Index

A C D F G H I L M N O P R S T U
All Classes and Interfaces|All Packages|Constant Field Values

A

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

Add pmid/awardNumber combination to set

addToOrCreateEntry(String, String) - Method in class org.eclipse.pass.loader.nihms.client.cache.UserPubSubmissionsCache

Add an item to an existing Map Entry or create a new one if one does not already exist

AWARD_NUMBER_FLD - Static variable in class org.eclipse.pass.loader.nihms.client.NihmsPassClientService

The field name for the award number

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.client.cache.GrantIdCache

Empty map

clear() - Method in class org.eclipse.pass.loader.nihms.client.cache.NihmsDepositIdCache

Empty map

clear() - Method in class org.eclipse.pass.loader.nihms.client.cache.NihmsRepositoryCopyIdCache

Empty map

clear() - Method in class org.eclipse.pass.loader.nihms.client.cache.PublicationIdCache

Empty map

clear() - Method in class org.eclipse.pass.loader.nihms.client.cache.UserPubSubmissionsCache

Empty map

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

Empty cache

clearCache() - Method in class org.eclipse.pass.loader.nihms.client.NihmsPassClientService

Remove all data from 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.

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

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

Check if it contains pmid/award number combination

createPublication(Publication) - Method in class org.eclipse.pass.loader.nihms.client.NihmsPassClientService

createRepositoryCopy(RepositoryCopy) - Method in class org.eclipse.pass.loader.nihms.client.NihmsPassClientService

Create a new RepositoryCopy in PASS

createSubmission(Submission) - Method in class org.eclipse.pass.loader.nihms.client.NihmsPassClientService

D

DEPOSIT_STATUS_REF_FLD - Static variable in class org.eclipse.pass.loader.nihms.client.NihmsPassClientService

The field name for the status ref of a deposit.

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

doUpdateDeposit() - 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

F

FileUtil - Class in org.eclipse.pass.loader.nihms.util

Utility class to support directory/filepath processing

findJournalByIssn(String) - Method in class org.eclipse.pass.loader.nihms.client.NihmsPassClientService

Look up Journal ID using ISSN

findMostRecentGrantByAwardNumber(String) - Method in class org.eclipse.pass.loader.nihms.client.NihmsPassClientService

Searches for Grant record using awardNumber.

findNihmsDepositbyNihmsId(String) - Method in class org.eclipse.pass.loader.nihms.client.NihmsPassClientService

Searches for a Deposit to NIHMS that matches a NihmsID

findNihmsDepositForSubmission(String) - Method in class org.eclipse.pass.loader.nihms.client.NihmsPassClientService

Searches for a NIHMS Deposit that matches a SubmissionID

findNihmsRepositoryCopyForPubId(String) - Method in class org.eclipse.pass.loader.nihms.client.NihmsPassClientService

Find NIHMS RepositoryCopy record for a publicationId

findNihmsSubmissionsByPublicationId(String) - Method in class org.eclipse.pass.loader.nihms.client.NihmsPassClientService

Find all Submissions with a publication that are associated with the NIHMS repository

findPublicationByDoi(String, String) - Method in class org.eclipse.pass.loader.nihms.client.NihmsPassClientService

Looks up publication using DOI, call should include pmid so that it can check publication cache first, then checks index for DOI

findPublicationByPmid(String) - Method in class org.eclipse.pass.loader.nihms.client.NihmsPassClientService

Looks up publication using PMID, since this is the most reliable field to match.

findSubmissionsByPublicationAndUserId(String, String) - Method in class org.eclipse.pass.loader.nihms.client.NihmsPassClientService

Searches for Submissions matching a specific publication and User Id (Submission.submitter)

formatDate(String, String) - Static method in class org.eclipse.pass.loader.nihms.util.ProcessingUtil

Formats a date to a ZonedDateTime according to pattern provided.

G

get(String) - Method in class org.eclipse.pass.loader.nihms.client.cache.GrantIdCache

Retrieve grantId by awardNumber

get(String) - Method in class org.eclipse.pass.loader.nihms.client.cache.NihmsDepositIdCache

Retrieve depositId by submissionId

get(String) - Method in class org.eclipse.pass.loader.nihms.client.cache.NihmsRepositoryCopyIdCache

Retrieve RepositoryCopyId by publicationId

get(String) - Method in class org.eclipse.pass.loader.nihms.client.cache.PublicationIdCache

Retrieve publicationId by pmid

get(String) - Method in class org.eclipse.pass.loader.nihms.client.cache.UserPubSubmissionsCache

Retrieve submissionIds by userIdPubId

getCsvFilePaths(Path) - Static method in class org.eclipse.pass.loader.nihms.util.FileUtil

Retrieve a list of files in a directory, filter by directory

getCurrentDirectory() - Static method in class org.eclipse.pass.loader.nihms.util.FileUtil

Gets directory that the app was run from

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

getDoi() - Method in class org.eclipse.pass.loader.nihms.entrez.PubMedEntrezRecord

Extract DOI from Entrez JSON as https://doi.org/10....

getEssn() - Method in class org.eclipse.pass.loader.nihms.entrez.PubMedEntrezRecord

Extracts ESSN from Entrez JSON record and returns it

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

getInstance() - Static method in class org.eclipse.pass.loader.nihms.client.cache.GrantIdCache

Get singleton instance of GrantIdCache

getInstance() - Static method in class org.eclipse.pass.loader.nihms.client.cache.NihmsDepositIdCache

Get singleton instance of NihmsDepositIdCache

getInstance() - Static method in class org.eclipse.pass.loader.nihms.client.cache.NihmsRepositoryCopyIdCache

Get singleton instance of NihmsRepositoryCopyIdCache

getInstance() - Static method in class org.eclipse.pass.loader.nihms.client.cache.PublicationIdCache

Get singleton instance of PublicationIdCache

getInstance() - Static method in class org.eclipse.pass.loader.nihms.client.cache.UserPubSubmissionsCache

Get singleton instance of UserPubSubmissionsCache

getIssn() - Method in class org.eclipse.pass.loader.nihms.entrez.PubMedEntrezRecord

Extracts ISSN from Entrez JSON record and returns it

getIssue() - Method in class org.eclipse.pass.loader.nihms.entrez.PubMedEntrezRecord

Extracts issue from Entrez JSON record and returns it

getPmid() - Method in class org.eclipse.pass.loader.nihms.entrez.PubMedEntrezRecord

Extracts PMID from Entrez JSON record and returns it

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

getTitle() - Method in class org.eclipse.pass.loader.nihms.entrez.PubMedEntrezRecord

Extracts title from Entrez JSON record and returns it

getVolume() - Method in class org.eclipse.pass.loader.nihms.entrez.PubMedEntrezRecord

Extracts volume from Entrez JSON record and returns it

GrantIdCache - Class in org.eclipse.pass.loader.nihms.client.cache

Caches awardNumber and grantId combination for easy lookup

H

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

Request for help/usage documentation

I

ISSNS_FLD - Static variable in class org.eclipse.pass.loader.nihms.client.NihmsPassClientService

The field name for the ISSN

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

N

NIHMS_DEP_STATUS_REF_PREFIX - Static variable in class org.eclipse.pass.loader.nihms.client.NihmsPassClientService

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

NihmsDepositIdCache - Class in org.eclipse.pass.loader.nihms.client.cache

Caches submission and depositId combination for easy lookup Note: cache only contains deposits for nihms

NihmsPassClientService - Class in org.eclipse.pass.loader.nihms.client

NIHMS PASS client service deals with interactions with the data via the PASS client and controls local data caches

NihmsPassClientService(PassClient) - Constructor for class org.eclipse.pass.loader.nihms.client.NihmsPassClientService

Constructor that allows a PassClient to be passed in

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(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

NihmsRepositoryCopyIdCache - Class in org.eclipse.pass.loader.nihms.client.cache

Caches publicationId and repositoryCopyId mapping for easy lookup Important: includes RepositoryCopies for NIHMS records only

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.

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

NIHMS Submission Loader CLI

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

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

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

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

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

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(SubmissionLoader, NihmsPublicationToSubmission, CompletedPublicationsCache) - Constructor for class org.eclipse.pass.loader.nihms.NihmsTransformLoadService

O

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

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

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

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

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

P

passClient() - Method in class org.eclipse.pass.loader.nihms.NihmsTransformLoadConfig

PmidLookup - Class in org.eclipse.pass.loader.nihms.entrez

Service to retrieve a PMID records from Entrez.

PmidLookup(Long, Long) - Constructor for class org.eclipse.pass.loader.nihms.entrez.PmidLookup

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

ProcessingUtil - Class in org.eclipse.pass.loader.nihms.util

General small utilities to tidy up data processing code.

PUBLICATION_FLD - Static variable in class org.eclipse.pass.loader.nihms.client.NihmsPassClientService

The field name for the publication

PublicationIdCache - Class in org.eclipse.pass.loader.nihms.client.cache

Caches pmid and publicationId combination for easy lookup

PubMedEntrezRecord - Class in org.eclipse.pass.loader.nihms.entrez

Class is instantiated by passing in a JSONObject from Entrez representing a PubMed article record.

PubMedEntrezRecord(JSONObject) - Constructor for class org.eclipse.pass.loader.nihms.entrez.PubMedEntrezRecord

Instantiate a PubMedRecord by passing in a JSONObject representing a single result from the PubMed database of the Entrez API.

put(String, String) - Method in class org.eclipse.pass.loader.nihms.client.cache.GrantIdCache

Add awardNumber/grantId combination to map

put(String, String) - Method in class org.eclipse.pass.loader.nihms.client.cache.NihmsDepositIdCache

Add deposit to map

put(String, String) - Method in class org.eclipse.pass.loader.nihms.client.cache.NihmsRepositoryCopyIdCache

Add publicationId to repositoryCopyId mapping

put(String, String) - Method in class org.eclipse.pass.loader.nihms.client.cache.PublicationIdCache

Add publication to map

put(String, Set<String>) - Method in class org.eclipse.pass.loader.nihms.client.cache.UserPubSubmissionsCache

Add userIdPubId/submissionIds combination to map

R

readDeposit(String) - Method in class org.eclipse.pass.loader.nihms.client.NihmsPassClientService

Retrieve full deposit record from database

readGrant(String) - Method in class org.eclipse.pass.loader.nihms.client.NihmsPassClientService

Retrieve full grant record from database

readPublication(String) - Method in class org.eclipse.pass.loader.nihms.client.NihmsPassClientService

Retrieve full publication record from database

readRepository(String) - Method in class org.eclipse.pass.loader.nihms.client.NihmsPassClientService

Retrieve repository record from database

readSubmission(String) - Method in class org.eclipse.pass.loader.nihms.client.NihmsPassClientService

Retrieve full Submission record

remove(String) - Method in class org.eclipse.pass.loader.nihms.client.cache.GrantIdCache

Remove a Grant from cache

remove(String) - Method in class org.eclipse.pass.loader.nihms.client.cache.NihmsDepositIdCache

Remove a Deposit from cache

remove(String) - Method in class org.eclipse.pass.loader.nihms.client.cache.NihmsRepositoryCopyIdCache

Remove a publicationId to repositoryCopyId mapping from cache

remove(String) - Method in class org.eclipse.pass.loader.nihms.client.cache.PublicationIdCache

Remove a Publication from cache

remove(String) - Method in class org.eclipse.pass.loader.nihms.client.cache.UserPubSubmissionsCache

Remove a Submission from cache

renameToDone(Path) - Static method in class org.eclipse.pass.loader.nihms.util.FileUtil

Rename file to append ".done" once it has been processed

REPOSITORY_FLD - Static variable in class org.eclipse.pass.loader.nihms.client.NihmsPassClientService

The field name for the repository

retrievePubMedRecord(String) - Method in class org.eclipse.pass.loader.nihms.entrez.PmidLookup

Retrieve PubMedRecord object for PMID record from NIH's Entrez API service.

retrievePubMedRecordAsJson(String) - Method in class org.eclipse.pass.loader.nihms.entrez.PmidLookup

Retrieve JSON for PMID record from NIH's Entrez API service.

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

S

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

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

setUpdateDeposoit(boolean) - 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.client.cache.GrantIdCache

Get number of cached grants

size() - Method in class org.eclipse.pass.loader.nihms.client.cache.NihmsDepositIdCache

Get number of cached deposits

size() - Method in class org.eclipse.pass.loader.nihms.client.cache.NihmsRepositoryCopyIdCache

Get number of cached mappings

size() - Method in class org.eclipse.pass.loader.nihms.client.cache.PublicationIdCache

Get number of cached publications

size() - Method in class org.eclipse.pass.loader.nihms.client.cache.UserPubSubmissionsCache

Get number of cached submissions

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

Get number of items in cache

SUBMISSION_FLD - Static variable in class org.eclipse.pass.loader.nihms.client.NihmsPassClientService

The field name for the submission

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

Supports initiation with specific client service

submissionStatusService(PassClient) - Method in class org.eclipse.pass.loader.nihms.NihmsTransformLoadConfig

SUBMITTER_FLD - Static variable in class org.eclipse.pass.loader.nihms.client.NihmsPassClientService

The field name for the submitter

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.

U

updateDeposit(Deposit) - Method in class org.eclipse.pass.loader.nihms.client.NihmsPassClientService

Update Deposit in PASS

updatePublication(Publication) - Method in class org.eclipse.pass.loader.nihms.client.NihmsPassClientService

Update Publication in PASS

updateRepositoryCopy(RepositoryCopy) - Method in class org.eclipse.pass.loader.nihms.client.NihmsPassClientService

Update RepositoryCopy in PASS

updateSubmission(Submission) - Method in class org.eclipse.pass.loader.nihms.client.NihmsPassClientService

Update Submission in PASS

UserPubSubmissionsCache - Class in org.eclipse.pass.loader.nihms.client.cache

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

A C D F G H I L M N O P R S T U
All Classes and Interfaces|All Packages|Constant Field Values