PhenoTips » Releases » Release for version phenotips-1.4.8

Release for version phenotips-1.4.8

Release Date: 09/07/2019
Released by:
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Use these icons to mark the release progress: cancel not done, accept done, error not done for a good reason (explain reason)
  • accept Check that you have the needed accounts
  • accept Verify that there are no open issues on GitHub for version phenotips-1.4.8
  • cancel Verify that the build passes on the CI Server
  • accept Close the Version on Jira
  • cancel Make sure the build machine has "rpmbuild" utility installed
  • accept Increase the amount of memory available to Maven: export MAVEN_OPTS="-Xmx2g -XX:MaxPermSize=256m"
  • accept Perform the release
  • accept Unzip the standalone distributions and perform a quick smoke test:
    • cancel Install and start phenotips on the following operating systems can you create a new patient? ( check the console window for errors)?
      • accept Linux
      • cancel OS
      • accept *Windows* 
    • accept Does the homepage display correctly?
    • cancel Do suggest widgets for vocabularies in Advanced filters work (Patients, Families, Studies, Groups)
    • cancel Do filters work as expected?
      • cancel in the Filtering panel of Browse all patients/families?
      • cancel in export and push dialogs?
      • cancel does "Delete all x" option work in the Filtering panels, Push and Export dialog?
    • cancel Can you add owner, collaborators and visibility to Browse all patients grid?
    • accept Does creating a new patient work?
    • accept Do hints work?
    • accept Does creating a pedigree from a patient page work?
      • accept Can you assign a patient to an existing family?
      • accept Can you create a new family for patient?
      • accept Does linking and un-linking patient to/from a pedigree node works?
        • accept Trying to a link a patient that is already in a family fails with a correct message?
      • accept Can you create a new patient record for an existing pedigree node?
      • accept Is "Life status" from the Patient record form in-sync with corresponding one in the pedigree? 
      • accept select a template
      • accept delete nodes
      • accept drag/drop diseases
      • accept turn the coloring of the group and on individual item
      • accept expand/collapse/close legend
      • accept drag/drop multi-generation relationships
      • accept create a sibling
      • accept use the children options menu
        • accept create multiple children of different genders
        • accept twins, triplets
        • accept "group"
        • accept mark individual/couple as infertile, as childless (using the bubble button)
      • accept does A&W menu appears when you hoover over the node?
        • accept does setting A&W, Alive and Deceased status works?
        • accept can you enter age and cause of death for deceased?
        • accept are all changes reflected on the node appearance and in the menu node form?
      • accept use the node menu form
        • accept change gender
        • accept change the adopted status and it updates the node appearance
        • accept change the alive and deceased status and it updates the node appearance
        • accept mark individual/couple as infertile, as childless (using the node menu)
        • accept change the carrier status
        • accept search for ethnicities (check auto-completion)
        • accept search for disorders
        • accept search for phenotypes
        • accept search for genes
        • accept add a comment in each tab
        • accept indicate a type of cancer with status and age at diagnosis and additional notes
      • accept Can you export pedigree as JSON, BOADICEA
      • accept Can you import pedigree using exported JSON
      • accept Does export as PED work, does disorder/cancer selection in the export menu work (when exporting as PED)?
      • accept Can you export pedigree as PDF, PNG and SVG?
      • cancel Does printing a pedigree work? (try different options e.g. anonymized, with/without legend, multiple pages, zoomed & panned, etc)
      • accept Does saving a pedigree work?
      • cancel Are saving failures for common reasons clearly communicated to the user?
        • cancel In a separate tab, log out of PhenoTips. Then try saving the pedigree in the pedigree editor. Does the editor correctly and visibly inform you that saving failed?
        • cancel From the terminal, shut down PhenoTips. Then try saving the pedigree. Does the editor correctly and visibly inform you that saving failed?
        • cancel (Restart PhenoTips and log back in to continue testing)
    • accept Are all saved pedigree edits present in the Patient form's corresponding fields?
    • accept Does re-editing a pedigree work?
    • accept Does the Pedigree and Family section show pedigree thumbnail with its action buttons?
    • accept Do all pedigree action buttons work as expected?
    • accept Does ethnicity suggestion box work? Does saving ethnicities work?
    • accept Does Other prenatal growth parameters and development search/suggestions work?
    • help Can you record allergies?
    • accept Do measurements work? Percentile computations? Charts?
    • accept Can you upload a previous medical report?
    • accept Can you search for a list of genes?
    • accept Can you upload a VCF file?
    • accept Are phenotype categories collapsed by default?
    • help Are the predefined phenotypes correctly displayed?
    • accept Does the Quick phenotype search work?
    • accept Can you enter free text in the Quick phenotype search and in predefined phenotype groups?
      • accept Does free text appears under proper category?
    • help Are Global mode of inheritance and Global age of onset collapsed by default?
    • help Are Global mode of inheritance and Global age of onset taken into account for diagnosis and "other phenotypes" suggestions?
    • accept Does adding phenotype details work?
    • help Do the diagnosis suggestions show up correctly (test with some phenotypes selected)?
    • cancel Do the gene suggestion show up correctly in the Gene Panels section (test selecting/deselecting phenotypes and negative genes option)?
    • cancel Are all 4 gene statuses (Candiate, Negative Confirmed causal, Carrier) listed in the gene status dropdown? 
    • cancel Does entering genes and variants work as expected?
      • cancel Do gene suggestions appear as expected (try entering partial gene name, alias or Ensembl ID)? 
    • accept Can you search for OMIM disorders/diagnosis suggestions?
    • accept Can you enter Clinical diagnosis?
    • accept Do search suggestions appear while typing Clinical and Final diagnosis?
    • accept Can you enter free text in Clinical and Final diagnosis fields?
    • accept Can you resolve the case?
    • accept Does the record save correctly?
    • accept Can you comment on patient record?
    • cancel Can you change patient permissions?
      • cancel Change visibility type works?
      • cancel Transfer ownership to a group works?
      • cancel Add/remove collaborators? Define/modify collaborator's access level?
    • cancel Collaborators cannot manage open patient records?
    • cancel Do patients with collaborators assigned show up on collaborator's PATIENTS SHARED WITH ME grid?
    • cancel Can you change family permissions?
      • cancel Change visibility type works?
      • cancel Transfer ownership to a group works?
      • cancel Add/remove collaborators? Define/modify collaborator's access level?
    • cancel Collaborators cannot manage open family records?
    • cancel Do families with collaborators assigned show up on collaborator's PATIENTS SHARED WITH ME grid?
    • cancel Add a required consent in the Administration section:
      • cancel Does patient form adhere to chosen consents?
      • cancel Can you update consents?
    • cancel Does the PDF export correctly?
    • cancel Does the Excel export correctly?
    • cancel Does the JSON export work?
      • cancel From the patient page?
      • cancel Form the All Data page?
    • cancel Does the JSON import work?
      • cancel From the patient page?
      • cancel Form the All patient records page?
    • cancel Can you open family page?
      • cancel Can you mark family as one with sensitive info?
      • cancel Does the modal with sensitive info pops up when expected?
      • cancel Can you update pedigree?
      • cancel When a patient is added to a pedigree, can all users who can edit the patient edit the family/pedigree?
      • cancel Do all action buttons work as expected?
      • cancel Can you delete a family record?
      • cancel When a patient is deleted (form the patient page), does the link get removed from pedigree image?
    • cancel Do the tables on the homepage and the All data table work?
    • cancel Does pushing a complete patient from one local instance to another work (exceptions are pedigree, medical reports, obstetric history, copy number variants, additional files)?
      • cancel Does pushing a new patient and updating existing work?
      • cancel Does pushing data to the version currently installed on Phenomecentral work (current->PCVersion)?
      • cancel Does pushing data from different PhenoTips versions work (latest 1.2->current, latest 1.3->current, previousMilestone->current)?
      • cancel Error handling when pushing patient records
        • cancel if server is unavailable?
        • cancel if incorrect credentials are used?
        • cancel if not authorized to push patients to the selected server?
      • cancel Does pushing to a server which has consents works?
        • cancel Is the list of available consents shown?
        • cancel Is there an error message and push prevented when one of the required consents is not selected?
      • cancel Does pushing multiple patients form All data page works?
        • cancel Do filters work as expected?
        • cancel  Are correct patients pushed?
    • cancel Does REST API work?
      • cancel Can you create a new patient? (Use any tool. From the command line: curl -u Admin:admin -H "Content-Type: application/json" -X POST -d '{}' http://localhost:8080/rest/patients , substituting {} with JSON obtaining from exporting patient as JSON)
      • cancel Can you update an existing patient via PUT to /rest/patients/id?
      • cancel Can you list all patients as well as individual ones?  GET for /rest/patients and /rest/patients/id
      • cancel Can you modify permissions (patients and families)?
        • cancel ownership?
        • cancel visibility?
        • cancel add/modify/remove collaborators?
      • cancel does the Vocabularies REST API works? 
      • cancel does the Families REST API works?
      • cancel does the Gene Panels REST API works? 
      • cancel does getTerm in HGNC vocabulary matches on exact input provided?
    • cancel does PhenoTips works for the guest user?
      • cancel can you create/edit/save/delete patient, family, pedigree?
      • cancel does export work?
  • cancel Release the MacOS DMG
  • cancel If branching a new version, remove the Clirr exclusions/ignores from the main pom.xml file, if any
  • cancel Update the extensions
  • cancel Update the Download page
  • cancel Upgrade playground.phenotips.org and other maintained instances
  • cancel Create blog post on phenotips.org
  • cancel Send the Announcement Mail
  • cancel Announce on Twitter with the PhenoTips account

Availability

PhenoTips® is freely available under the terms of the the GNU Affero General Public License, version 3.0.

 Download the latest release
 Play with our demo
 Get the source code

Contact

 Ask for free support (by volunteers):
support@phenotips.org
 Inquire about commercial support:
info@gene42.com
 Follow us on twitter:
@phenotips

PhenoTips® is an exclusive trademark of Gene42 Inc.