The SKR Web API has been designed to allow you to interact with our web-based
Scheduler using our Batch and Interactive facilities. Interactive access is currently only
available for the MetaMap and SemRep programs.
There 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
specify the username and password within the program to eliminate the need for
prompting when running.
For a list of the available options, please select the appropriate program name:
MetaMap and
MTI.
GenericBatch.java
Example program for submitting a new Generic Batch with Validation job
("GenericObject(true)" turns on validation) request to the Scheduler to
run. You will be prompted for your username and password and if they
are alright, the job is submitted to the Scheduler and the results are
returned in the String "results" below.
This example shows how to setup a basic Generic Batch with Validation job
with a small file (sample.txt) with ASCII MEDLINE formatted citations as
input data. You must set the Email_Address variable and use the
UpLoad_File
to specify the data to be processed. This example also shows the user
setting the SilentEmail option which tells the Scheduler to NOT send
email upon completing the job.
This example is set to run the MTI (Medical Text Indexer) program using
the -opt1L_DCMS and -E options. You can also setup any environment
variables
that will be needed by the program by setting the Batch_Env field.
NOTE:
The "-E" option/argument is very important and should be included
with whatever program (MetaMap, SemRep, MTI) you decided to run!
The reason is that this
version of the Generic Batch does validation and the -E option tells
the various programs to include a marker denoting when a successful
result has been found.
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GenericBatchNew.java
Same as GenericBatch.java above, except you can enter any of the
options and the inputfile on the command line. The usage of the
program and available options are listed below:
usage: GenericBatchNew [options] inputFilename
allowed options:
--email <address> : set email address. (required option)
--command <name> : batch command: metamap, semrep, etc. (default: MTI -opt1_DCMS -E)
--note <notes> : batch notes
--silent : don't send email after job completes.
--silent-errors : Silent on Errors
--singleLineInput : Single Line Delimited Input
--singleLinePMID : Single Line Delimited Input w/ID
--priority : request a Run Priority Level: 0, 1, or 2
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MMInteractive.java
This example shows how to setup a basic Interactive MetaMap request.
This runs the latest version of MetaMap with 1011 (2010AB) version
of the UMLS Metathesaurus ("KSOURCE", "1011"), with "ignore_word_order" (-i)
and "all_derivational_variants" (D) set as arguments to MetaMap. The
default "Human Readable" output will be produced.
NOTE:
The "-E" option/argument is NOT required for Interactive use.
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SRInteractive.java
This example shows how to setup a basic Interactive SemRep request.
This runs the latest version of SemRep with Full Fielded Output (-D).
NOTE:
The "-E" option/argument is NOT required for Interactive use.
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| GenericBatchUser.java
This example is the same as "GenericBatchNew.java" above, except that the
username and password are set in the program so that the user is not
prompted when the program runs. Please Note: Although we understand
the operational need for being able to specify the username and password
within a program, you must also be aware of the security risks when using
this setup. Please take care to secure the software you create using this
option.
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| MMInteractiveUser.java
This example is the same as "MMInteractive.java" above, except that the
username and password are set in the program so that the user is not
prompted when the program runs. Please Note: Although we understand
the operational need for being able to specify the username and password
within a program, you must also be aware of the security risks when using
this setup. Please take care to secure the software you create using this
option.
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