PubMed Search and Solr storage

Created: 2013-07-25 14:38:20 Last updated: 2013-08-26 14:13:59

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Based on the work of Fisher: This workflow takes in a search term, are passed to the eSearch function and searched for in PubMed. I extended by removing outputs and text extraction and addded an automatic Solr storage process using a post.jar, specified by the user. Before running this workflow, make sure that a solr server is up and running and the variable attached to the SolrImport process contains the correct path.

Dependencies:

- Solr

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Workflow Components

Authors (1)

Titles (1)

Descriptions (1)

Dependencies (0)

Inputs (4)

Name	Description
search_term	I want to find all abstracts that contain the words:
end_date	The found articles should be older then ____:
start_date	The found articles should not be older then ____.
maximum_articles	I want a maximum of ____ articles. 10 is set as default for testing. More then 100 is good for a normal run.

Processors (8)

Name	Type	Description
pubmed_database	stringconstant	Which database is being used. Value pubmed
extractPMID	localworker	This process extracts the pubmed IDS based on the eSearch run. Script import org.dom4j.Document; import org.dom4j.Node; import org.dom4j.io.SAXReader; SAXReader reader = new SAXReader(false); reader.setIncludeInternalDTDDeclarations(false); reader.setIncludeExternalDTDDeclarations(false); Document document = reader.read(new StringReader(xmltext)); List nodelist = document.selectNodes(xpath); // Process the elements in the nodelist ArrayList outputList = new ArrayList(); ArrayList outputXmlList = new ArrayList(); String val = null; String xmlVal = null; for (Iterator iter = nodelist.iterator(); iter.hasNext();) { Node element = (Node) iter.next(); xmlVal = element.asXML(); val = element.getStringValue(); if (val != null && !val.equals("")) { outputList.add(val); outputXmlList.add(xmlVal); } } List nodelist=outputList; List nodelistAsXML=outputXmlList;
xpath	stringconstant	Value /[local-name(.)='eSearchResult']/[local-name(.)='IdList']/*[local-name(.)='Id']
run_eSearch	wsdl	Wsdl http://eutils.ncbi.nlm.nih.gov/entrez/eutils/soap/eutils.wsdl Wsdl Operation run_eSearch
parametersXML_eFecth	xmlsplitter
Retrive_abstracts	workflow	This nested workflow was part of Fishers workflow, but has been decreased in size. This workflow is about storing the xmll files from eFetch and doesn't require to extract the plain text abstract like the original workflow did.
SolrImport	externaltool	SolrImport takes the path of the txt file and stores this in a Solr database. Make sure that the Solr database is running and that the correct path is inside the variable. If Solr is running locally you can check if the files have been stored by browsing to the following location:http://localhost:8983/solr/#/ Solr can be downloaded at: http://lucene.apache.org/solr/
pathToPostJar	stringconstant	This is the path to the Post.jar that Solr uses to import it's documents. Value /run/media/sander/Second Space/Downloads/solr-4.3.1/example/exampledocs/post.jar

Beanshells (0)

Outputs (3)

Name	Description
AbstractXML	This is the XML of the extracted abstracts that will be stored in Solr. The user can use this to make sure the correct content is being stored.
SolrImport_STDERR	This is the standerdized error from Solr. If there were any errors while running Solr then the values will turn red. Red is generally considered to be a bad colour.
SolrImport_STDOUT	This is the standerdized output from Solr.

Datalinks (14)

Source	Sink
xpath:value	extractPMID:xpath
run_eSearch:parameters	extractPMID:xml-text
parametersXML_eFecth:output	run_eSearch:parameters
pubmed_database:value	parametersXML_eFecth:db
search_term	parametersXML_eFecth:term
end_date	parametersXML_eFecth:maxdate
start_date	parametersXML_eFecth:mindate
maximum_articles	parametersXML_eFecth:RetMax
extractPMID:nodelist	Retrive_abstracts:pubmed_ids
Retrive_abstracts:AbstractXML	SolrImport:inputFile
pathToPostJar:value	SolrImport:pathToPostJar
Retrive_abstracts:AbstractXML	AbstractXML
SolrImport:STDERR	SolrImport_STDERR
SolrImport:STDOUT	SolrImport_STDOUT

Coordinations (0)

Information Workflow Type

Taverna 2

Information Uploader

Sander van boom

Information License

All versions of this Workflow are licensed under:

Information Version 1 (earliest) (of 5)

Information Credits (1)

(People/Groups)

Sander van boom

Information Attributions (1)

(Workflows/Files)

PubMed Search

Information Tags (6)

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Information Shared with Groups (1)

Concept profile generation pipeline

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Information Favourited By (1)

Sander van boom

Information Statistics

4130 viewings

1414 downloads

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Citations (0)

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Version History

In chronological order:

PubMed Search and Solr storage

Created by Sander van boom on Thursday 25 July 2013 14:38:20 (UTC)
PubMed Search and Solr storage

Created by Sander van boom on Thursday 01 August 2013 15:26:25 (UTC)

Revision comment:

Added an automatic update check (to prevent downloading the same file twice) and basic provenance to the outputfile.
PubMed Search and Solr storage

Created by Sander van boom on Tuesday 06 August 2013 11:25:43 (UTC)

Revision comment:

Updated the workflow with more provenance data and fixed a couple of bugs of the workflow.
It should be working properly (famous last words) and until there are any bugreports or requests, this will be the final version.
The only planned addition will be additonal documentation.
PubMed Search and Solr storage

Created by Sander van boom on Wednesday 07 August 2013 12:59:21 (UTC)

Revision comment:

Added an extra input port that gives the user the posibility to change their working directory.
PubMed Search and Solr storage

Created by Sander van boom on Friday 09 August 2013 11:57:11 (UTC)

Revision comment:

There was a bug in previous versions that didn't store the Solr data correctly. Creating a nested workflow that extracts and store the files and imports them in Solr was a simple update that solved the problem. Currently only the title and the ID of the abstract are being stored. This is because the example schema of Solr allows these tags. If you want more information being stored then you should add extra xpaths and change your basic Solr Schema. Later on I might add more information or provide additional documentation on how to do this yourself.

Reviews (1)

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Eelke van der Horst

Title: Thanks!

Rating: 4 out of 5

Created: 2013-08-26 14:13:59 | Updated: 2013-08-26 14:13:59

A nice workflow for gathering our in-house document corpus and metadata.

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PubMed Search and Solr storage

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