{"id":18285285,"url":"https://github.com/seandavi/map_to_mesh_with_mti","last_synced_at":"2026-05-19T03:21:50.872Z","repository":{"id":136334898,"uuid":"245916050","full_name":"seandavi/map_to_mesh_with_mti","owner":"seandavi","description":"Use the MTI tooling from NCBI to map UMLS and MESH terms to arbitrary text. 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HTML PUBLIC \"-//W3C//DTD HTML 4.01 Transitional//EN\"\u003e\n\u003chtml\u003e\n\u003chead\u003e\n\u003cmeta http-equiv=\"Content-Type\" content=\"text/html; charset=windows-1252\"\u003e\n\u003ctitle\u003eSemantic Knowledge Representation Web API Overview\u003c/title\u003e\n\u003cSCRIPT LANGUAGE=\"JavaScript\"\u003e\n\n\u003c!--- hide script from old browsers\n\nfunction displayMsg(text) {\n  msgWindow=window.open(\"\", \"message\", \n    \"screenX=300,screenY=300,outerWidth=500,outerHeight=500,scrollbars=yes,resizable=yes\")\n  msgWindow.document.close();\n  msgWindow.document.open();\n  msgWindow.document.write();\n  msgWindow.document.write (\"\u003chead\u003e\u003ctitle\u003eMessage Window\u003c/title\u003e\u003c/head\u003e\")\n  msgWindow.document.write (\"\u003cbody bgcolor=white\u003e\")\n  msgWindow.document.write (\"\u003cform method=post\u003e\")\n  msgWindow.document.write (\"\u003cbig\u003e\" + text + \"\u003cbr\u003e\u003cbr\u003e\")\n  msgWindow.document.write (\"\u003ccenter\u003e\")\n  msgWindow.document.write (\"\u003cinput type=button value=OK onClick=\\\"window.close();\\\"\u003e\")\n  msgWindow.document.write (\"\u003c/center\u003e\u003c/form\u003e\u003c/body\u003e\")\n}\n\nfunction toggleDisplay(options, which) {\n   if(options[0].selected) {\n      var block = document.getElementById(which);\n      block.style.display = \"none\";\n   }\n\n   else {\n      var block = document.getElementById(which);\n      block.style.display = \"block\";\n   }\n}\n// end hiding from old browsers --\u003e\n\n\u003c/SCRIPT\u003e\n\u003c/head\u003e\n\n\u003cbody bgcolor=papayawhip\u003e\n\u003ctable border=\"0\" width=100%\u003e\n   \u003ctr\u003e\n     \u003ctd align=center\u003e\n       \u003cimg border=0 src=\"./doc/SKR_Web_API.jpg\"\n           alt=\"SKR Web API Logo\" title=\"SKR Web API Logo\"\u003e\n     \u003c/td\u003e\n   \u003c/tr\u003e\n\u003c/table\u003e\n\n\u003chr noshade\u003e\n\n\u003cfont size=+1\u003e\u003cb\u003e\u003cu\u003eContents:\u003c/u\u003e\u003c/b\u003e\u003c/font\u003e\u003cbr\u003e\n\n\u003ctable border=0\u003e\n  \u003ctr\u003e\n     \u003ctd valign=top\u003e\n       \u003cfont color=blue\u003e\n         \u003cul\u003e\n          \u003cli\u003e\u003cfont color=black point-size=12\u003e\n              \u003ca href=\"#Prequisites\"\u003ePrerequisites and Notices\u003c/a\u003e\u003c/font\u003e\u003cbr\u003e\n\n          \u003cli\u003e\u003cfont color=black point-size=12\u003e\n              \u003ca href=\"#Installation\"\u003eInstallation\u003c/a\u003e\u003c/font\u003e\u003cbr\u003e\n        \u003c/ul\u003e\n       \u003c/font\u003e\n     \u003c/td\u003e\n\n     \u003ctd valign=top\u003e\n       \u003cfont color=blue\u003e\n         \u003cul\u003e\n          \u003cli\u003e\u003cfont color=black point-size=12\u003e\n              \u003ca href=\"#Overview\"\u003eOverview of What Happens\u003c/a\u003e\u003c/font\u003e\u003cbr\u003e\n\n          \u003cli\u003e\u003cfont color=black point-size=12\u003e\n               \u003ca href=\"#Examples\"\u003eExample Programs\u003c/a\u003e\u003c/font\u003e\u003cbr\u003e\n\n          \u003cli\u003e\u003cfont color=black point-size=12\u003e\n               \u003ca href=\"#Samples\"\u003eSample Batch Commands\u003c/a\u003e\u003c/font\u003e\u003cbr\u003e\n        \u003c/ul\u003e\n       \u003c/font\u003e\n     \u003c/td\u003e\n\n     \u003ctd valign=top\u003e\n       \u003cfont color=blue\u003e\n         \u003cul\u003e\n          \u003cli\u003e\u003cfont color=black point-size=12\u003e\n               \u003ca href=\"#HowTo\"\u003eHow to Compile and Run\u003c/a\u003e\u003c/font\u003e\u003cbr\u003e\n\n          \u003cli\u003e\u003cfont color=black point-size=12\u003e\n               \u003ca href=\"#Notes\"\u003eProgramming Notes\u003c/a\u003e\u003c/font\u003e\u003cbr\u003e\n \n          \u003cli\u003e\u003cfont color=black point-size=12\u003e\n               \u003ca href=\"doc/index.html\"\u003eJavadoc for SKR Web API\u003c/a\u003e\u003c/font\u003e\u003cbr\u003e\n       \u003c/ul\u003e\n       \u003c/font\u003e\n     \u003c/td\u003e\n  \u003c/tr\u003e\n\u003c/table\u003e\n\u003cdiv align=center\u003e\nWhenever you see \n\u003cimg border=0 align=ABSMIDDLE src=\"./doc/quest.gif\" \n  width=14 height=14 alt=\"Information Mark Symbol\"\n  title=\"Information Mark Symbol\"\u003e in the text below, it means that additional\ninformation is available by selecting the symbol.\n\u003c/div\u003e\n\n\u003chr noshade\u003e\n\u003cfont size=+1\u003e\u003cb\u003e\u003cu\u003e\n\u003ca name=\"Introduction\"\u003eIntroduction:\u003c/a\u003e\u003c/u\u003e\u003c/b\u003e\u003c/font\u003e\u003cbr\u003e\nThis Java-based API to the Semantic Knowledge Representation (SKR) Scheduler facility was created to provide users with the ability to programmatically submit jobs to the Scheduler Batch and Interactive facilities instead of using the web-based interface.\n\u003cbr\u003e\u003cbr\u003e\n\n\u003cfont size=+1\u003e\u003cb\u003e\u003cu\u003e\n\u003ca name=\"Background\"\u003eBackground:\u003c/a\u003e\u003c/u\u003e\u003c/b\u003e\u003c/font\u003e\u003cbr\u003e\nThe SKR Project was initiated at NLM in order to develop programs to provide usable semantic representation of biomedical free text by building on resources currently available at the library.\n\u003cbr\u003e\u003cbr\u003e\n\nThe SKR project is concerned with reliable and effective management of the information encoded in natural language texts. The project develops programs that provide usable semantic representation of biomedical text by building on resources currently available at the Library, especially the UMLS knowledge sources and the natural language processing tools provided by the SPECIALIST system.\n\u003cbr\u003e\u003cbr\u003e\n\nTwo programs in particular, MetaMap and SemRep, are being evaluated and enhanced and applied to a variety of problems in the management of biomedical information. These include automatic indexing of MEDLINE citations, concept-based query expansion, analysis of complex Metathesaurus strings, accurate identification of the terminology and relationships in anatomical documents, and the extraction of chemical binding relations from biomedical text.\n\u003cbr\u003e\u003cbr\u003e\n\n\u003cfont size=+1\u003e\u003cb\u003e\u003cu\u003e\n\u003ca name=\"TPAL\"\u003eThird Party and Associated Licenses Used:\u003c/a\u003e\u003c/u\u003e\u003c/b\u003e\u003c/font\u003e\u003cbr\u003e\n  For specifics on the licensing and copyright information on each of these\n  packages, please visit their respective link.  Notices/Attributions will\n  also be found in the source code when and where required.\u003cbr\u003e\n\n  \u003cul\u003e\n    \u003cli\u003eThe http*.jar files are from the Apache\n        HttpComponents\u003csup\u003e\u003cfont size=-1\u003e\u0026#174;\u003c/font\u003e\u003c/sup\u003e project\n        (\u003ca href=\"http://hc.apache.org\"\u003ehttp://hc.apache.org\u003c/a\u003e/)\n        which is under the Apache License, Version 2.0\n       (\u003ca \n     href=\"http://www.apache.org/licenses\"\u003ehttp://www.apache.org/licenses\u003c/a\u003e/).\n       \u003cbr\u003e\u003cbr\u003e\n\n    \u003cli\u003eThe Json libraries are from JSON.org (\u003ca\n        href=\"http://json.org\"\u003ehttp://json.org\u003c/a\u003e/) which uses the\n        JSON License (\u003ca class=\"link\"\nhref=\"http://www.json.org/license.html\"\u003ehttp://www.json.org/license.html\u003c/a\u003e)\n       \u003cbr\u003e\u003cbr\u003e\n\n    \u003cli\u003eThe Password Masking in the Java Programming Language software is from\n        \u003ca\n    href=\"http://java.sun.com/developer/technicalArticles/Security/pwordmask/\"\u003e\n        http://java.sun.com/developer/technicalArticles/Security/pwordmask/\u003c/a\u003e.\n        Author: Qusay H. Mahmoud with contributions from Alan Sommerer\n        \u003cbr\u003e\u003cbr\u003e\n\n     \u003cli\u003eInformation on the CAS RESTful API Protocol used by this API can be found at:\n\u003ca href=\"https://wiki.jasig.org/display/CASUM/RESTful+API\"\u003ehttps://wiki.jasig.org/display/CASUM/RESTful+API\u003c/a\u003e .\n\n  \u003c/ul\u003e\n\n\u003chr noshade\u003e\n\n\u003cfont size=+1\u003e\u003cb\u003e\u003cu\u003e\n\u003ca name=\"Prerequisites\"\u003ePrerequisites and Notices:\u003c/a\u003e\u003c/u\u003e\u003c/b\u003e\u003c/font\u003e\n\n\u003ctable border=1 bgcolor=red\u003e\n  \u003ctr\u003e\n    \u003ctd bgcolor=white\u003e\n      \u003cdiv align=center\u003e\u003cb\u003ePlease Note\u003c/b\u003e\u003c/div\u003e\n      This software is produced by an agency of the U.S. Government, and\n      by statute is not subject to copyright in the United States.  Recipients\n      of this software assume all responsibilities associated with its\n      operation, modification, and maintenance.\n    \u003c/td\u003e\n  \u003c/tr\u003e\n\u003c/table\u003e\n\n\u003ctable border=\"1\" bgcolor=tan\u003e\n  \u003ctr bgcolor=moccasin\u003e\n     \u003ctd colspan=2 align=center\u003e\n      Users are responsible for compliance with the UMLS Metathesaurus\n      License Agreement.\n\n      \u003cbr\u003e\u003cbr\u003e\n      To use the SKR Web API, you must have accepted the terms of the\n      \u003ca href=\"https://uts.nlm.nih.gov/license.html\"\u003eUMLS Metathesaurus\n      License Agreement\u003c/a\u003e, which requires you to respect the copyrights\n      of the constituent vocabularies and to file a brief annual report on\n      your use of the UMLS. You also must have activated\n      a \u003ca href=\"https://uts.nlm.nih.gov\"\u003eUMLS Terminology Services (UTS)\u003c/a\u003e\n      account.  For information on how we use UTS authentication please select\n      the Info icon to the right:\n      \u003ca href=\"http://skr.nlm.nih.gov/Help/umlsks.shtml\"\u003e\n        \u003cimg border=0 align=ABSMIDDLE src=\"./doc/quest.gif\" \n             width=18 height=18\n             alt=\"Information Mark Symbol: Help about UTS accounts\"\n             title=\"Information Mark Symbol: Help about UTS accounts\"\u003e\u003c/a\u003e\n\n      \u003cbr\u003e\u003cbr\u003e\n      For details of the licenses see the\n      \u003ca href=\"https://uts.nlm.nih.gov/license.html\"\u003eUMLS Metathesaurus\n      License Agreement\u003c/a\u003e and\u003cbr\u003e\n      \u003ca href=\"http://www.nlm.nih.gov/databases/umls.html\"\u003eHow to License\n      and Access the Unified Medical Language System� (UMLS�) Data\u003c/a\u003e.\n     \u003c/td\u003e\n  \u003c/tr\u003e\n\u003c/table\u003e\n\u003chr noshade\u003e\n\n\u003cul type=square\u003e\n \u003cli\u003e A running version of Java.\n      \u003ca href=\"javascript:displayMsg('If you are only going to use Java\u003csup\u003e\u0026trade;\u003c/sup\u003e for running the SKR Web API program, you will only need the Java Runtime Environment (JRE).  The following link will take you to the Sun Java 2 Platform, Standard Edition download web page.  From that web page, select the latest (non Beta) version of JRE typically entitled something similar to the following: \u003cem\u003eJava 2, Runtime Environment, Standard Edition, v1.4.2 (JRE)\u003c/em\u003e.\u003cbr\u003e\u003cbr\u003e If you are going to use Java for augmenting the SKR Web API or for your own Java based programming, it is recommended that you download the Java SDK.\u003cbr\u003e\u003cbr\u003e\u003cb\u003ePlease Note:\u003c/b\u003e In either case, you will be required to review and accept a disclaimer before downloading is allowed for the Java software.\u003cbr\u003e\u003cbr\u003e\u003ca href=http://www.java.sun.com/j2se target=Java\u003e Java 2 Platform, Standard Edition Download Page\u003c/a\u003e');\"\u003e\n          \u003cimg border=0 align=ABSMIDDLE width=14 height=14\n           src=\"./doc/quest.gif\"\n           alt=\"Information Mark Symbol: Help about Java\"\n           title=\"Information Mark Symbol: Help about Java\"\u003e\u003c/a\u003e\n      We have tested and confirmed that the SKR Web API\n      program compiles and runs under the following versions of Java:\n      \u003cul type=disc\u003e\n        \u003cli\u003e 1.6.0\n      \u003c/ul\u003e\n     \u003cbr\u003e\n\n \u003cli\u003e We have tested and confirmed that the SKR Web API program runs on the\n      following operating systems:\n      \u003cul type=disc\u003e\n        \u003cli\u003e Linux\n        \u003cli\u003e Microsoft Windows XP, 7\n        \u003cli\u003e Mac OS/X\n      \u003c/ul\u003e\n     \u003cbr\u003e\n\n  \u003cli\u003e Apache's Jakarta Project Ant\n           \u003ca href=\"javascript:displayMsg('\u003cb\u003eTo find out which version of\n           Ant you are running, type the following in a command window.\u003cbr\u003e\u003cbr\u003e\n           \u003cpre\u003e     ant -version\u003c/pre\u003e\u003c/b\u003e\u003cbr\u003e\u003cbr\u003eThe following link will take\n           you to the Apache Jakarta Ant web page.\n           From that web site, select the \u003ci\u003eLatest Release\u003c/i\u003e that you would\n           like to install.\u003cbr\u003e\u003cbr\u003e\n           \u003ca href=http://jakarta.apache.org/ant/index.html target=ANT\u003eAnt \n           Download Page\u003c/a\u003e');\"\u003e\n          \u003cimg border=0 align=ABSMIDDLE width=14 height=14\n           src=\"./doc/quest.gif\"\n           alt=\"Information Mark Symbol: Help about Ant\"\n           title=\"Information Mark Symbol: Help about Ant\"\u003e\u003c/a\u003e\n           program is \u003cu\u003eonly\u003c/u\u003e required if you wish to modify\n           and/or compile the SKR Web API source code using the\n           existing build file:\n      \u003cul type=disc\u003e\n        \u003cli\u003e 1.6 or better\n      \u003c/ul\u003e\n         \u003cbr\u003e\n\n \u003cli\u003e Your data in a recognized format.  Please see the\n      \u003ca href=\"http://skr.nlm.nih.gov/Help/help.shtml#File%20Formats\"\u003eSupported\n      File Formats\u003c/a\u003e section of the SKR Help Information web page for\n      detailed information and examples of valid input formats.\n\u003c/ul\u003e\n\u003chr noshade\u003e\n\n\u003cfont size=+1\u003e\u003cb\u003e\u003cu\u003e\n\u003ca name=\"Installation\"\u003eInstallation:\u003c/a\u003e\u003c/u\u003e\u003c/b\u003e\u003c/font\u003e\u003cbr\u003e\u003cbr\u003e\nTo install the SKR Web API, do the following:\u003cbr\u003e\n  \u003col start=1 type=\"1\"\u003e\n    \u003cli\u003e Make a top level directory to store the SKR Web API program.\n         \u003cbr\u003e\u003cbr\u003e\n\n    \u003cli\u003e Go to the \u003ca href=\"http://skr.nlm.nih.gov/SKR_API\"\u003eSKR Web API\u003c/a\u003e page\n         from the \u003ca href=\"http://skr.nlm.nih.gov/\"\u003eSKR\u003c/a\u003e homepage.\n         \u003cbr\u003e\u003cbr\u003e\n\n    \u003cli\u003e Download the latest version of the SKR Web API into the\n         directory created in #1.\n         \u003cbr\u003e\u003cbr\u003e\n\n    \u003cli\u003e Change directory to the directory created in #1\n         \u003cbr\u003e\u003cbr\u003e\n\n    \u003cli\u003e Extract the jar files from the downloaded jar file - SKR_Web_API_V2_0.jar.\n         \u003cul type=\"disc\"\u003e\n           \u003cli\u003e\u003cb\u003eOn Windows:\u003c/b\u003eRun winzip, pkzip, or zip on the\n                downloaded file.\n                \u003cbr\u003e\u003cbr\u003e\n           \u003cli\u003e\u003cb\u003eOn Unix:\u003c/b\u003eRun the java jar program on the\n                jar file: \u003cb\u003ejava sun.tools.jar.Main xf SKR_Web_API_V2_0.jar\u003c/b\u003e\n         \u003c/ul\u003e\n\n         \u003cbr\u003e\n    \u003cli\u003eThis will create a directory called \"SKR_Web_API_V2_0\"\n        in the directory you created in #1 and\n         fill it with all of the program files needed.\n         \u003cbr\u003e\u003cbr\u003e\n\n    \u003cli\u003eNow, change to this new directory: \u003cb\u003ecd SKR_Web_API_V2_0\u003c/b\u003e\n         \u003cbr\u003e\u003cbr\u003e\n\n    \u003cli\u003eYou are now ready to run.  Look at the example programs in the\n        \"examples\" subdirectory for ideas on what to do.\n  \u003c/ol\u003e\n\n\u003chr noshade\u003e\n\n\u003cfont size=+1\u003e\u003cb\u003e\u003cu\u003e\n\u003ca name=\"Overview\"\u003eOverview of What Happens:\u003c/a\u003e\u003c/u\u003e\u003c/b\u003e\u003c/font\u003e\n\n \u003cp\u003e\n  The SKR Web API has been designed to allow you to interact with our web-based \nScheduler using our Batch and Interactive facilities.  Interactive access is currently only\navailable for the MetaMap and SemRep programs.\n\n\u003cul type=square\u003e\n \u003cli\u003e\u003cb\u003eBatch Jobs have three main phases:\u003c/b\u003e\n   \u003col type=\"1\"\u003e\n     \u003cli\u003e Request is made for a new batch job and the SKR Web API submits the\n          job.\u003cbr\u003e\u003cbr\u003e\n\n     \u003cli\u003e Program waits for job to finish.  This is done by monitoring the\n          Scheduler queue to see when the job exits the queue.  The program\n          sleeps for 10 seconds after each check of the queue so that it\n          doesn't become a nuisance process.\u003cbr\u003e\u003cbr\u003e\n\n     \u003cli\u003e Once the job has left the Scheduler queue, the program then checks\n          to see if the \"text.out.done\" file exists in the job result\n          directory.  If it does, then the results file \"text.out\" is returned\n          as a String to the calling method.  If the \"text.out.done\" file\n          doesn't exist, an error has occurred and the program exits.\n   \u003c/ol\u003e\u003cbr\u003e\n\n \u003cli\u003e\u003cb\u003eInteractive Jobs only have two main phases:\u003c/b\u003e\n   \u003col type=\"1\"\u003e\n     \u003cli\u003e Request is made for a new interactive job and the SKR Web API submits the\n          job.\u003cbr\u003e\u003cbr\u003e\n\n     \u003cli\u003e Program waits for job to finish and returns the result as a String\n          to the calling method.  Interactive jobs don't really enter the\n          Scheduler - they are run from the command line.  The API simply\n          waits for the command to return a result without having to worry\n          about the Scheduler queue, etc., providing the fastest mechanism for\n          receiving results.\u003cbr\u003e\u003cbr\u003e\n\n     \u003cli\u003e \u003cb\u003eNote:\u003c/b\u003e \u003ci\u003eInteractive jobs will only accept a single\n          item up to 10,000 characters in length to process - anything\n          larger will generate an error.\u003c/i\u003e\n   \u003c/ol\u003e\n\u003c/ul\u003e\n\n\u003chr noshade\u003e\n\n\u003cfont size=+1\u003e\u003cb\u003e\u003cu\u003e\n\u003ca name=\"Examples\"\u003eExample Programs:\u003c/a\u003e\u003c/u\u003e\u003c/b\u003e\u003c/font\u003e\n\n\u003cp\u003e\nThere are six example programs included in the \"examples\" directory to illustrate how to incorporate the SKR Web API into your application.  Two of the examples (GenericBatch.java and GenericBatchNew.java) show how to access the Scheduler Batch facility.  MMInteractive and SRInteractive.java examples show how to access Interactive MetaMap and Interactive SemRep respectively.  The last two examples GenericBatchUser.java and MMInteractiveUser.java illustrate how to\nspecify the username and password within the program to eliminate the need for\nprompting when running.\n\n\u003cbr\u003e\u003cbr\u003e\nFor a list of the available options, please select the appropriate program name:\n \u003ca href=\"http://metamap.nlm.nih.gov/MM09_Usage.shtml\"\n    target=helpSKROpts\u003eMetaMap\u003c/a\u003e and  \n  \u003ca href=\"http://skr.nlm.nih.gov/resource/NewMTIBatch_help_info.html\"\n     target=helpMTIOpts\u003eMTI\u003c/a\u003e.\n\n\u003cbr\u003e\u003cbr\u003e\n\n\u003ctable border=1 bgcolor=tan\u003e\n  \u003ctr bgcolor=white\u003e\n   \u003ctd\u003e\u003cb\u003eGenericBatch.java\u003c/b\u003e\n       Example program for submitting a new Generic Batch with Validation job\n       (\"GenericObject(true)\" turns on validation) request to the Scheduler to\n       run.  You will be prompted for your username and password and if they\n       are alright, the job is submitted to the Scheduler and the results are\n       returned in the String \"results\" below.\n       \u003cbr\u003e\u003cbr\u003e\n       This example shows how to setup a basic Generic Batch with Validation job\n       with a small file (sample.txt) with ASCII MEDLINE formatted citations as\n       input data. You must set the Email_Address variable and use the\n       UpLoad_File\n       to specify the data to be processed.  This example also shows the user\n       setting the SilentEmail option which tells the Scheduler to NOT send\n       email upon completing the job.\n       \u003cbr\u003e\u003cbr\u003e\n       This example is set to run the MTI (Medical Text Indexer) program using\n       the -opt1L_DCMS and -E options. You can also setup any environment\n       variables\n       that will be needed by the program by setting the Batch_Env field.\n       \u003cbr\u003e\u003cbr\u003e\n       \u003cb\u003eNOTE:\u003c/b\u003e\n          The \"-E\" option/argument is very important and should be included\n          with whatever program (MetaMap, SemRep, MTI) you decided to run!\n          The reason is that this\n          version of the Generic Batch does validation and the -E option tells\n          the various programs to include a marker denoting when a successful\n          result has been found.\n   \u003c/td\u003e\n  \u003c/tr\u003e\n\n  \u003ctr bgcolor=steelblue\u003e\n   \u003ctd\u003e\u003cfont point-size=4\u003e\u0026nbsp;\u003c/font\u003e\u003c/td\u003e\n  \u003c/tr\u003e\n\n  \u003ctr bgcolor=white\u003e\n   \u003ctd\u003e\u003cb\u003eGenericBatchNew.java\u003c/b\u003e\n       Same as GenericBach.java above, except you can enter any of the\n       options and the inputfile on the command line.  The usage of the\n       program and available options are listed below:\n\u003cdiv class=\"block\"\u003e\u003cpre\u003e\nusage: GenericBatchNew [options] inputFilename\n  allowed options: \n    --email \u0026lt;address\u0026gt; : set email address. (required option)\n    --command \u0026lt;name\u0026gt; : batch command: metamap, semrep, etc. (default: MTI -opt1_DCMS -E)\n    --note \u0026lt;notes\u0026gt; : batch notes \n    --silent : don't send email after job completes.\n    --silent-errors : Silent on Errors\n    --singleLineInput : Single Line Delimited Input\n    --singleLinePMID : Single Line Delimited Input w/ID\n    --priority : request a Run Priority Level: 0, 1, or 2\n\u003c/pre\u003e\u003c/div\u003e\n\n       \u003cb\u003eNOTE:\u003c/b\u003e\n          The \"-E\" option/argument is very important and should be included\n          with whatever program you decided to run!  The reason is that this\n          version of the Generic Batch does validation and the -E option tells\n          the various programs to include a marker denoting when a successful\n          result has been found.\n   \u003c/td\u003e\n  \u003c/tr\u003e\n\n  \u003ctr bgcolor=steelblue\u003e\n   \u003ctd\u003e\u003cfont point-size=4\u003e\u0026nbsp;\u003c/font\u003e\u003c/td\u003e\n  \u003c/tr\u003e\n\n  \u003ctr bgcolor=white\u003e\n   \u003ctd\u003e\u003cb\u003eMMInteractive.java\u003c/b\u003e\n   This example shows how to setup a basic Interactive MetaMap request.\n   This runs the latest version of MetaMap with 1011 (2010AB) version\n   of the UMLS Metathesaurus (\"KSOURCE\", \"1011\"), with \"ignore_word_order\" (-i)\n   and \"all_derivational_variants\" (D) set as arguments to MetaMap.  The\n   default \"Human Readable\" output will be produced.\n\n       \u003cbr\u003e\u003cbr\u003e\n       \u003cb\u003eNOTE:\u003c/b\u003e\n          The \"-E\" option/argument is \u003cu\u003eNOT\u003c/u\u003e required for Interactive use.\n   \u003c/td\u003e\n  \u003c/tr\u003e\n\n  \u003ctr bgcolor=steelblue\u003e\n   \u003ctd\u003e\u003cfont point-size=4\u003e\u0026nbsp;\u003c/font\u003e\u003c/td\u003e\n  \u003c/tr\u003e\n\n  \u003ctr bgcolor=white\u003e\n   \u003ctd\u003e\u003cb\u003eSRInteractive.java\u003c/b\u003e\n   This example shows how to setup a basic Interactive SemRep request.\n   This runs the latest version of SemRep with Full Fielded Output (-D).\n\n       \u003cbr\u003e\u003cbr\u003e\n       \u003cb\u003eNOTE:\u003c/b\u003e\n          The \"-E\" option/argument is \u003cu\u003eNOT\u003c/u\u003e required for Interactive use.\n   \u003c/td\u003e\n  \u003c/tr\u003e\n\n  \u003ctr bgcolor=steelblue\u003e\n   \u003ctd\u003e\u003cfont point-size=4\u003e\u0026nbsp;\u003c/font\u003e\u003c/td\u003e\n  \u003c/tr\u003e\n\n  \u003ctr bgcolor=white\u003e\n   \u003ctd\u003e\u003cb\u003eGenericBatchUser.java\u003c/b\u003e\n   This example is the same as \"GenericBatchNew.java\" above, except that the\n   username and password are set in the program so that the user is not\n   prompted when the program runs.  \u003cb\u003ePlease Note:\u003c/b\u003e Although we understand\n   the operational need for being able to specify the username and password\n   within a program, you must also be aware of the security risks when using\n   this setup.  Please take care to secure the software you create using this\n   option.\n   \u003c/td\u003e\n  \u003c/tr\u003e\n\n  \u003ctr bgcolor=steelblue\u003e\n   \u003ctd\u003e\u003cfont point-size=4\u003e\u0026nbsp;\u003c/font\u003e\u003c/td\u003e\n  \u003c/tr\u003e\n\n  \u003ctr bgcolor=white\u003e\n   \u003ctd\u003e\u003cb\u003eMMInteractiveUser.java\u003c/b\u003e\n   This example is the same as \"MMInteractive.java\" above, except that the\n   username and password are set in the program so that the user is not\n   prompted when the program runs.  \u003cb\u003ePlease Note:\u003c/b\u003e Although we understand\n   the operational need for being able to specify the username and password\n   within a program, you must also be aware of the security risks when using\n   this setup.  Please take care to secure the software you create using this\n   option.\n   \u003c/td\u003e\n  \u003c/tr\u003e\n\u003c/table\u003e\n\n\u003chr noshade\u003e\n\n\u003cfont size=+1\u003e\u003cb\u003e\u003cu\u003e\n\u003ca name=\"Samples\"\u003eSample Batch Commands:\u003c/a\u003e\u003c/u\u003e\u003c/b\u003e\u003c/font\u003e\n\n\u003cul type=square\u003e\n  \u003cli\u003e Default MetaMap call (latest version of MetaMap, strict data model,\n       current UMLS Knowledge Source, human readable output,\n       and best mappings only):\n       \u003cdiv style=\"background-color:white; border:2px solid #ADADAD\"\u003e\n       metamap -E\n       \u003c/div\u003e\n       \u003cbr\u003e\n\n  \u003cli\u003e MetaMap formatted XML output call (latest version of MetaMap,\n       strict data model, current UMLS Knowledge Source, Formatted XML output,\n       and best mappings only) showing both short and long form of the\n       XML option:\n       \u003cdiv style=\"background-color:white; border:2px solid #ADADAD\"\u003e\n       metamap -% format -E\u003cbr\u003e\n       \u0026nbsp;\u0026nbsp;or\u003cbr\u003e\n       metamap --XML format -E\n       \u003c/div\u003e\n       \u003cbr\u003e\n\n  \u003cli\u003e Specify Semantic Types to Restrict MetaMap too (latest version of\n       MetaMap, strict data model, current UMLS Knowledge Source,\n       human readable output, best mappings only, only allow \"Disease or\n       Syndrome\", \"Finding\", and \"Injury or Poisoning\" Semantic Types):\n       \u003cdiv style=\"background-color:white; border:2px solid #ADADAD\"\u003e\n       metamap -J \"dsyn,fndg,inpo\" -E\u003cbr\u003e\n       \u003c/div\u003e\n       \u003cbr\u003e\n\n  \u003cli\u003e Default MTI call (latest version of MTI, use PubMed Related Articles\n       first and TexTool as backup for PRC, and default output):\n       \u003cdiv style=\"background-color:white; border:2px solid #ADADAD\"\u003e\n       MTI -opt1L_DCMS -E\n       \u003c/div\u003e\n       \u003cbr\u003e\n\n  \u003cli\u003e Default SemRep call (latest version of SemRep with Full Fielded Output):\n       \u003cdiv style=\"background-color:white; border:2px solid #ADADAD\"\u003e\n       semrep -D -E\n       \u003c/div\u003e\n       \u003cbr\u003e\n\u003c/ul\u003e\n\n\u003chr noshade\u003e\n\n\u003cfont size=+1\u003e\u003cb\u003e\u003cu\u003e\n\u003ca name=\"HowTo\"\u003eHow to Compile and Run:\u003c/a\u003e\u003c/u\u003e\u003c/b\u003e\u003c/font\u003e\n\n\u003cul type=square\u003e\n  \u003cli\u003e To compile the source jar file and/or any of the examples using Ant\n       - change to the top-level directory and run:\n       \u003cdiv style=\"background-color:white; border:2px solid #ADADAD\"\u003e\n       ant jar\n       \u003c/div\u003e\n       \u003cbr\u003e\n\n  \u003cli\u003e To compile any of the examples \u003cu\u003ewithout\u003c/u\u003e Ant, change to\n       the examples directory first:\n       \u003cbr\u003e\n       \u003cdiv style=\"background-color:white; border:2px solid #ADADAD\"\u003e\n       cd examples\u003cbr\u003e\u003cbr\u003e\n       \u003cb\u003eUnix:\u003c/b\u003e\u003cbr\u003e\njavac -cp ../classes:../lib/skrAPI.jar:../lib/commons-logging-1.1.1.jar:../lib/httpclient-cache-4.1.1.jar:../lib/httpcore-nio-4.1.jar:../lib/httpclient-4.1.1.jar:../lib/httpcore-4.1.jar:../lib/httpmime-4.1.1.jar -d ../classes GenericBatch.java\u003cbr\u003e\u003cbr\u003e\n\nor, you can use the \"compile.sh\" script provided\u003cbr\u003e\u003cbr\u003e\n\u0026nbsp;\u0026nbsp;\u0026nbsp;\u0026nbsp;\u0026nbsp;../compile.sh GenericBatch.java\u003cbr\u003e\u003cbr\u003e\n\n\n       \u003cb\u003eWindows:\u003c/b\u003e\u003cbr\u003e\njavac -cp ..\\classes;..\\lib\\skrAPI.jar;..\\lib\\commons-logging-1.1.1.jar;..\\lib\\httpclient-cache-4.1.1.jar;..\\lib\\httpcore-nio-4.1.jar;..\\lib\\httpclient-4.1.1.jar;..\\lib\\httpcore-4.1.jar;..\\lib\\httpmime-4.1.1.jar -d ..\\classes GenericBatch.java\u003cbr\u003e\u003cbr\u003e\n\n       \u003c/div\u003e\u003cbr\u003e\n\n  \u003cli\u003e To run any of the examples, change to the examples directory first:\n       \u003cbr\u003e\n       \u003cdiv style=\"background-color:white; border:2px solid #ADADAD\"\u003e\n       cd examples\u003cbr\u003e\u003cbr\u003e\n       \u003cb\u003eUnix:\u003c/b\u003e\u003cbr\u003e\njava -cp ../classes:../lib/skrAPI.jar:../lib/commons-logging-1.1.1.jar:../lib/httpclient-cache-4.1.1.jar:../lib/httpcore-nio-4.1.jar:../lib/httpclient-4.1.1.jar:../lib/httpcore-4.1.jar:../lib/httpmime-4.1.1.jar GenericBatch\u003cbr\u003e\u003cbr\u003e\n\njava -cp ../classes:../lib/skrAPI.jar:../lib/commons-logging-1.1.1.jar:../lib/httpclient-cache-4.1.1.jar:../lib/httpcore-nio-4.1.jar:../lib/httpclient-4.1.1.jar:../lib/httpcore-4.1.jar:../lib/httpmime-4.1.1.jar GenericBatchNew --email your@email inputFilename\u003cbr\u003e\u003cbr\u003e\n\nor, you can use the \"run.sh\" script provided\u003cbr\u003e\u003cbr\u003e\n\u0026nbsp;\u0026nbsp;\u0026nbsp;\u0026nbsp;\u0026nbsp;../run.sh GenericBatch\u003cbr\u003e\u003cbr\u003e\n\u0026nbsp;\u0026nbsp;\u0026nbsp;\u0026nbsp;\u0026nbsp;../run.sh GenericBatchNew --email your@email inputFilename\u003cbr\u003e\u003cbr\u003e\n\n\n       \u003cb\u003eWindows:\u003c/b\u003e\u003cbr\u003e\njava -cp ..\\classes;..\\lib\\skrAPI.jar;..\\lib\\commons-logging-1.1.1.jar;..\\lib\\httpclient-cache-4.1.1.jar;..\\lib\\httpcore-nio-4.1.jar;..\\lib\\httpclient-4.1.1.jar;..\\lib\\httpcore-4.1.jar;..\\lib\\httpmime-4.1.1.jar GenericBatch\u003cbr\u003e\u003cbr\u003e\n\njava -cp ..\\classes;..\\lib\\skrAPI.jar;..\\lib\\commons-logging-1.1.1.jar;..\\lib\\httpclient-cache-4.1.1.jar;..\\lib\\httpcore-nio-4.1.jar;..\\lib\\httpclient-4.1.1.jar;..\\lib\\httpcore-4.1.jar;..\\lib\\httpmime-4.1.1.jar GenericBatchNew --email your@email filename\u003cbr\u003e\u003cbr\u003e\n\n       \u003c/div\u003e\n\u003c/ul\u003e\n\n\u003chr noshade\u003e\n\n\u003cfont size=+1\u003e\u003cb\u003e\u003cu\u003e\n\u003ca name=\"Notes\"\u003eProgramming Notes:\u003c/a\u003e\u003c/u\u003e\u003c/b\u003e\u003c/font\u003e\n\u003cbr\u003e\u003cbr\u003e\n\n\u003ctable border=1 bgcolor=white\u003e\n  \u003ctr bgcolor=steelblue\u003e\n    \u003cth colspan=4\u003e\u003cfont color=white point-size=12\u003eRequired Fields\u003c/font\u003e\u003c/th\u003e\n  \u003c/tr\u003e\n\n  \u003ctr\u003e\n    \u003cth\u003e\u003cfont point-size=10\u003eGeneral Description\u003c/font\u003e\u003c/th\u003e\n    \u003cth\u003e\u003cfont point-size=10\u003eName\u003c/font\u003e\u003c/th\u003e\n    \u003cth\u003e\u003cfont point-size=10\u003eType\u003c/font\u003e\u003c/th\u003e\n  \u003c/tr\u003e\n\n  \u003ctr\u003e\n    \u003ctd\u003e\u003cfont point-size=10\u003eEmail Address\u003c/font\u003e\u003c/td\u003e\n    \u003ctd\u003e\u003cfont point-size=10\u003eEmail_Address\u003c/font\u003e\u003c/td\u003e\n    \u003ctd\u003e\u003cfont point-size=10\u003eString\u003c/font\u003e\u003c/td\u003e\n  \u003c/tr\u003e\n\n  \u003ctr\u003e\n    \u003ctd\u003e\u003cfont point-size=10\u003eFile to Upload\u003c/font\u003e\u003c/td\u003e\n    \u003ctd\u003e\u003cfont point-size=10\u003eUpLoad_File\u003c/font\u003e\u003c/td\u003e\n    \u003ctd\u003e\u003cfont point-size=10\u003eString\u003c/font\u003e\u003c/td\u003e\n  \u003c/tr\u003e\n\u003c/table\u003e\n\n\u003cbr\u003e\u003cbr\u003e\n\n\u003ctable border=1 bgcolor=white\u003e\n  \u003ctr bgcolor=steelblue\u003e\n    \u003cth colspan=4\u003e\u003cfont color=white point-size=12\u003eOptional Fields\u003c/font\u003e\n    \u003c/th\u003e\n  \u003c/tr\u003e\n\n\n  \u003ctr\u003e\n    \u003cth\u003e\u003cfont point-size=10\u003eGeneral Description\u003c/font\u003e\u003c/th\u003e\n    \u003cth\u003e\u003cfont point-size=10\u003eName\u003c/font\u003e\u003c/th\u003e\n    \u003cth\u003e\u003cfont point-size=10\u003eType\u003c/font\u003e\u003c/th\u003e\n  \u003c/tr\u003e\n\n  \u003ctr\u003e\n    \u003ctd\u003e\u003cfont point-size=10\u003eSilent on Errors\u003c/font\u003e\n      \u003ca href=\"javascript:displayMsg('\u003cb\u003e\u003cu\u003e\u003ccenter\u003eSilent on Errors\n        Option\u003c/center\u003e\u003c/u\u003e\u003c/b\u003e\u003cbr\u003e\n        Normal Scheduler operation inserts an ERROR marker in the result\n        when an error occurs during the processing of\n        a job.  The line looks similar to the following:\u003cbr\u003e\u003cbr\u003e\n        [23412]: *** ERROR *** ERROR *** ERROR ***\u003cbr\u003e\u003cbr\u003e\n        The error line denotes the item number that caused the error\n        and is a placeholder for the results.\u003cbr\u003e\u003cbr\u003e\n        By selecting the \u003ci\u003eSilent on Errors\u003c/i\u003e option, you force \n        the Scheduler to \u003cb\u003e\u003cu\u003eNOT\u003c/u\u003e\u003c/b\u003e print this placeholder in \n        the results.');\"\u003e\n       \u003cimg border=0 align=ABSMIDDLE src=\"./doc/quest.gif\" \n       width=14 height=14\n       alt=\"Question Mark Symbol: Help about Silent on Errors\"\n       title=\"Question Mark Symbol: Help about Silent on Errors\"\u003e\u003c/a\u003e\n       \u003c/td\u003e\n       \u003ctd\u003e\u003cfont point-size=10\u003eESilent\u003c/font\u003e\u003c/td\u003e\n       \u003ctd\u003e\u003cfont point-size=10\u003eBoolean\u003c/font\u003e\u003c/td\u003e\n      \u003c/tr\u003e\n\n  \u003ctr\u003e\n    \u003ctd\u003e\u003cfont point-size=10\u003eSingle Line Delimited Input\u003c/font\u003e\n       \u0026nbsp;\n       \u003ca href=\"javascript:displayMsg('\u003cb\u003e\u003cu\u003e\u003ccenter\u003eSingle Line Delimited\n        Input\u003c/center\u003e\u003c/u\u003e\u003c/b\u003e\u003cbr\u003e\n        Normal Scheduler operation assumes that each input element\n        (free text or MEDLINE citation) is separated from the next\n        element by a blank line.\u003cbr\u003e\u003cbr\u003e\n        By selecting the \u003ci\u003eSingle Line Delimited Input\u003c/i\u003e option, \n        you are telling the Scheduler to treat each line of the input\n        file as a separate input item and to ignore blank lines in\n        the file.\u003cbr\u003e\u003cbr\u003eFor Example,\u003cbr\u003e\u003cbr\u003eLine one to process\u003cbr\u003eLine two to\n        process');\"\u003e\n        \u003cimg border=0 align=ABSMIDDLE src=\"./doc/quest.gif\" \n        width=14 height=14\n       alt=\"Question Mark Symbol: Help about Single Line Delimited Input\"\n       title=\"Question Mark Symbol: Help about Single Line Delimited Input\"\u003e\u003c/a\u003e\n       \u003c/td\u003e\n       \u003ctd\u003e\u003cfont point-size=10\u003eSingLine\u003c/font\u003e\u003c/td\u003e\n       \u003ctd\u003e\u003cfont point-size=10\u003eBoolean\u003c/font\u003e\u003c/td\u003e\n      \u003c/tr\u003e\n\n  \u003ctr\u003e\n    \u003ctd\u003e\u003cfont point-size=10\u003eSingle Line Delimited Input w/ID\u003c/font\u003e\n      \u003ca href=\"javascript:displayMsg('\u003cb\u003e\u003cu\u003e\u003ccenter\u003eSingle Line Delimited\n        Input w/ ID\u003c/center\u003e\u003c/u\u003e\u003c/b\u003e\u003cbr\u003e\n        Normal Scheduler operation assumes that each input element\n        (free text or MEDLINE citation) is separated from the next\n        element by a blank line.\u003cbr\u003e\u003cbr\u003e\n        By selecting the \u003ci\u003eSingle Line Delimited Input w/ ID\u003c/i\u003e option, \n        you are telling the Scheduler to treat each line of the input\n        file as a separate input item, identify the first field of each line\n        as an identification marker, and to ignore blank lines in\n        the file.\u003cbr\u003e\u003cbr\u003eFor Example,\u003cbr\u003e\u003cbr\u003e00000001|Line one to process\u003cbr\u003e\n        00000002|Line two to process');\"\u003e\n        \u003cimg border=0 align=ABSMIDDLE src=\"./doc/quest.gif\" \n        width=14 height=14\n       alt=\"Question Mark Symbol: Help about Single Line Delimited Input w/ ID\"\n       title=\"Question Mark Symbol: Help about Single Line Delimited Input w/ ID\"\u003e\u003c/a\u003e\n    \u003c/td\u003e\n    \u003ctd\u003e\u003cfont point-size=10\u003eSingLinePMID\u003c/font\u003e\u003c/td\u003e\n    \u003ctd\u003e\u003cfont point-size=10\u003eBoolean\u003c/font\u003e\u003c/td\u003e\n  \u003c/tr\u003e\n\n  \u003ctr\u003e\n    \u003ctd\u003e\u003cfont point-size=10\u003eRequested Run Priority Level\u003c/font\u003e\n      \u003ca href=\"javascript:displayMsg('\u003cb\u003e\u003cu\u003e\u003ccenter\u003eRequested Run Priority\u003c/center\u003e\u003c/u\u003e\u003c/b\u003e\u003cbr\u003e0 - Normal Priority\u003cbr\u003e1 - Medium Priority\u003cbr\u003e\n        2 - High Priority\u003cbr\u003e\u003cbr\u003e\n        Users will normally run with Normal priority since only users with\n        specific authorization are allowed to specify either of the higher\n        priorities.  Medium priority provides the job with roughly 10 times\n        the processing time of any Normal priority jobs in the queue.  High\n        priority means that the job will take over the entire queue until\n        it has completed processing.');\"\u003e\n        \u003cimg border=0 align=ABSMIDDLE src=\"./doc/quest.gif\" \n        width=14 height=14\n       alt=\"Question Mark Symbol: Help about Requested Run Priority Levels\"\n       title=\"Question Mark Symbol: Help about Requested Run Priority Levels\"\u003e\u003c/a\u003e\n    \u003c/td\u003e\n    \u003ctd\u003e\u003cfont point-size=10\u003eRPriority\u003c/font\u003e\u003c/td\u003e\n    \u003ctd\u003e\u003cfont point-size=10\u003eString\u003c/font\u003e\u003c/td\u003e\n  \u003c/tr\u003e\n\n  \u003ctr\u003e\n    \u003ctd\u003e\u003cfont point-size=10\u003eNo Completion Email\u003c/font\u003e\n      \u003ca href=\"javascript:displayMsg('\u003cb\u003e\u003cu\u003e\u003ccenter\u003eNo Completion Email\u003c/center\u003e\u003c/u\u003e\u003c/b\u003e\u003cbr\u003eNormal behavior is for the Scheduler to email\n        the user whenever a job finishes.  This option tells the Scheduler\n        to not do this.');\"\u003e\n        \u003cimg border=0 align=ABSMIDDLE src=\"./doc/quest.gif\" \n        width=14 height=14\n       alt=\"Question Mark Symbol: Help about the No Completion Email option\"\n       title=\"Question Mark Symbol: Help about the No Completion Email option\"\u003e\u003c/a\u003e\n    \u003c/td\u003e\n    \u003ctd\u003e\u003cfont point-size=10\u003eSilentEmail\u003c/font\u003e\u003c/td\u003e\n     \u003ctd\u003e\u003cfont point-size=10\u003eBoolean\u003c/font\u003e\u003c/td\u003e\n  \u003c/tr\u003e\n\u003c/table\u003e\n\n\u003cul type=square\u003e\n  \u003cli\u003eYou \"should\" catch \"RuntimeException\" exceptions in your program\n      since this is what the SKR Web API throws internally when it encounters\n      an error.  See example below for try/catch sample.\n  \u003cbr\u003e\u003cbr\u003e\n\n  \u003cli\u003eYou must specify an Email Address.  This is used for logging as well\n      as notification when Batch jobs finish, or if there are problems with\n      a job.\n  \u003cbr\u003e\u003cbr\u003e\n\n  \u003cli\u003eYou must specify the UpLoad_File field.\n  \u003cbr\u003e\u003cbr\u003e\n\n  \u003cli\u003eValid Batch job priorities are \"0\", \"1\", or \"2\".  Where \"0\" represents\n      Normal priority, \"1\" represents Medium, and \"2\" represents High\n      priority. Medium and High priorities are reserved and you must have the\n      proper permissions to use them.\n  \u003cbr\u003e\u003cbr\u003e\n\n  \u003cli\u003eExplanation of setting up a basic SKR Web API program. The following\n      description details the steps to setting up a simple SKR Web API job to\n      send a small file to the Scheduler and receive a result back.\n      See the GenericBatch.java program file in the examples directory for the\n      full program.\u003cbr\u003e\u003cbr\u003e\n      \u003col type=1\u003e\n       \u003cli\u003eThe first thing you need to do is create a job object for the type\n           of program you want to run.\u003cbr\u003e\u003cbr\u003e\n           \u003cdiv style=\"background-color:white; border:2px solid #ADADAD\"\u003e\n           \u003ccode\u003eGenericObject myGenericObj = new GenericObject();\u003c/code\u003e\n           \u003c/div\u003e\u003cbr\u003e\n           This creates a Generic Batch job object with Validation.\n           \u003cbr\u003e\u003cbr\u003e\n\n        \u003cli\u003eThe next thing to do is setup any of the required or batch specific\n            fields.\u003cbr\u003e\u003cbr\u003e\n            \u003cdiv style=\"background-color:white; border:2px solid #ADADAD\"\u003e\n            \u003ccode\u003e\n             myGenericObj.setField(\"Email_Address\", \"yourEmailAddress\");\u003cbr\u003e\n             myGenericObj.setField(\"SilentEmail\", true);\u003cbr\u003e\n             myGenericObj.setField(\"Batch_Command\", \"MTI -opt1L_DCMS -E\");\u003cbr\u003e\n             myGenericObj.setField(\"UpLoad_File\", \"./sample.txt\");\n            \u003c/code\u003e\n            \u003c/div\u003e\u003cbr\u003e\n            This tells the job object what your email address is (required),\n            tells the Scheduler that we don't want to be notified after the\n            job completes (SilentEmail), we want to run the MTI command with\n            \"-opt1L_DCMS -E\" as options, and that we want to use the local\n            file \"sample.txt\" as the input data to be processed (UpLoad_File).\n           \u003cbr\u003e\u003cbr\u003e\n\n        \u003cli\u003eNow we are finally ready to actually submit the Batch job and\n            receive our results back.  We surround this submission code with\n            a try/catch for any \"RuntimeException\" exceptions that might be\n            thrown back to us from the SKR Web API program.\n            \u003cbr\u003e\u003cbr\u003e\n            \u003cdiv style=\"background-color:white; border:2px solid #ADADAD\"\u003e\n            \u003ccode\u003e\n            try\u003cbr\u003e\n            {\u003cbr\u003e\n            \u0026nbsp;\u0026nbsp;\u0026nbsp;String results = myGenericObj.handleSubmission();\u003cbr\u003e\n            \u0026nbsp;\u0026nbsp;\u0026nbsp;System.out.print(results);\u003cbr\u003e\n\n            } catch (RuntimeException ex) {\u003cbr\u003e\n            \u0026nbsp;\u0026nbsp;\u0026nbsp;System.err.println(\"\");\u003cbr\u003e\n            \u0026nbsp;\u0026nbsp;\u0026nbsp;System.err.print(\"An ERROR has occurred while processing your\");\u003cbr\u003e\n            \u0026nbsp;\u0026nbsp;\u0026nbsp;System.err.println(\" request, please review any\");\u003cbr\u003e\n            \u0026nbsp;\u0026nbsp;\u0026nbsp;System.err.print(\"lines beginning with \\\"Error:\\\" above and the\");\u003cbr\u003e\n            \u0026nbsp;\u0026nbsp;\u0026nbsp;System.err.println(\" trace below for indications of\");\u003cbr\u003e\n            \u0026nbsp;\u0026nbsp;\u0026nbsp;System.err.println(\"what may have gone wrong.\");\u003cbr\u003e\n            \u0026nbsp;\u0026nbsp;\u0026nbsp;System.err.println(\"\");\u003cbr\u003e\n            \u0026nbsp;\u0026nbsp;\u0026nbsp;System.err.println(\"Trace:\");\u003cbr\u003e\n            \u0026nbsp;\u0026nbsp;\u0026nbsp;ex.printStackTrace();\u003cbr\u003e\n            } // catch\u003cbr\u003e\n            \u003c/code\u003e\n            \u003c/div\u003e\n            \u003cbr\u003e\n            This calls the job object routine that takes care of the job from\n            submission, monitoring, cleaning up, and returning a result.\n      \u003c/ol\u003e\n\u003c/ul\u003e\n\u003c/body\u003e\n\n\u003c/html\u003e\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fseandavi%2Fmap_to_mesh_with_mti","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fseandavi%2Fmap_to_mesh_with_mti","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fseandavi%2Fmap_to_mesh_with_mti/lists"}