Index

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A

add(String, String) - Method in class org.eclipse.pass.loader.nihms.CompletedPublicationsCache

Add pmid/awardNumber combination to set

C

calcRepoCopyStatus(NihmsPublication, CopyStatus) - Static method in class org.eclipse.pass.loader.nihms.NihmsPublicationToSubmission

Determines a new deposit status based on various dates populated in the NIHMS publication If the status registered in PASS is further along than NIHMS thinks we are, roll back to what NIHMS says and log the fact as a warning.

clear() - Method in class org.eclipse.pass.loader.nihms.CompletedPublicationsCache

Empty cache

CompletedPublicationsCache - Class in org.eclipse.pass.loader.nihms

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.

contains(String, String) - Method in class org.eclipse.pass.loader.nihms.CompletedPublicationsCache

Check if it contains pmid/award number combination

D

doUpdate() - Method in class org.eclipse.pass.loader.nihms.SubmissionDTO

doUpdatePublication() - Method in class org.eclipse.pass.loader.nihms.SubmissionDTO

doUpdateRepositoryCopy() - Method in class org.eclipse.pass.loader.nihms.SubmissionDTO

doUpdateSubmission() - Method in class org.eclipse.pass.loader.nihms.SubmissionDTO

G

getGrantId() - Method in class org.eclipse.pass.loader.nihms.SubmissionDTO

getInstance() - Static method in class org.eclipse.pass.loader.nihms.CompletedPublicationsCache

Get singleton instance of cache

getPublication() - Method in class org.eclipse.pass.loader.nihms.SubmissionDTO

getRepositoryCopy() - Method in class org.eclipse.pass.loader.nihms.SubmissionDTO

getSubmission() - Method in class org.eclipse.pass.loader.nihms.SubmissionDTO

H

help - Variable in class org.eclipse.pass.loader.nihms.NihmsTransformLoadCLI

Request for help/usage documentation

L

load(SubmissionDTO) - Method in class org.eclipse.pass.loader.nihms.SubmissionLoader

Load the data in the NihmsSubmissionDTO to the database.

loadFromFile() - Method in class org.eclipse.pass.loader.nihms.CompletedPublicationsCache

Load contents of cache file into memory from file

M

main(String[]) - Static method in class org.eclipse.pass.loader.nihms.NihmsTransformLoadCLI

This is the main entry point for the NihmsTransformLoadCLI application.

N

NihmsCsvProcessor - Class in org.eclipse.pass.loader.nihms

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.

NihmsCsvProcessor(Path, NihmsStatus) - Constructor for class org.eclipse.pass.loader.nihms.NihmsCsvProcessor

Set the file path to the NIHMS CSV to read in and the status of the NIHMS deposit

NihmsPublicationToSubmission - Class in org.eclipse.pass.loader.nihms

Does the heavy lifting of data transform work, converting a NihmsPublication to a NihmsSubmissionDTO (submission + deposits) for loading to the database

NihmsPublicationToSubmission() - Constructor for class org.eclipse.pass.loader.nihms.NihmsPublicationToSubmission

Constructor uses defaults for client service and pmid lookup

NihmsPublicationToSubmission(NihmsPassClientService, PmidLookup) - Constructor for class org.eclipse.pass.loader.nihms.NihmsPublicationToSubmission

Constructor initiates with the required NIHMS Client Service and PMID lookup Useful to pass in an existing clientService to reuse cache

nihmsStatus(Path) - Static method in class org.eclipse.pass.loader.nihms.NihmsCsvProcessor

Cycles through Submission status types, and matches it to the filepath to determine the status of the rows in the CSV file.

NihmsTransformLoadApp - Class in org.eclipse.pass.loader.nihms

Coordinates loading of csv files and passing into load and transform routine

NihmsTransformLoadApp(Set<NihmsStatus>) - Constructor for class org.eclipse.pass.loader.nihms.NihmsTransformLoadApp

Constructor for the NihmsTransformLoadApp

NihmsTransformLoadCLI - Class in org.eclipse.pass.loader.nihms

NIHMS Submission Loader CLI

NihmsTransformLoadCLI() - Constructor for class org.eclipse.pass.loader.nihms.NihmsTransformLoadCLI

NihmsTransformLoadService - Class in org.eclipse.pass.loader.nihms

Service that takes a filepath, gets the csvs there, and transforms/loads the data according to a list of statuses to be processed.

NihmsTransformLoadService() - Constructor for class org.eclipse.pass.loader.nihms.NihmsTransformLoadService

Default constructor for NihmsTransformLoadService

NihmsTransformLoadService(NihmsPassClientService, PmidLookup, SubmissionStatusService) - Constructor for class org.eclipse.pass.loader.nihms.NihmsTransformLoadService

Option to inject dependencies

O

org.eclipse.pass.loader.nihms - package org.eclipse.pass.loader.nihms

P

processCsv(Consumer<NihmsPublication>) - Method in class org.eclipse.pass.loader.nihms.NihmsCsvProcessor

Cycles through the CSV that is loaded, converting to a NihmsPublication, and then using the consumer provided to process the record

R

run() - Method in class org.eclipse.pass.loader.nihms.NihmsTransformLoadApp

Run the transform and load process

S

setGrantId(String) - Method in class org.eclipse.pass.loader.nihms.SubmissionDTO

setPublication(Publication) - Method in class org.eclipse.pass.loader.nihms.SubmissionDTO

setRepositoryCopy(RepositoryCopy) - Method in class org.eclipse.pass.loader.nihms.SubmissionDTO

setSubmission(Submission) - Method in class org.eclipse.pass.loader.nihms.SubmissionDTO

setUpdatePublication(boolean) - Method in class org.eclipse.pass.loader.nihms.SubmissionDTO

setUpdateRepositoryCopy(boolean) - Method in class org.eclipse.pass.loader.nihms.SubmissionDTO

setUpdateSubmission(boolean) - Method in class org.eclipse.pass.loader.nihms.SubmissionDTO

size() - Method in class org.eclipse.pass.loader.nihms.CompletedPublicationsCache

Get number of items in cache

SubmissionDTO - Class in org.eclipse.pass.loader.nihms

Data transfer object to hold the various components of a NIHMS Submission up to the point of update or create.

SubmissionDTO() - Constructor for class org.eclipse.pass.loader.nihms.SubmissionDTO

SubmissionLoader - Class in org.eclipse.pass.loader.nihms

Creates / updates the Submission, RepositoryCopy, Publication, and Deposit in the database as needed

SubmissionLoader() - Constructor for class org.eclipse.pass.loader.nihms.SubmissionLoader

Initiates with default client service

SubmissionLoader(NihmsPassClientService, SubmissionStatusService) - Constructor for class org.eclipse.pass.loader.nihms.SubmissionLoader

Supports initiation with specific client service

T

transform(NihmsPublication) - Method in class org.eclipse.pass.loader.nihms.NihmsPublicationToSubmission

Does the heavy lifting of converting a NihmsPublication record into the NihmsSubmissionDTO that is needed for the NihmsLoader

transformAndLoadFiles(Set<NihmsStatus>) - Method in class org.eclipse.pass.loader.nihms.NihmsTransformLoadService

Goes through list of files in directory specified and processes those that have a NihmsStatus that matches a row in statusesToProcess.

transformAndLoadNihmsPub(NihmsPublication) - Method in class org.eclipse.pass.loader.nihms.NihmsTransformLoadService

Takes pub record from CSV loader, transforms it then passes transformed record to the loader.

A C D G H L M N O P R S T
All Classes and Interfaces|All Packages