A D E F G H I J L M N O P S T V

A

Article() - Constructor for class org.dataconservancy.pass.deposit.model.DepositMetadata.Article

D

DepositFile - Class in org.dataconservancy.pass.deposit.model

Represents a file that was uploaded by a user into PASS; e.g.

DepositFile() - Constructor for class org.dataconservancy.pass.deposit.model.DepositFile

DepositFileType - Enum in org.dataconservancy.pass.deposit.model

The semantic type of a file.

DepositManifest - Class in org.dataconservancy.pass.deposit.model

Accounts for every file in a submission.

DepositManifest() - Constructor for class org.dataconservancy.pass.deposit.model.DepositManifest

DepositMetadata - Class in org.dataconservancy.pass.deposit.model

Encapsulates required and optional metadata for submitting a manuscript.

DepositMetadata() - Constructor for class org.dataconservancy.pass.deposit.model.DepositMetadata

DepositMetadata.Article - Class in org.dataconservancy.pass.deposit.model

DepositMetadata.IssnPubType - Class in org.dataconservancy.pass.deposit.model

ISSN associated with a publication type

DepositMetadata.Journal - Class in org.dataconservancy.pass.deposit.model

Journal-related metadata fields

DepositMetadata.Manuscript - Class in org.dataconservancy.pass.deposit.model

Manuscript-related metadata fields

DepositMetadata.Person - Class in org.dataconservancy.pass.deposit.model

A Person associated with the submission, their names and role

DepositMetadata.PERSON_TYPE - Enum in org.dataconservancy.pass.deposit.model

Person type: identifies person's role as submitter, PI/co-PI or author

DepositSubmission - Class in org.dataconservancy.pass.deposit.model

Encapsulates a submission to the target system, including the manuscript and supplement files, metadata describing the manuscript, authors, and the journal of publication, and a manifest cataloging every file in the submission.

DepositSubmission() - Constructor for class org.dataconservancy.pass.deposit.model.DepositSubmission

doi - Variable in class org.dataconservancy.pass.deposit.model.DepositMetadata.Article

DOI for the final version of the article, if known.

E

email - Variable in class org.dataconservancy.pass.deposit.model.DepositMetadata.Person

embargoLiftDate - Variable in class org.dataconservancy.pass.deposit.model.DepositMetadata.Article

equals(Object) - Method in class org.dataconservancy.pass.deposit.model.DepositFile

equals(Object) - Method in class org.dataconservancy.pass.deposit.model.DepositMetadata.IssnPubType

equals(Object) - Method in class org.dataconservancy.pass.deposit.model.DepositSubmission

F

firstName - Variable in class org.dataconservancy.pass.deposit.model.DepositMetadata.Person

fullName - Variable in class org.dataconservancy.pass.deposit.model.DepositMetadata.Person

G

getArticleMetadata() - Method in class org.dataconservancy.pass.deposit.model.DepositMetadata

getConstructedName() - Method in class org.dataconservancy.pass.deposit.model.DepositMetadata.Person

Returns the assembled name for the person using the first/middle/last names.

getDoi() - Method in class org.dataconservancy.pass.deposit.model.DepositMetadata.Article

getEmail() - Method in class org.dataconservancy.pass.deposit.model.DepositMetadata.Person

getEmbargoLiftDate() - Method in class org.dataconservancy.pass.deposit.model.DepositMetadata.Article

getFiles() - Method in class org.dataconservancy.pass.deposit.model.DepositManifest

getFiles() - Method in class org.dataconservancy.pass.deposit.model.DepositSubmission

getFirstName() - Method in class org.dataconservancy.pass.deposit.model.DepositMetadata.Person

getFullName() - Method in class org.dataconservancy.pass.deposit.model.DepositMetadata.Person

Returns the supplied "full" name string for the person.

getId() - Method in class org.dataconservancy.pass.deposit.model.DepositSubmission

getIssn() - Method in class org.dataconservancy.pass.deposit.model.DepositMetadata.Journal

Deprecated.

getIssnPubTypes() - Method in class org.dataconservancy.pass.deposit.model.DepositMetadata.Journal

getIssue() - Method in class org.dataconservancy.pass.deposit.model.DepositMetadata.Article

getJournalId() - Method in class org.dataconservancy.pass.deposit.model.DepositMetadata.Journal

getJournalMetadata() - Method in class org.dataconservancy.pass.deposit.model.DepositMetadata

getJournalTitle() - Method in class org.dataconservancy.pass.deposit.model.DepositMetadata.Journal

getJournalType() - Method in class org.dataconservancy.pass.deposit.model.DepositMetadata.Journal

getLabel() - Method in class org.dataconservancy.pass.deposit.model.DepositFile

getLastName() - Method in class org.dataconservancy.pass.deposit.model.DepositMetadata.Person

getLocation() - Method in class org.dataconservancy.pass.deposit.model.DepositFile

getManifest() - Method in class org.dataconservancy.pass.deposit.model.DepositSubmission

getManuscriptMetadata() - Method in class org.dataconservancy.pass.deposit.model.DepositMetadata

getManuscriptUrl() - Method in class org.dataconservancy.pass.deposit.model.DepositMetadata.Manuscript

getMetadata() - Method in class org.dataconservancy.pass.deposit.model.DepositSubmission

getMiddleName() - Method in class org.dataconservancy.pass.deposit.model.DepositMetadata.Person

getMsAbstract() - Method in class org.dataconservancy.pass.deposit.model.DepositMetadata.Manuscript

getName() - Method in class org.dataconservancy.pass.deposit.model.DepositFile

getName() - Method in class org.dataconservancy.pass.deposit.model.DepositMetadata.Person

Returns the "total" name for the person, regardless of how that name was supplied.

getName() - Method in class org.dataconservancy.pass.deposit.model.DepositSubmission

getNihmsId() - Method in class org.dataconservancy.pass.deposit.model.DepositMetadata.Manuscript

getPersons() - Method in class org.dataconservancy.pass.deposit.model.DepositMetadata

getPublicationDate() - Method in class org.dataconservancy.pass.deposit.model.DepositMetadata.Journal

getPublisherName() - Method in class org.dataconservancy.pass.deposit.model.DepositMetadata.Journal

getReversedName() - Method in class org.dataconservancy.pass.deposit.model.DepositMetadata.Person

Returns the last-name-first version of the "total" name for a person whose name was supplied as a combination of a first, a last and an optional middle name.

getTitle() - Method in class org.dataconservancy.pass.deposit.model.DepositMetadata.Article

getTitle() - Method in class org.dataconservancy.pass.deposit.model.DepositMetadata.Manuscript

getType() - Method in class org.dataconservancy.pass.deposit.model.DepositFile

getType() - Method in class org.dataconservancy.pass.deposit.model.DepositMetadata.Person

getTypeDescription() - Method in enum org.dataconservancy.pass.deposit.model.JournalPublicationType

getVolume() - Method in class org.dataconservancy.pass.deposit.model.DepositMetadata.Article

H

hashCode() - Method in class org.dataconservancy.pass.deposit.model.DepositFile

hashCode() - Method in class org.dataconservancy.pass.deposit.model.DepositMetadata.IssnPubType

hashCode() - Method in class org.dataconservancy.pass.deposit.model.DepositSubmission

I

isPublisherPdf() - Method in class org.dataconservancy.pass.deposit.model.DepositMetadata.Manuscript

isShowPublisherPdf() - Method in class org.dataconservancy.pass.deposit.model.DepositMetadata.Manuscript

issn - Variable in class org.dataconservancy.pass.deposit.model.DepositMetadata.IssnPubType

issn - Variable in class org.dataconservancy.pass.deposit.model.DepositMetadata.Journal

Deprecated.

IssnPubType(String, JournalPublicationType) - Constructor for class org.dataconservancy.pass.deposit.model.DepositMetadata.IssnPubType

issnPubTypes - Variable in class org.dataconservancy.pass.deposit.model.DepositMetadata.Journal

ISSN mapped to journal publication type

issue - Variable in class org.dataconservancy.pass.deposit.model.DepositMetadata.Article

The publication's issue in which the article appears

J

Journal() - Constructor for class org.dataconservancy.pass.deposit.model.DepositMetadata.Journal

journalId - Variable in class org.dataconservancy.pass.deposit.model.DepositMetadata.Journal

NLM title abbreviation

JournalPublicationType - Enum in org.dataconservancy.pass.deposit.model

Journal type: electronic or print

journalTitle - Variable in class org.dataconservancy.pass.deposit.model.DepositMetadata.Journal

NLM full journal title

journalType - Variable in class org.dataconservancy.pass.deposit.model.DepositMetadata.Journal

Journal type, always set to nlm-ta

L

lastName - Variable in class org.dataconservancy.pass.deposit.model.DepositMetadata.Person

M

Manuscript() - Constructor for class org.dataconservancy.pass.deposit.model.DepositMetadata.Manuscript

manuscriptUrl - Variable in class org.dataconservancy.pass.deposit.model.DepositMetadata.Manuscript

URL to the manuscript, if known.

middleName - Variable in class org.dataconservancy.pass.deposit.model.DepositMetadata.Person

msAbstract - Variable in class org.dataconservancy.pass.deposit.model.DepositMetadata.Manuscript

A brief abstract of the manuscript

N

nihmsId - Variable in class org.dataconservancy.pass.deposit.model.DepositMetadata.Manuscript

Internal NIHMS submission ID; null unless this is a re-submission

O

org.dataconservancy.pass.deposit.model - package org.dataconservancy.pass.deposit.model

Provides the basic model for the submission of article manuscripts and supplement data to NIHMS.

P

parseTypeDescription(String) - Static method in enum org.dataconservancy.pass.deposit.model.JournalPublicationType

Parse an Extension from the string form as it would be used in a file name.

Person() - Constructor for class org.dataconservancy.pass.deposit.model.DepositMetadata.Person

Person(DepositMetadata.Person) - Constructor for class org.dataconservancy.pass.deposit.model.DepositMetadata.Person

publicationDate - Variable in class org.dataconservancy.pass.deposit.model.DepositMetadata.Journal

Date of publication

publisherName - Variable in class org.dataconservancy.pass.deposit.model.DepositMetadata.Journal

Name of publisher

publisherPdf - Variable in class org.dataconservancy.pass.deposit.model.DepositMetadata.Manuscript

true if the submission includes the the publisher's final PDF version of the manuscript

pubType - Variable in class org.dataconservancy.pass.deposit.model.DepositMetadata.IssnPubType

S

setArticleMetadata(DepositMetadata.Article) - Method in class org.dataconservancy.pass.deposit.model.DepositMetadata

setDoi(URI) - Method in class org.dataconservancy.pass.deposit.model.DepositMetadata.Article

setEmail(String) - Method in class org.dataconservancy.pass.deposit.model.DepositMetadata.Person

setEmbargoLiftDate(ZonedDateTime) - Method in class org.dataconservancy.pass.deposit.model.DepositMetadata.Article

setFiles(List<DepositFile>) - Method in class org.dataconservancy.pass.deposit.model.DepositManifest

setFiles(List<DepositFile>) - Method in class org.dataconservancy.pass.deposit.model.DepositSubmission

setFirstName(String) - Method in class org.dataconservancy.pass.deposit.model.DepositMetadata.Person

setFullName(String) - Method in class org.dataconservancy.pass.deposit.model.DepositMetadata.Person

Stores a single string containing the person's entire name.

setId(String) - Method in class org.dataconservancy.pass.deposit.model.DepositSubmission

setIssn(String) - Method in class org.dataconservancy.pass.deposit.model.DepositMetadata.Journal

Deprecated.

setIssnPubTypes(Map<String, DepositMetadata.IssnPubType>) - Method in class org.dataconservancy.pass.deposit.model.DepositMetadata.Journal

setIssue(String) - Method in class org.dataconservancy.pass.deposit.model.DepositMetadata.Article

setJournalId(String) - Method in class org.dataconservancy.pass.deposit.model.DepositMetadata.Journal

setJournalMetadata(DepositMetadata.Journal) - Method in class org.dataconservancy.pass.deposit.model.DepositMetadata

setJournalTitle(String) - Method in class org.dataconservancy.pass.deposit.model.DepositMetadata.Journal

setLabel(String) - Method in class org.dataconservancy.pass.deposit.model.DepositFile

setLastName(String) - Method in class org.dataconservancy.pass.deposit.model.DepositMetadata.Person

setLocation(String) - Method in class org.dataconservancy.pass.deposit.model.DepositFile

setManifest(DepositManifest) - Method in class org.dataconservancy.pass.deposit.model.DepositSubmission

setManuscriptMetadata(DepositMetadata.Manuscript) - Method in class org.dataconservancy.pass.deposit.model.DepositMetadata

setManuscriptUrl(URL) - Method in class org.dataconservancy.pass.deposit.model.DepositMetadata.Manuscript

setMetadata(DepositMetadata) - Method in class org.dataconservancy.pass.deposit.model.DepositSubmission

setMiddleName(String) - Method in class org.dataconservancy.pass.deposit.model.DepositMetadata.Person

setMsAbstract(String) - Method in class org.dataconservancy.pass.deposit.model.DepositMetadata.Manuscript

setName(String) - Method in class org.dataconservancy.pass.deposit.model.DepositFile

setName(String) - Method in class org.dataconservancy.pass.deposit.model.DepositSubmission

setNihmsId(String) - Method in class org.dataconservancy.pass.deposit.model.DepositMetadata.Manuscript

setPersons(List<DepositMetadata.Person>) - Method in class org.dataconservancy.pass.deposit.model.DepositMetadata

setPublicationDate(String) - Method in class org.dataconservancy.pass.deposit.model.DepositMetadata.Journal

setPublisherName(String) - Method in class org.dataconservancy.pass.deposit.model.DepositMetadata.Journal

setPublisherPdf(boolean) - Method in class org.dataconservancy.pass.deposit.model.DepositMetadata.Manuscript

setShowPublisherPdf(boolean) - Method in class org.dataconservancy.pass.deposit.model.DepositMetadata.Manuscript

setTitle(String) - Method in class org.dataconservancy.pass.deposit.model.DepositMetadata.Article

setTitle(String) - Method in class org.dataconservancy.pass.deposit.model.DepositMetadata.Manuscript

setType(DepositFileType) - Method in class org.dataconservancy.pass.deposit.model.DepositFile

setType(DepositMetadata.PERSON_TYPE) - Method in class org.dataconservancy.pass.deposit.model.DepositMetadata.Person

setVolume(String) - Method in class org.dataconservancy.pass.deposit.model.DepositMetadata.Article

showPublisherPdf - Variable in class org.dataconservancy.pass.deposit.model.DepositMetadata.Manuscript

true if DepositMetadata.Manuscript.publisherPdf is true and if the publisher's final PDF version should be used in lieu of the NIHMS-generated PDF in PubMed Central.

T

title - Variable in class org.dataconservancy.pass.deposit.model.DepositMetadata.Article

The title of the article

title - Variable in class org.dataconservancy.pass.deposit.model.DepositMetadata.Manuscript

The title of the manuscript

toString() - Method in class org.dataconservancy.pass.deposit.model.DepositFile

toString() - Method in class org.dataconservancy.pass.deposit.model.DepositMetadata.IssnPubType

toString() - Method in class org.dataconservancy.pass.deposit.model.DepositMetadata

toString() - Method in class org.dataconservancy.pass.deposit.model.DepositSubmission

toString() - Method in enum org.dataconservancy.pass.deposit.model.JournalPublicationType

type - Variable in class org.dataconservancy.pass.deposit.model.DepositMetadata.Person

The role for this person.

V

valueOf(String) - Static method in enum org.dataconservancy.pass.deposit.model.DepositFileType

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.dataconservancy.pass.deposit.model.DepositMetadata.PERSON_TYPE

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.dataconservancy.pass.deposit.model.JournalPublicationType

Returns the enum constant of this type with the specified name.

values() - Static method in enum org.dataconservancy.pass.deposit.model.DepositFileType

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.dataconservancy.pass.deposit.model.DepositMetadata.PERSON_TYPE

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.dataconservancy.pass.deposit.model.JournalPublicationType

Returns an array containing the constants of this enum type, in the order they are declared.

volume - Variable in class org.dataconservancy.pass.deposit.model.DepositMetadata.Article

The publication volume in which the article appears

A D E F G H I J L M N O P S T V