All Classes and Interfaces
Classes
Class
Description
This controls a simple local text file containing a list of compliant "pmid|grantNumber" combinations
that are considered DONE and therefore require no re-processing.
Utility class to support directory/filepath processing
Caches awardNumber and grantId combination for easy lookup
NIHMS CSV Reader expects a Submissions CSV from the NIHMS site and will read it into a List,
mapping the relevant fields to the NihmsPublication model.
Caches submission and depositId combination for easy lookup
Note: cache only contains deposits for nihms
NIHMS PASS client service deals with interactions with the data via the PASS client and controls local data caches
Does the heavy lifting of data transform work, converting a NihmsPublication to a
NihmsSubmissionDTO (submission + deposits) for loading to the database
Caches publicationId and repositoryCopyId mapping for easy lookup
Important: includes RepositoryCopies for NIHMS records only
NIHMS Submission Loader CLI
Service that takes a filepath, gets the csvs there, and transforms/loads the data according to a
list of statuses to be processed.
Service to retrieve a PMID records from Entrez.
General small utilities to tidy up data processing code.
Caches pmid and publicationId combination for easy lookup
Class is instantiated by passing in a JSONObject from Entrez representing a PubMed
article record.
Data transfer object to hold the various components of a NIHMS Submission up to the point of
update or create.
Creates / updates the Submission, RepositoryCopy, Publication, and Deposit in the database as needed
Caches userIdPubId as concatenated string with the list of submissions relevant to that combination to ensure
all relevant submissions are retrieved regardless of whether index is up to date with most recent etl records