated with new string key.

[olle]

Design update:

• It was decided to label the field set with the strategy selection as "Advanced options", and hide its contents by default.
• As the current msInspect form only contains one field set (the description text area has the same appearance as a fieldset GUI item, but is a TitledWindow), the "Advanced options" field set cannot by hidden, as class GUIConverter only supports this feature if the form has several field sets. This rule makes sense in most cases, except when other GUI elements like TitledWindow also exist. In order to allow the show/hide toggle feature for a single field set when appropriate, class Fieldset will be updated with a new private instance variable Boolean singleFieldsetToggleAllowed with public accessor methods. The default value of singleFieldsetToggleAllowed will be false, and will therefore not change the appearance of forms if not specifically called for.

[olle]

(In [4090]) Refs #711. Refs #668. Field set show/hide toggle updated to allow the feature for single field sets, if specifically called for:

1. Class/file gui/form/Fieldset.java in client/servlet/ updated with new private instance variable Boolean singleFieldsetToggleAllowed with public accessor methods. The default value of singleFieldsetToggleAllowed is false, and will therefore not change the appearance of forms if not specifically called for.

2. Class/file gui/web/GUIConverter.java in client/servlet/ updated in public method Tag convert(org.proteios.gui.form.Form w) to allow the show/hide toggle feature for a single field set, if value of singleFieldsetToggleAllowed is true.

[olle]

(In [4091]) Refs #668. Support for running msInspect feature detection from Proteios SE updated by labeling field set with strategy selection as "Advanced options", and hide its contents by default:

1. Class/file action/file/UseSpectrumFileForMsInspectSearchExtension.java in client/servlet/ updated in protected method void runMe() by labeling field set with strategy selection as "Advanced options", and hide its contents by default.

2. English dictionary file locale/en/dictionary in client/servlet/ updated with new string key.

[olle]

(In [4095]) Refs #668. Outermost Ant build.xml file updated for target "dist-jar" to include files msinspect.properties*, when copying files from directory client/servlet/conf/ to dist/ProteiosSE-*-dev/www/WEB-INF/classes/. Files in the latter directory are copied to directory $CATALINA_HOME/webapps/proteios/www/WEB-INF/classes/ when script "./install.sh --force" is run from directory dist/ProteiosSE-*-dev/.

[olle]

(In ​[22]) Proteios SE manual wiki page ​Proteios SE server administration updated by addition of introductory section for configuration of Proteios SE access to external programs. Previous section "Search Engine configuration" renamed "Search Engine Configuration - General" and placed as subsection to the new section. The change was motivated by only part of the supported external programs being "search engines" in the strict sense.

[olle]

(In ​[23]) Proteios SE manual wiki page ​Proteios SE server administration updated by addition of new section on configuration of msInspect feature detection.

[olle]

Design update:

• Failure to download a local copy of a large file is not uncommon. If this happens, up to 3 attempts should be made to copy the file. If the copying did not succeed after 3 attempts, the job should terminate, preferably with a message informing the user of the cause.

[olle]

(In [4141]) Refs #668. Class/file plugins/RunMsInspectPlugin.java in plugin/ updated to make a number of attempts to make a local file copy, and if still not successful, the job terminates with a message explaining the cause:

1. New private instance variable String errorInfo added. Default value is null.

2. New private constant int MAX_NUMBER_OF_FILE_UPLOAD_TRIES added, with value set to 3.

3. Private method void msInspectSearchLocal(...) updated to make up to MAX_NUMBER_OF_FILE_UPLOAD_TRIES attempts to make a local file copy, and if still not successful, the job terminates with a message explaining the cause.

[olle]

(In [4143]) Refs #668. Class/file plugins/RunMsInspectPlugin.java in plugin/ updated by extracting creation of temporary local file copy into its own method. Also renaming of some variables and constants to more appropriate names, and removal of unused imports, inner classes, and methods:

1. Private method void msInspectSearchLocal(...) updated by extracting creation of temporary local file copy into new private method boolean makeTemporaryLocalFileCopy(File sourceFile, String localFilePath).

2. New private method boolean makeTemporaryLocalFileCopy(File sourceFile, String localFilePath) added. It performs a number of attempts to make a temporary local file copy of a file item.

3. Private constant int MAX_NUMBER_OF_FILE_UPLOAD_TRIES renamed to the more appropriate MAX_NUMBER_OF_FILE_COPY_ATTEMPTS.

4. Private inner class FileItemPartSource, private method void addStringPart(String name, String value, List<Part> list), and private method String updateCommand(String cmd, String option, String value) removed, since they are not used.

[olle]

(In [4164]) Refs #668. Class/file plugins/RunMsInspectPlugin.java in plugin/ updated to set correct MIME type for uploaded tab-separated value (tsv) output file:

1. Private method void uploadMsInspectOutputFile(String directoryPath, String outputFileName, String filenameOfUploadedFile, Integer dirId, String descr) updated to set MIME type for uploaded tab-separated value (tsv) output file to the correct "text/plain", instead of "text/xml".

[olle]

(In [4165]) Refs #668. Refs #746. Class/file plugins/RunMsInspectPlugin.java in plugin/ updated in javadoc:

1. Public method void setInputFileSizeInBytes(long inputFileSizeInBytes) updated in javadoc by fix of typo.

[olle]

Ticket closed as a first version of support for running msInspect from Proteios SE has been added.

[olle]

(In [4175]) Refs #749. Refs #668. Refs #744. Refs #356. Refs #287. First version of support for starting feature detection from the menu:

1. Class/file gui/MainMenu.java in client/servlet/ updated:
   a. Private method Node createProjectMenu() updated by adding cascade menu for performing feature detection.

2. New class/file action/file/PerformMsInspectSearch.java in client/servlet/ added. It displays the file selection form and then forwards the action to class UseSpectrumFileForMsInspectSearchExtension.

3. New class/file action/file/PerformOpenMsSearch.java in client/servlet/ added. It displays the file selection form and then forwards the action to class UseSpectrumFileForOpenMsSearchExtension.

4. English dictionary file locale/en/dictionary in client/servlet/ updated with new entries for various string keys.

[olle]

(In [4176]) Refs #748. Refs #749. Refs #668. Running feature detection using msInspect updated to support disabling the functionality via the configuration file:

1. msInspect properties template file conf/msinspect.properties.in in client/servlet/ updated with new option "msinspect.local.disabled", that should be set to "yes" or "no".

2. Class/file action/file/PerformMsInspectSearch.java in client/servlet/ updated to implement the ExtensionDisableInterface. New public method boolean fetchExtensionDisabledFlag() retrieves the disable flag by calling the fetchExtensionDisabledFlag() method of an instance of UseSpectrumFileForMsInspectSearchExtension.

3. Class/file action/file/UseSpectrumFileForMsInspectSearchExtension.java in client/servlet/ updated to implement the ExtensionDisableInterface. New public method boolean fetchExtensionDisabledFlag() retrieves the disable flag from the msInspect properties file. If the properties file is missing, true is returned, while if the disable option is missing, false is returned for backwards compatibility.

[olle]

(In ​[26]) Proteios SE manual wiki page ​Proteios SE server administration updated in configuration of msInspect feature detection with new parameter msinspect.local.disabled.

[olle]

(In [4180]) Refs #668. Proteios SE update bat-file for MS Windows updated to create msInspect properties file msinspect.properties from template file msinspect.properties.in, if not existing:

1. Proteios SE update bat-file update_proteios-win.bat in misc/install/ updated to create msInspect properties file msinspect.properties from template file msinspect.properties.in, if not existing.

[olle]

(In [4186]) Refs #668. Class/file plugins/RunMsInspectPlugin.java in plugin/ updated by removal of unused imports and exchanging log4j logger "org.proteios.plugins.RunMsInspectPlugin" for "org.proteios.io", which is used in most plug-ins.

[olle]

Design update:

• The uploaded msInspect feature file should include the file extension of the original spectrum file in the filename, but the file extension should be extended with "peptides.tsv", e.g. spectrum file "sample.mzML" results in feature file "sample.mzML.peptides.tsv", while "sample.mzXML" results in "sample.mzXML.peptides.tsv". This is essential for the msInspect importer in Proteios SE to find the spectrum file related to a feature file.

[olle]

(In [4187]) Refs #668. Class/file plugins/RunMsInspectPlugin.java in plugin/ updated to always include original file extension of spectrum file in name of uploaded feature file:

1. Private method void msInspectSearchLocal(Request request, Response response, ...) updated to always include original file extension of spectrum file in name of uploaded feature file, e.g. spectrum file "sample.mzML" results in feature file "sample.mzML.peptides.tsv", while "sample.mzXML" results in "sample.mzXML.peptides.tsv".

[olle]

(In [4188]) Refs #752. Refs #668. Refs #614. Refs #287. Support for running msInspect feature detection from Proteios SE updated with option to import the created feature file directly:

1. Class/file action/file/UseSpectrumFileForMsInspectSearchExtension.java in client/servlet/ updated with new check box for option to import created feature file. The check box is coupled to new valid parameter VBoolean RunMsInspect.VMSINSPECTIMPORTRESULTS. Default is to not import the feature file directly.

2. Class/file action/msInspect/RunMsInspect.java in client/servlet/ updated:
   a. New valid parameter VBoolean VMSINSPECTIMPORTRESULTS added.
   b. Protected method void runMe() updated to retrieve the value of valid parameter VBoolean VMSINSPECTIMPORTRESULTS, and if the value is true create an import job after the feature detection job. The path of the feature file to be created is transferred to the import job as a string job parameter. Jobs are created by calling new private methods Job createMsInspectJob(...) and Job createMsInspectImportJob(...).
   c. New private method Job createMsInspectJob(DbControl dc, File spectrumFile, ... , Job blockerJob) added. It creates an msInspect job.
   d. New private method Job createMsInspectImportJob(DbControl dc, String featureFilePathStr, String featureFileName, Job blockerJob) added. It creates an msInspect import job.

3. Class/file plugins/MsInspectFeatureImporter.java in plugin/ updated:{{BR]]a. Public method void run(Request request, Response response, ProgressReporter progress) updated to retrieve value of feature file path from a string job parameter and obtain the feature file from this, in case the File value retrieved from a File job parameter is null.

4. English dictionary file locale/en/dictionary in client/servlet/ updated with new string keys.

[olle]

(In [4193]) Refs #668. Class/file action/file/UseSpectrumFileForMsInspectSearchExtension.java in client/servlet/ updated in info test regarding filename of created result file:

1. Protected method void runMe() updated in info test regarding filename of created result file.

[olle]

(In ​[2]) Proteios SE manual wiki page ​Feature Detection updated in configuration of msInspect feature detection regarding file extension of result file.

[olle]

(In [4210]) Refs #668. Class/file action/file/UseSpectrumFileForMsInspectSearchExtension.java in client/servlet/ updated in protected method void runMe() by fix of typo in comment.

[Fredrik Levander]

(In [4346]) Refs #668. Removed unnecessary system output.