Editing PatternQuery:Command Line (section)

= Running the Offline Service =
-----------------------
Just download the latest release of [http://webchem.ncbr.muni.cz/Platform/PatternQuery/DownloadService PatternQuery application]. A simple [http://webchem.ncbr.muni.cz/Platform/PatternQuery/CmdExample demo] is available as well. The service can be executed using the command (latest .NET Framework required): 
<pre>WebChemistry.Queries.Service.exe workingFolder configuration.json</pre>
In Linux (where available) and MacOS, the latest version the Mono Framework (http://mono-project.com/) must be used to run the application:
<pre>mono WebChemistry.Queries.Service.exe workingFolder configuration.json</pre>

Both of the commands immediately executes a calculation, which produces all the output into the <code>workingFolder</code>. A further description can be found when running the program with the <code>--help</code> option. e.g.

<pre>WebChemistry.Queries.Service.exe --help</pre> or <pre>mono WebChemistry.Queries.Service.exe --help</pre>

== Configuration ==
The configuration is specified using the JSON format.

=== Configuration Example ===
This is the general shape of the JSON input configuration.
<pre>{
  "InputFolders": [
    "c:\\TestData\\PDB\\SampleSet1"
  ],
  "Queries": [
    {
      "Id": "NAGs",
      "QueryString": "Residues(\"NAG\")"
    },
    {
      "Id": "MANs",
      "QueryString": "Residues('MAN')"
    }
  ],
  "StatisticsOnly": false,
  "CSAPath": "c:\\data\\csa.dat",
  "MaxParallelism": 8
}</pre>

There has to be exactly one configuration file for each validation run. Every value, as well as settings' names, is surrounded in quotation marks (" " or ' '). Backslashes (\) have to be escaped (\\). File system paths can be absolute as well as relative (/ works as well in paths).

=== Attributes ===
* '''InputFolders''' [ String[] ]
: ''A list of folders containing the input structures.''

* '''Queries''' [ [[#QueryInfo_details|QueryInfo]] ]
: ''A list of queries.''

* '''StatisticsOnly''' [ Boolean ]
: ''If `true`, the files with fragments are not exported.''

* '''CSAPath''' [ String ]
: ''Optional path to a file with CSA database that allows the CSA() query to work. The file is a CSV file that must contain the columns `PdbID, SiteNumber, ResidueName, ChainId, ResidueNumber, ...`''

* '''MaxParallelism''' [ Int32 ], Default value = 8
: ''The maximum number of structures that can be processed simultaneously.''

=== Descriptions ===
===== <span id='QueryInfo_details'>QueryInfo</span> =====
* '''Id''' [ String ]
: ''A unique identifier of the query.''

* '''QueryString''' [ String ]
: ''The query expression.''


== Output Description ==

=== General Structure ===
* '''[WorkingDirectory]''' - ''Working directory of the application.''
:* '''result''' - ''Contains the result of the computation.''
:: '''log.txt''' - ''Contains the console output of the application.''
:: '''status.json''' - ''Contains general information of the computation (running time, version, etc.).''

=== MotiveQuery Specific Structure ===
* '''result''' - ''Folder with computation result''
:* '''query_id''' - ''Folder for each query named by its unique id.''
::* '''patterns''' - ''Folder with patterns stored in PDB format.''
:::: '''data.json''' - ''Information about the result in JSON format.''
:::: '''patterns.csv''' - ''Information about the patterns in CSV format.''
:::: '''metadata_summary.csv''' - ''Information about the metadata (origin organism, EC number, etc.) in CSV format.''
:::: '''structures.csv''' - ''Information about structures that contain the given patterns in CSV format.''
:: '''structures.csv''' - ''Information about all structures that were queried in CSV format.''
:: '''structures.json''' - ''Information about all structures that were queried in JSON format.''
:: '''summary.json''' - ''Summary information (number of found patterns, etc.) about the computation in JSON format.''