PhenoTips » Releases » Release for version phenotips-1.4-milestone-4

Release for version phenotips-1.4-milestone-4

Release Date: 04/06/2018
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-milestone-4
  • accept Verify that the build passes on the CI Server
  • accept Close the Version on Jira
  • accept 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:
    • accept install and start phenotips on Linux, OS and Windows ( check the console window for errors)?
      • accept can you create a new patient? ( check console window) 
    • 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?
    • cancel Does creating a new patient work?
    • cancel 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 pedigre/ 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 colouring 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
      • cancel Can you export pedigree as JSON, BOADICEA
      • cancel Can you import pedigree using exported JSON
      • cancel Does export as PED work, does disorder/cancer selection in the export menu work (when exporting as PED)?
      • cancel 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)
      • cancel 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)
    • cancel Are all saved pedigree edits present in the Patient form's corresponding fields?
    • cancel Does re-editing a pedigree work?
    • cancel Does the Pedigree and Family section show pedigree thumbnail with its action buttons?
    • cancel Do all pedigree action buttons work as expected?
    • cancel Does ethnicity suggestion box work? Does saving ethnicities work?
    • cancel Does Other prenatal growth parameters and development search/suggestions work?
    • cancel Can you record allergies?
    • cancel Do measurements work? Percentile computations? Charts?
    • cancel Can you upload a previous medical report?
    • cancel Can you search for a list of genes?
    • cancel Can you upload a VCF file?
    • cancel Are phenotype categories collapsed by default?
    • cancel Are the predefined phenotypes correctly displayed?
    • cancel Does the Quick phenotype search work?
    • cancel Can you enter free text in the Quick phenotype search and in predefined phenotype groups?
      • cancel Does free text appears under proper category?
    • cancel Are Global mode of inheritance and Global age of onset collapsed by default?
    • cancel Are Global mode of inheritance and Global age of onset taken into account for diagnosis and "other phenotypes" suggestions?
    • cancel Does adding phenotype details work?
    • cancel 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)? 
    • cancel Can you search for OMIM disorders/diagnosis suggestions?
    • cancel Can you enter Clinical diagnosis?
    • cancel Do search suggestions appear while typing Clinical and Final diagnosis?
    • cancel Can you enter free text in Clinical and Final diagnosis fields?
    • cancel Can you resolve the case?
    • cancel Does the record save correctly?
    • cancel 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
  • error If branching a new version, remove the Clirr exclusions/ignores from the main pom.xml file, if any
  • accept 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