Pivotal ID # 184977702: Assign DOIs Automatically

[jhoanmanuelms]

https://www.pivotaltracker.com/story/show/184977702

• Validate the required DOI fields
• Perform the request to register the DOI for the submission

[Juan-EBI]

Looking great please check comments

[Juan-EBI]

you an use created doi extension bellow.

[jhoanmanuelms]

The thing is the find method from the Attributable returns null either if the attribute is not present or the value itself is null and at this point, we are only concerned about the attribute presence

[Juan-EBI]

I would recomend to use functions so it becomes

        val headers = httpHeadersOf(contentType to MULTIPART_FORM_DATA)
        val body = linkedMultiValueMapOf(
            USER_PARAM to properties.user,
            PASSWORD_PARAM to properties.password,
            OPERATION_PARAM to OPERATION_PARAM_VALUE,
            FILE_PARAM to FileSystemResource(requestFile)
        )  

[jhoanmanuelms]

This is a great functionality but it's part of the bio-webclient module which is not used in the submitter module and I think it shouldn't be. Instead, I moved this method to commons-http which seems like the best place for this general functionality to be so it can be used in every module.

[Juan-EBI]

LGTM please consider comments

[Juan-EBI]

looks like you need to sync this part with last merge

[Juan-EBI]

Please consider

    private fun getContributors(sub: Submission): List<Contributor> {
        val organizations = getOrganizations(sub).associateBy({ it.accNo }, { it.name })
        val contributors = sub.allSections().filter { it.type == AUTHOR_TYPE }
        return contributors
            .map { it.asContributor(organizations) }
            .ifEmpty { throw MissingDoiFieldException(AUTHOR_TYPE) }
    }

    private fun Section.asContributor(organizations: Map<String, String>): Contributor {
        val names = requireNotNull(find(NAME_ATTR)) { throw InvalidAuthorNameException() }
        val org = requireNotNull(find(AFFILIATION_ATTR)) { throw MissingAuthorAffiliationException() }
        val affiliation = requireNotNull(organizations[org]) { throw InvalidAuthorAffiliationException(names, org) }
        val (name, surname) = names.split("\\s".toRegex())
        return Contributor(
            name = name,
            surname = surname,
            affiliation = affiliation,
            orcid = find(ORCID_ATTR)
        )
    }

    private fun getOrganizations(sub: Submission): List<Organization> {
        return sub
            .allSections().filter { it.type == ORG_TYPE }
            .map { it.asOrganization() }
            .ifEmpty { throw MissingDoiFieldException(ORG_TYPE) }
    }

    private fun Section.asOrganization(): Organization {
        val accNo = requireNotNull(accNo) { throw InvalidOrgException() }
        val name = requireNotNull(find(NAME_ATTR)) { throw InvalidOrgNameException(accNo) }
        return Organization(accNo, name)
    }