CPGP Peregrine Get Abstracts Create tables
Created: 2014-05-27 11:29:40
Last updated: 2014-06-30 09:15:55
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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 (1)
Inputs (2)
| Name |
Description |
| Ontology_input |
A Skos formated dictionary/thesaurus of predefined concepts.
|
| 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 (3)
| Name |
Type |
Description |
| Peregrine indexer |
workflow |
The nested workflow Peregrine Indexer uses a java peregrine skos cli.jar file to index the occurence of concepts in documents.
The Peregrine indexer program can be downloaded from trac.nbic.nl/biosemantics/downloads.
Install LVG2013Lite. See: https://trac.nbic.nl/biosemantics/wiki/Peregrine%20SKOS%20CLI
Copy properties file from production.properties which can be downloaded from: 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
Change the normalizer.lvg.properties and normalizer.lvg.binaryCache properties to point to the LVG installation path.
normalizer.lvg.properties =/home/path/to/lvg2013lite/data/config/config/lvg.properties normalizer.lvg.binaryCahce=/home/path/to/lvg2013lite/standartNormCache2013.bin
Have MySQL installed with a database called mydb or please create one.
Have mysql-connector-java-5.1.28-bin.jar or better placed in the local JAR files.
|
| Create Tables |
workflow |
This nested workflows create the necessary tables for inserting the generated values. The following tables are created:
- Co-occurence table
This table will consist out of
- Occurence table
- Uncertainty coefficient table
- Inner product table
- Big table |
| Get_abstracts |
workflow |
A nested workflow to retrieve abstracts from a sql table. |
Beanshells (9)
| Name |
Description |
Inputs |
Outputs |
| Beanshell_SQL_generate_table_UC |
A Beanshell script that generates a table for the uncertainty coefficient values. |
time_stamp
|
output
|
| Beanshell_SQL_CREATE_last_big_table |
|
timestamp
|
out1
|
| Beanshell_SQL_query_generator_Concept_Doc_occurence |
A Beanshell script that generates a Sql statement to INSERT
the concept URI and document URI in the table named after the timestamp/tablename the workflow started.
It uses a database called mydb. If there is not a database/schema named mydb, please create one. |
table_name
concept_occurence_document
|
out1
|
| Beanshell_extract_uri_doc_and_abstract |
A Beanshell script which loops through the input to seperate the Document URIs and Abstract URIs. |
Input
|
doc_uri
abstracts
|
| Beanshell_remove_dot_and_put_correct_doc_uri_in_con_occ_doc |
A Beanshell script that replaces the temp created Taverna file with the correct Document URI. |
concept_occurence_document
doc_uri
|
out1
|
| Beanshell_generate_SQL_occurence_concept_doc_table |
A Beanshell script which generates a sql statement to CREATE a TABLE.
TABLE name is the input of the timestamp.
The table consists out of 4 columns: concept_occ_doc_id, concept_uri, occurence_uri and doc_uri.
Where as concept_occ_doc_id is the PRIMARY KEY and AUTOINCREMENTED.
Every other column has a VARCHAR(200)
|
timeStamp
|
Table_sql
|
| Beanshell_get_timestamp |
A Beanshell script which retreives the time the program started.
As in year, month, day, hour, minutes and seconds in military time. |
|
timeStamp
|
| Beanshell_generate_SQL_table_inner_product |
|
timestamp
|
out1
|
| Beanshell_SQL_create_table_co_occurence |
|
timestamp
|
out1
|
Outputs (2)
| Name |
Description |
| end |
|
| indexer_output |
|
Datalinks (8)
| Source |
Sink |
| Create Tables:timeStamp |
Peregrine indexer:table_name |
| Ontology_input |
Peregrine indexer:ontology |
| Get_abstracts:db_results |
Peregrine indexer:Input |
| db_properties |
Peregrine indexer:propertyString |
| db_properties |
Create Tables:db_properties |
| db_properties |
Get_abstracts:propertyString |
| Peregrine indexer:output |
end |
| Peregrine indexer:indexer_output |
indexer_output |
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