Updating to Reggie 4.6

• The YubiKey v1.3 (or later) extension is required for the delivery client login to work.

• Install the latest pipeline scripts. The nextseq_status.sh script has been updated with support for searching multiple run archives (see #901). The new script is not compatible with the old version. Download the script from ​http://baseplugins.thep.lu.se/browser/other/pipeline/trunk and save it on the computation cluster in the location specified by the <pipeline-scripts><path> setting in reggie-config.xml.

The following steps should be made after updating Reggie

1. Add user accounts to the 'SCAN-B Lab' group

Due to the "Report delivery system" (#891) the update has removed the Everyone group from using the web client. The SCAN-B Lab group has been created as a replacement and must be used instead. User accounts that need to access BASE/Reggie via the regular web client interface must thus be added to the SCAN-B Lab group. The ROOT user and other Administrator accounts are not affected.

2. Setting up user accounts for the report delivery client

User accounts that are created for the report delivery client should be configured according to the specification below:

• Member of the Guest role
• Member of the SCAN-B Delivery group AND one site-specific group (eg. Malmö, Lund or any other site)
• A YubiKey is required for logging in with the delivery client

The delivery client login page is available at the location <root>/extensions/reggie.jar/delivery/index.jsp, where <root> is the regular BASE web client login. For example: https://base.server.domain/base/extensions/reggie.jar/delivery/index.jsp.

3. Adding referral form template info for referral form generation

The referral form generation uses template PDF files for creating the forms. A template contains all information except SCAN-B ID text and barcodes, which are added, when the complete form is generated. In order for the patient curator to be able to replace templates with new versions, the template files are placed in the BASE file system. Also, in order to support variations in the text and layout of templates for different sites (other than the SCAN-B text and barcodes), templates for different sites are placed in separate sub-directories:

• The template top directory is /home/SCANB/ReferralFormTemplatesInUse/.
• Each site has a sub-directory named after the site's SCAN-B prefix. e.g. /home/SCANB/ReferralFormTemplatesInUse/88/ for Uppsala with prefix "88".

The application identifies a template's type based on the start of its filename:

• For a template file to be used, the filename must begin with a string defined for its referral form type in reggie-config.xml, tag referral-form-generation, sub-tag template-filename-start.
• A start string should be unique and not be a sub-string of another start string.
• A start string should not include version information, and normally not site-specific information.
• A form template filename, however, is recommended to contain version information in part of the filename following the start string, since the complete filenames of used templates for a referral form generation session are included in an entry in the referral form generation log file.
• When generating referral forms for a site, the application looks for templates of all type of forms. If no template file with a valid filename is found for a specific form type and site, that form type is skipped in the output.

3.1. Update reggie-config.xml with start of referral form template filenames for different form types

In reggie-config.xml, tag referral-form-generation, sub-tag template-filename-start, add start of template filenames for the following tags:

Form type XML Tag	Example of start of template filenames
<patient-info>	Patinfo
<clinical-chemistry-biopsy>	KlinKemBiopsy-SCAN-B-remiss
<clinical-chemistry-blood>	KlinKem-SCAN-B-blood-biobanken_remiss
<clinical-chemistry-blood-lundcopy>	KlinKem-SCAN-B-blood-biobanken-lundkopia_remiss
<clinical-chemistry-bcblood>	KlinKem-SCAN-B-bcblood-remiss
<middle-needle-biopsy>	PathBiopsy-SCAN-B-remiss
<clinical-chemistry>	Klinkem-SCAN-B-remiss
<clinical-pathology>	Path-SCAN-B-remiss
<consent-report>	Consent-SCAN-B-remiss

As an example, the patient info form template may have the full filename "Patinfo_3_0_120109_SCAN-B.pdf", and the clinical pathology form template the full filename "Path-SCAN-B-remiss_v7.pdf".

3.2. Copy referral form template files to use to sub-directory for each site

For all form types supported for a site, copy the corresponding form template PDF file to the sub-directory for the site. For the first release, the following table may be of help:

Form type XML	Supported by site[s]
patient-info	All
clinical-chemistry-biopsy	All
clinical-chemistry-blood	Uppsala (88) only
clinical-chemistry-blood-lundcopy	Uppsala (88) only
clinical-chemistry-bcblood	Lund (11) only
middle-needle-biopsy	All
clinical-chemistry	All except Uppsala (88)
clinical-pathology	All
consent-report	All