CPGP Summary table
Created: 2014-05-27 11:50:57
Last updated: 2014-06-30 09:25:29
Part of the CPGP to make a summary of all the mysql tables and inserted value for better overview
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Authors (1)
Titles (1)
| Concept Profile Generation Pipeline |
Descriptions (1)
| Requirements:
Have MySQL installed with a database called mydb or please create one.
Have a mysql connector file. This can be downloaded from mysql.com.
Rename the downloaded file to mysql-connector-java.jar and place it in the the local lib file of Taverna as written on the dependencies tab.
Choose this dependency by rightclicking a beanshell script and selecting it for the whole workflow as system classloader.
Download the Peregrine SKOS CLI from: https://trac.nbic.nl/biosemantics/downloads
Install LVG2013Lite. See: https://trac.nbic.nl/biosemantics/wiki/Peregrine%20SKOS%20CLI
Change lvg.properties
LVG_DIR=/home/path/to/lvg2013lite/
This file can be found in:
/home/path/to/lvg2013lite/data/config/lvg.properties
Copy properties file from production.properties which can be found on: https://trac.nbic.nl/biosemantics/wiki/Peregrine%20SKOS%20CLI
Change the normalizer.lvg.properties and normalizer.lvg.binaryCache properties to point to the LVG installation path.
This file can be obtained from https://trac.nbic.nl/biosemantics/wiki/Peregrine%20SKOS%20CLI
Have Peregrine indexer installed locally and give it the correct path in the component named "Indexer_tool". Which can be found in the nested workflow named Peregrine indexer.
If using a Windows machine please install cygwin. Set cygwin in the $PATH of the environment variabale.
Go to taverna File --> preferences --> Tool invocation --> set modify on explicit locations --> edit a default local to Shell: C:\Windows\system32\cmd.exe /c and save that. -->Set Modify on: symbolic locations --> edit --> choose default local and save.
Have JAVA_HOME C:\Program Files\jdk 1.7.0 in environment variabale when using Windows.
The nested workflow Get_abstract uses a sql command to retrieve abstracts which presumes that it uses the mydb database. Please change this when using a other sql database. |
Dependencies (0)
Inputs (1)
| Name |
Description |
| db_properties |
Please load a file in as seen in the example where the user, password, url (which is the database it should use), and driver is stated.
|
Processors (2)
| Name |
Type |
Description |
| Summarize Big Table |
workflow |
A nested workflow to retrieve the calculated co-occurence, occurence, uncertainty coefficient and inner product values. These values are inserted into one table to summarize and quick access. |
| Text_constant |
stringconstant |
Valuealpha |
Beanshells (2)
| Name |
Description |
Inputs |
Outputs |
| Beanshell_SQL_Generate_INSERT_INTO_big_table |
A Beanshell script that generates SQL statements to insert two concepts and their given co-occurence, uncertainty coefficientcy and inner product values into the table. |
timestamp
in1
|
out1
|
| Beanshell_SQL_statement_get_last_table_data_input |
A Beanshell that generates SQL statements to retrieve the inner product of two concept profiles, the co-occurence of the concepts and the uncertainty coefficient. |
timestamp
|
out1
|
Datalinks (3)
| Source |
Sink |
| db_properties |
Summarize Big Table:propertyString |
| Text_constant:value |
Summarize Big Table:timestamp |
| Summarize Big Table:resultList |
end |
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