Journal Loader
Last updated
Last updated
The Journal Loader is responsible for pulling data from (PMC) and the , and making the appropriate updates to PASS.
The Journal Loader parses the PMC type A journal .csv file, and/or the .txt file, and syncs with the repository by taking the following actions:
Adds journals if they do not already exist
Updates PMC method A participation if it differs from the corresponding resource in the repository.
Development of the Journal Loader
Programming in Java
Basic understanding of the NLM journal loader
Running the Journal Loader
CLI commands
Using Java system properties to launch the journal loader. Note: Replace the version number in the jar name with the specific version you are using.
The following may be provided as system properties on the command line -Dprop-value.
pass.core.url The base URL for the pass-core REST API such as http://localhost:8080
pass.core.user The pass-core backend user.
pass.core.password The pass-core backend user password.
dryRun Do not add or update resources in the repository, just give statistics of resources that would be added or updated
LOG.* Adjust the logging level of a particular component, e.g. LOG.org.eclipse.pass=WARN
Initialization:
The Main class initializes the application and calls the BatchJournalFinder and LoaderEngine to start processing.
File Processing:
BatchJournalFinder processes each file using the appropriate reader (MedlineReader, NihTypeAReader).
The load method in BatchJournalFinder initiates the process, collects files to be processed.
Data Loading:
Processed journal data is passed to LoaderEngine to be loaded into the target system.
If a journal is not found then a new one will be created, otherwise it will update the journal.
The following resources are the sources of the journal data that is loaded into pass:
pmc URL of the PMC "type A" journal .csv file, for example:
medline URL of the Medline journal file, for example:
Journal loader is simple to configure. It will run on any system that can run Java applications and does not require external account setup. The two sources of data PMC Type A Journals and MEDLINE, do not require accounts to access the data. Similar to the and , the Journal Loader is run using .