PhenoTips » Releases » Release for version phenotips-1.4.2
From version 1.1
edited by Sergiu Dumitriu
on 2018/12/12 18:35
To version 2.1
edited by Sergiu Dumitriu
on 2018/12/12 18:37
Change comment: There is no comment for this version

Content changes

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1 +{{velocity}}
2 +#set ($object = $doc.getObject("ReleaseCode.ReleaseClass"))
3 +#set ($version = $object.getProperty("version").getValue())
4 +{{/velocity}}
5 +
6 +{{info}}Use these icons to mark the release progress: (x) not done, (/) done, (!) not done for a good reason (explain reason){{/info}}
7 +
8 +* (/) Check that you have the [[needed accounts>>Release.ReleasePlanHelp||anchor="HSetupyouridentity"]]
9 +* (/) Verify that there are no {{velocity}}[[open issues on GitHub for version $version>>https://github.com/phenotips/phenotips/milestones]]{{/velocity}}
10 +* (/) Verify that [[the build passes on the CI Server>>https://ci.phenotips.org/job/phenotips/]]
11 +* (/) Close the Version on [[Jira>>https://phenotips.atlassian.net/plugins/servlet/project-config/PT/versions]]
12 +* (/) Make sure the build machine has "rpmbuild" utility installed
13 +* (/) Increase the amount of memory available to Maven: ##export MAVEN_OPTS="-Xmx2g -XX:MaxPermSize=256m"##
14 +* (/) [[Perform the release>>Release.ReleasePlanHelp||anchor="HBuildtherelease"]]
15 +* (x) Unzip the standalone distributions and perform a quick smoke test:
16 +** (x) install and start phenotips on Linux, OS and Windows ( check the console window for errors)?
17 +*** (x) can you create a new patient? ( check console window)
18 +** (x) Does the homepage display correctly?
19 +** (x) Do suggest widgets for vocabularies in Advanced filters work (Patients, Families, Studies, Groups)
20 +** (x) Do filters work as expected?
21 +*** (x) in the Filtering panel of Browse all patients/families?
22 +*** (x) in export and push dialogs?
23 +*** (x) does "Delete all x" option work in the Filtering panels, Push and Export dialog?
24 +** (x) Can you add owner, collaborators and visibility to Browse all patients grid?
25 +** (x) Does creating a new patient work?
26 +** (x) Do hints work?
27 +** (x) Does creating a pedigree from a patient page work?
28 +*** (x) Can you assign a patient to an existing family?
29 +*** (x) Can you create a new family for patient?
30 +*** (x) Does linking and un-linking patient to/from a pedigree node works?
31 +**** (x) Trying to a link a patient that is already in a family fails with a correct message?
32 +*** (x) Can you create a new patient record for an existing pedigree node?
33 +*** (x) Is "Life status" from the Patient record form in-sync with corresponding one in the pedigree?
34 +*** (x) select a template
35 +*** (x) delete nodes
36 +*** (x) drag/drop diseases
37 +*** (x) turn the colouring of the group and on individual item
38 +*** (x) expand/collapse/close legend
39 +*** (x) drag/drop multi-generation relationships
40 +*** (x) create a sibling
41 +*** (x) use the children options menu
42 +**** (x) create multiple children of different genders
43 +**** (x) twins, triplets
44 +**** (x) "group"
45 +**** (x) mark individual/couple as infertile, as childless (using the bubble button)
46 +*** (x) does A&W menu appears when you hoover over the node?
47 +**** (x) does setting A&W, Alive and Deceased status works?
48 +**** (x) can you enter age and cause of death for deceased?
49 +**** (x) are all changes reflected on the node appearance and in the menu node form?
50 +*** (x) use the node menu form
51 +**** (x) change gender
52 +**** (x) change the adopted status and it updates the node appearance
53 +**** (x) change the alive and deceased status and it updates the node appearance
54 +**** (x) mark individual/couple as infertile, as childless (using the node menu)
55 +**** (x) change the carrier status
56 +**** (x) search for ethnicities (check auto-completion)
57 +**** (x) search for disorders
58 +**** (x) search for phenotypes
59 +**** (x) search for genes
60 +**** (x) add a comment in each tab
61 +**** (x) indicate a type of cancer with status and age at diagnosis and additional notes
62 +*** (x) Can you export pedigree as JSON, BOADICEA
63 +*** (x) Can you import pedigree using exported JSON
64 +*** (x) Does export as PED work, does disorder/cancer selection in the export menu work (when exporting as PED)?
65 +*** (x) Can you export pedigree as PDF, PNG and SVG?
66 +*** (x) Does printing a pedigree work? (try different options e.g. anonymized, with/without legend, multiple pages, zoomed & panned, etc)
67 +*** (x) Does saving a pedigree work?
68 +*** (x) Are saving failures for common reasons clearly communicated to the user?
69 +**** (x) 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?
70 +**** (x) From the terminal, shut down PhenoTips. Then try saving the pedigree. Does the editor correctly and visibly inform you that saving failed?
71 +**** (x) (Restart PhenoTips and log back in to continue testing)
72 +** (x) Are all saved pedigree edits present in the Patient form's corresponding fields?
73 +** (x) Does re-editing a pedigree work?
74 +** (x) Does the Pedigree and Family section show pedigree thumbnail with its action buttons?
75 +** (x) Do all pedigree action buttons work as expected?
76 +** (x) Does ethnicity suggestion box work? Does saving ethnicities work?
77 +** (x) Does ##Other## prenatal growth parameters and development search/suggestions work?
78 +** (x) Can you record allergies?
79 +** (x) Do measurements work? Percentile computations? Charts?
80 +** (x) Can you upload a previous medical report?
81 +** (x) Can you search for a list of genes?
82 +** (x) Can you upload a VCF file?
83 +** (x) Are phenotype categories collapsed by default?
84 +** (x) Are the predefined phenotypes correctly displayed?
85 +** (x) Does the //Quick phenotype search// work?
86 +** (x) Can you enter free text in the //Quick phenotype search// and in predefined phenotype groups?
87 +*** (x) Does free text appears under proper category?
88 +** (x) Are Global mode of inheritance and Global age of onset collapsed by default?
89 +** (x) Are Global mode of inheritance and Global age of onset taken into account for diagnosis and "other phenotypes" suggestions?
90 +** (x) Does adding phenotype details work?
91 +** (x) Do the diagnosis suggestions show up correctly (test with some phenotypes selected)?
92 +** (x) Do the gene suggestion show up correctly in the Gene Panels section (test selecting/deselecting phenotypes and negative genes option)?
93 +** (x) Are all 4 gene statuses (##Candiate, Negative Confirmed causal, Carrier##) listed in the gene status dropdown?
94 +** (x) Does entering genes and variants work as expected?
95 +*** (x) Do gene suggestions appear as expected (try entering partial gene name, alias or Ensembl ID)?
96 +** (x) Can you search for OMIM disorders/diagnosis suggestions?
97 +** (x) Can you enter Clinical diagnosis?
98 +** (x) Do search suggestions appear while typing Clinical and Final diagnosis?
99 +** (x) Can you enter free text in Clinical and Final diagnosis fields?
100 +** (x) Can you resolve the case?
101 +** (x) Does the record save correctly?
102 +** (x) Can you comment on patient record?
103 +** (x) Can you change patient permissions?
104 +*** (x) Change visibility type works?
105 +*** (x) Transfer ownership to a group works?
106 +*** (x) Add/remove collaborators? Define/modify collaborator's access level?
107 +** (x) Collaborators cannot manage open patient records?
108 +** (x) Do patients with collaborators assigned show up on collaborator's PATIENTS SHARED WITH ME grid?
109 +** (x) Can you change family permissions?
110 +*** (x) Change visibility type works?
111 +*** (x) Transfer ownership to a group works?
112 +*** (x) Add/remove collaborators? Define/modify collaborator's access level?
113 +** (x) Collaborators cannot manage open family records?
114 +** (x) Do families with collaborators assigned show up on collaborator's PATIENTS SHARED WITH ME grid?
115 +** (x) Add a required consent in the Administration section:
116 +*** (x) Does patient form adhere to chosen consents?
117 +*** (x) Can you update consents?
118 +** (x) Does the PDF export correctly?
119 +** (x) Does the Excel export correctly?
120 +** (x) Does the JSON export work?
121 +*** (x) From the patient page?
122 +*** (x) Form the //All Data// page?
123 +** (x) Does the JSON import work?
124 +*** (x) From the patient page?
125 +*** (x) Form the //All patient records// page?
126 +** (x) Can you open family page?
127 +*** (x) Can you mark family as one with sensitive info?
128 +*** (x) Does the modal with sensitive info pops up when expected?
129 +*** (x) Can you update pedigree?
130 +*** (x) When a patient is added to a pedigree, can all users who can edit the patient edit the family/pedigree?
131 +*** (x) Do all action buttons work as expected?
132 +*** (x) Can you delete a family record?
133 +*** (x) When a patient is deleted (form the patient page), does the link get removed from pedigree image?
134 +** (x) Do the tables on the homepage and the //All data// table work?
135 +** (x) Does pushing a complete patient from one local instance to another work (##exceptions are pedigree, medical reports, obstetric history, copy number variants, additional files##)?
136 +*** (x) Does pushing a new patient and updating existing work?
137 +*** (x) Does pushing data to the version currently installed on Phenomecentral work (##current##->##PCVersion##)?
138 +*** (x) Does pushing data from different PhenoTips versions work (##latest 1.2##->##current##, ##latest 1.3##->##current##, ##previousMilestone##->##current##)?
139 +*** (x) Error handling when pushing patient records
140 +**** (x) if server is unavailable?
141 +**** (x) if incorrect credentials are used?
142 +**** (x) if not authorized to push patients to the selected server?
143 +*** (x) Does pushing to a server which has consents works?
144 +**** (x) Is the list of available consents shown?
145 +**** (x) Is there an error message and push prevented when one of the required consents is not selected?
146 +*** (x) Does pushing multiple patients form //All data// page works?
147 +**** (x) Do filters work as expected?
148 +**** (x) Are correct patients pushed?
149 +** (x) Does REST API work?
150 +*** (x) 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)
151 +*** (x) Can you update an existing patient via ##PUT## to ##/rest/patients/id##?
152 +*** (x) Can you list all patients as well as individual ones? ##GET## for ##/rest/patients## and ##/rest/patients/id##
153 +*** (x) Can you modify permissions (patients and families)?
154 +**** (x) ownership?
155 +**** (x) visibility?
156 +**** (x) add/modify/remove collaborators?
157 +*** (x) does the Vocabularies REST API works?
158 +*** (x) does the Families REST API works?
159 +*** (x) does the Gene Panels REST API works?
160 +*** (x) does getTerm in HGNC vocabulary matches on exact input provided?
161 +** (x) does PhenoTips works for the guest user?
162 +*** (x) can you create/edit/save/delete patient, family, pedigree?
163 +*** (x) does export work?
164 +* (x) Release the MacOS DMG
165 +* (x) If branching a new version, remove the Clirr exclusions/ignores from the main ##pom.xml## file, if any
166 +* (x) [[Update the extensions>>Extension.WebHome]]
167 +* (x) Update the Download page
168 +* (x) Upgrade ##playground.phenotips.org## and other maintained instances
169 +* (x) [[Create blog post on phenotips.org>>Blog.WebHome]]
170 +* (x) Send the Announcement Mail
171 +* (x) Announce on Twitter with the [[PhenoTips account>>https://twitter.com/PhenoTips/]]

Availability

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

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