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  1. PT-3708

Automatic layout may leave pedigree in an un-saveable un-exportable state

    Details

    • Type: Bug
    • Status: Closed
    • Priority: Major
    • Resolution: Fixed
    • Affects Version/s: 1.4-milestone-4
    • Fix Version/s: 1.4-rc-1
    • Component/s: None
    • Labels:
      None
    • Sprint:

      Description

      For some very specific pedigrees after an automatic layout is performed the pedigree can not be saved or exported

      Sample pedigree in new Phenotips JSON format:

      {"JSON_version":"1.0","members":[{"id":0,"pedigreeProperties":{"cancers":[{"qualifiers":[{"numericAgeAtDiagnosis":"","notes":"","ageAtDiagnosis":"","laterality":"","primary":true},{"numericAgeAtDiagnosis":10,"notes":"need to google this one","ageAtDiagnosis":"10","laterality":"","primary":true}],"id":"HP:0025432","label":"Acanthoma","affected":true}],"carrierStatus":"affected","nodeNumber":"III-2"},"properties":{"phenotips_version":"1.4-milestone-4","sex":"U","external_id":"","patient_name":{"first_name":"","last_name":""},"life_status":"alive","date_of_birth":{},"date_of_death":{},"genes":[{"gene":"AMELX","id":"ENSG00000125363","status":"candidate"},{"gene":"ATP6V1B2","id":"ENSG00000147416","status":"solved"},{"gene":"ACAP1","id":"ENSG00000072818","status":"carrier"}],"features":[{"id":"HP:0031316","label":"Abnormal ventricular myocardium morphology","type":"phenotype","observed":"yes"}],"nonstandard_features":[],"disorders":[{"id":"MIM:107680","label":"APOLIPOPROTEIN A-I"}],"family_history":{"consanguinity":false}}},{"id":1,"pedigreeProperties":{"cancers":[{"qualifiers":[{"numericAgeAtDiagnosis":"","notes":"","ageAtDiagnosis":"","laterality":"","primary":true}],"id":"HP:0100013","label":"Breast","affected":true}],"carrierStatus":"affected","nodeNumber":"II-4"},"properties":{"date":"2018-06-04T18:50:40.000Z","prenatal_perinatal_history":{"gestation":null},"apgar":{},"notes":{"family_history":"","prenatal_development":"","indication_for_referral":"","genetic_notes":"","medical_history":"","diagnosis_notes":""},"ethnicity":{"maternal_ethnicity":[],"paternal_ethnicity":[]},"genes":[{"gene":"BDNF-AS","id":"ENSG00000245573","status":"candidate"},{"gene":"BNIP3P36","id":"ENSG00000271661","status":"solved"},{"gene":"BANF1P4","id":"ENSG00000223828","status":"carrier"}],"life_status":"alive","sex":"F","clinical-diagnosis":[],"solved":{"status":"unsolved"},"reporter":"Admin","external_id":"","last_modified_by":"Admin","clinicalStatus":"affected","disorders":[{"id":"MIM:109540","label":"B-CELL GROWTH FACTOR"}],"features":[{"id":"HP:0010976","label":"B lymphocytopenia","type":"phenotype","observed":"yes"}],"report_id":"P0000010","meta":{"hgnc_version":"2017-07-17T02:26:39.671Z","omim_version":"2017-05-08T16:25:23.918Z","ordo_version":"2.3","hpo_version":"releases/2017-12-12","phenotips_version":"1.4-milestone-4"},"contact":[{"institution":"http://phenotips.org/","name":"Administrator","id":"xwiki:XWiki.Admin","email":"support@phenotips.org"}],"last_modification_date":"2018-06-04T18:50:40.000Z","patient_name":{"first_name":"","last_name":""},"specificity":{"date":"2018-06-04T16:44:32.345Z","score":0,"server":"monarchinitiative.org"},"nonstandard_features":[],"phenotips_version":"1.4-milestone-4","date_of_birth":{},"date_of_death":{},"family_history":{"consanguinity":false}}},{"id":2,"pedigreeProperties":{"cancers":[{"qualifiers":[{"numericAgeAtDiagnosis":"","notes":"","ageAtDiagnosis":"","laterality":"","primary":true}],"id":"HP:0100273","label":"Colon","affected":true}],"carrierStatus":"affected","nodeNumber":"II-3"},"properties":{"phenotips_version":"1.4-milestone-4","sex":"M","external_id":"","patient_name":{"first_name":"","last_name":""},"life_status":"alive","date_of_birth":{},"date_of_death":{},"genes":[{"gene":"CTSV","id":"ENSG00000136943","status":"candidate"},{"gene":"C6orf48","id":"ENSG00000204387","status":"solved"},{"gene":"CACTIN","id":"ENSG00000105298","status":"carrier"}],"features":[{"id":"HP:0009373","label":"Type C brachydactyly","type":"phenotype","observed":"yes"}],"nonstandard_features":[],"disorders":[{"id":"MIM:211750","label":"C SYNDROME"}],"family_history":{"consanguinity":false}}},{"id":3,"pedigreeProperties":{"cancers":[{"qualifiers":[{"numericAgeAtDiagnosis":"","notes":"","ageAtDiagnosis":"","laterality":"","primary":true}],"id":"HP:0100273","label":"Colon","affected":true}],"carrierStatus":"affected","nodeNumber":"I-3"},"properties":{"date":"2018-06-04T18:51:44.000Z","prenatal_perinatal_history":{"gestation":null},"apgar":{},"notes":{"family_history":"","prenatal_development":"","indication_for_referral":"","genetic_notes":"","medical_history":"","diagnosis_notes":""},"ethnicity":{"maternal_ethnicity":[],"paternal_ethnicity":[]},"genes":[{"gene":"CTSV","id":"ENSG00000136943","status":"candidate"},{"gene":"C6orf48","id":"ENSG00000204387","status":"solved"},{"gene":"CACTIN","id":"ENSG00000105298","status":"carrier"}],"life_status":"alive","sex":"M","clinical-diagnosis":[],"solved":{"status":"unsolved"},"reporter":"Admin","external_id":"","last_modified_by":"Admin","clinicalStatus":"affected","disorders":[{"id":"MIM:211750","label":"C 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G"}],"family_history":{"consanguinity":false}}},{"id":10,"pedigreeProperties":{"nodeNumber":"I-1"},"properties":{"phenotips_version":"1.4-milestone-4","sex":"F","external_id":"","patient_name":{"first_name":"","last_name":""},"life_status":"alive","date_of_birth":{},"date_of_death":{},"genes":[],"features":[],"nonstandard_features":[],"disorders":[],"family_history":{"consanguinity":false}}},{"id":12,"pedigreeProperties":{"carrierStatus":"affected","nodeNumber":"II-1"},"properties":{"phenotips_version":"1.4-milestone-4","sex":"M","external_id":"","patient_name":{"first_name":"Clone1","last_name":""},"life_status":"alive","date_of_birth":{},"date_of_death":{},"genes":[{"gene":"GAPDHP16","id":"ENSG00000225502","status":"candidate"},{"gene":"GALNT7","id":"ENSG00000109586","status":"solved"},{"gene":"TRP-GGG1-1","id":"HGNC:35026","status":"candidate"},{"gene":"gg","id":"gg","status":"candidate"},{"gene":"gg-gg-gg","id":"gg-gg-gg","status":"carrier"}],"features":[{"id":"HP:0011892","label":"Vitamin K deficiency","type":"phenotype","observed":"yes"}],"nonstandard_features":[{"label":"g","type":"phenotype","observed":"yes"}],"disorders":[{"id":"MIM:609887","label":"GLAUCOMA 1, OPEN ANGLE, G"}],"family_history":{"consanguinity":false}}},{"id":14,"pedigreeProperties":{"nodeNumber":"II-2"},"properties":{"phenotips_version":"1.4-milestone-4","sex":"F","external_id":"","patient_name":{"first_name":"","last_name":""},"life_status":"alive","date_of_birth":{},"date_of_death":{},"genes":[],"features":[],"nonstandard_features":[],"disorders":[],"family_history":{"consanguinity":false}}},{"id":16,"pedigreeProperties":{"carrierStatus":"affected","nodeNumber":"III-1"},"properties":{"date":"2018-06-04T17:19:32.000Z","parental_names":{"paternal_first_name":"","maternal_first_name":"","paternal_last_name":"","maternal_last_name":""},"apgar":{},"notes":{"family_history":"","prenatal_development":"","indication_for_referral":"","genetic_notes":"","medical_history":"","diagnosis_notes":""},"ethnicity":{"maternal_ethnicity":[],"paternal_ethnicity":[]},"date_of_birth":{},"solved":{"status":"unsolved"},"external_id":"","clinicalStatus":"affected","disorders":[{"id":"MIM:609887","label":"GLAUCOMA 1, OPEN ANGLE, G"}],"features":[{"id":"HP:0011892","label":"Vitamin K 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              • Assignee:
                asm Andriy Misyura
                Reporter:
                asm Andriy Misyura
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                • Created:
                  Updated:
                  Resolved: