Skip to content

Commit 59b2870

Browse files
SeriousHorncatfatimarabab
SeriousHorncat
and
fatimarabab
authored
Alliance genome animal model schema update (#211)
* Revised the animal model cards to supprt new alliance genome animal models json schema and continue support for earlier versions of the schema; added a shared fixtures directory to share between unit tests, and use parameterized unit tests for vitest to cover large number of situational casses for the cards and their rendering * updated the card tests to test using several different models pulled from existing annotations * Linkouts within the animal model card titles to the direct animal model from its source datasource.;Added additional animal model to animal model test fixtures; attempted to have the scroll bar be inside the card so that all 4 corners of the card are rounded (incomplete, reach goal) * [Bug] Fixing the Styling of the Alliance Genome Cards (#210) * Fixed the CSS of the Alliance Genome Card component to match the original Figma design. * Met with team to review options for short term solution for overflow; we decided to overflow the center content for now, streamlined the spacing for lines and elements; tidying everything up * Found a few things to cleanup while drafting the PR * A new import test fixture that takes an existing cpam analysis and swaps a variant & gene with another one, so that there is an analysis that has one matching variant&gene but an additional non-existing variant&gene. * Fixed zebrafish annotation configuration for summaries bug --------- Co-authored-by: Rabab Fatima <rfatima@uab.edu>
1 parent 51155ef commit 59b2870

10 files changed

Lines changed: 1166 additions & 319 deletions

File tree

‎CHANGELOG.md‎

Lines changed: 3 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -16,10 +16,13 @@
1616
- Rosalution page titles reflect the name of the analysis being viewed. Annotation pages include the analysis' name
1717
along with the selected gene and variant.
1818
- The build version of Rosalution is in the footer of each Rosalution page after login
19+
- Animal model cards are backwards compatible with past and current versions of the JSON schema from Alliance Genome.
20+
- Animal model card titles linkout directly to the animal model from their source database if the URL is available.
1921

2022
### Bugs
2123

2224
- Missing Favicon with rosalution's logo on each Rosalution page now present
25+
- Fixed the styling of Alliance Genome Cards in the Annotation View to display text in a more distinct and readable format.
2326

2427
## 0.8.6
2528

‎backend/annotation-render-layout.json‎

Lines changed: 36 additions & 6 deletions
Original file line numberDiff line numberDiff line change
@@ -568,14 +568,24 @@
568568
"props": {
569569
"label": "AG Summary"
570570
}
571-
},
571+
}
572+
]
573+
},
574+
{
575+
"class": "",
576+
"datasets": [
572577
{
573578
"dataset": "Rat_Alliance_Genome_RGD_Summary",
574579
"type": "text-dataset",
575580
"props": {
576581
"label": "RGD Summary"
577582
}
578-
},
583+
}
584+
]
585+
},
586+
{
587+
"class": "",
588+
"datasets": [
579589
{
580590
"dataset": "Rat_Alliance_Genome_Models",
581591
"type": "card-dataset"
@@ -617,14 +627,24 @@
617627
"props": {
618628
"label": "AG Summary"
619629
}
620-
},
630+
}
631+
]
632+
},
633+
{
634+
"class": "",
635+
"datasets": [
621636
{
622637
"dataset": "Mouse_Alliance_Genome_MGI_Summary",
623638
"type": "text-dataset",
624639
"props": {
625640
"label": "MGI Summary"
626641
}
627-
},
642+
}
643+
]
644+
},
645+
{
646+
"class": "",
647+
"datasets": [
628648
{
629649
"dataset": "Mouse_Alliance_Genome_Models",
630650
"type": "card-dataset"
@@ -666,14 +686,24 @@
666686
"props": {
667687
"label": "AG Summary"
668688
}
669-
},
689+
}
690+
]
691+
},
692+
{
693+
"class": "",
694+
"datasets": [
670695
{
671696
"dataset": "Zebrafish_Alliance_Genome_ZFIN_Summary",
672697
"type": "text-dataset",
673698
"props": {
674699
"label": "ZFIN Summary"
675700
}
676-
},
701+
}
702+
]
703+
},
704+
{
705+
"class": "",
706+
"datasets": [
677707
{
678708
"dataset": "Zebrafish_Alliance_Genome_Models",
679709
"type": "card-dataset"

‎etc/fixtures/import/dev-test-analysis-C-PAM0084-alternate-duplicate.json‎

Lines changed: 160 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,160 @@
1+
{
2+
"date": "2022-12-27T16:32:19.000Z",
3+
"parental_names": {
4+
"paternal_first_name": "",
5+
"maternal_first_name": "",
6+
"paternal_last_name": "",
7+
"maternal_last_name": ""
8+
},
9+
"apgar": {},
10+
"notes": {
11+
"family_history": "",
12+
"prenatal_development": "",
13+
"indication_for_referral": "",
14+
"genetic_notes": "",
15+
"medical_history": "",
16+
"diagnosis_notes": ""
17+
},
18+
"ethnicity": {
19+
"maternal_ethnicity": [],
20+
"paternal_ethnicity": []
21+
},
22+
"date_of_birth": {
23+
"year": 2014
24+
},
25+
"solved": {
26+
"status": "unsolved"
27+
},
28+
"external_id": "CPAM0084-duplicate-again",
29+
"variants": [
30+
{
31+
"start_position": "7100249",
32+
"evidence": [
33+
"rare"
34+
],
35+
"gene": "ENSG00000132535",
36+
"chromosome": "17",
37+
"inheritance": "unknown",
38+
"end_position": "7100249",
39+
"transcript": "NM_001365.4",
40+
"sanger": "NA",
41+
"zygosity": "heterozygous",
42+
"interpretation": "likely_pathogenic",
43+
"reference_genome": "GRCh37",
44+
"protein": "p.Glu347ArgTer12",
45+
"effect": "deletion_frameshift",
46+
"cdna": "c.1039del",
47+
"segregation": "NA"
48+
},
49+
{
50+
"evidence": [
51+
"reported"
52+
],
53+
"gene": "ENSG00000198563",
54+
"chromosome": "6X",
55+
"inheritance": "NA",
56+
"transcript": "NM_004640.7",
57+
"sanger": "NA",
58+
"zygosity": "heterozygous",
59+
"interpretation": "pathogenic",
60+
"reference_genome": "GRCh37",
61+
"protein": "p.Gly92Asp",
62+
"cdna": "c.275G>A"
63+
}
64+
],
65+
"clinicalStatus": "affected",
66+
"disorders": [],
67+
"features": [
68+
{
69+
"id": "HP:0000739",
70+
"label": "Anxiety",
71+
"type": "phenotype",
72+
"observed": "yes"
73+
},
74+
{
75+
"id": "HP:0000750",
76+
"label": "Delayed speech and language development",
77+
"type": "phenotype",
78+
"observed": "yes"
79+
},
80+
{
81+
"id": "HP:0001249",
82+
"label": "Intellectual disability",
83+
"type": "phenotype",
84+
"observed": "yes"
85+
},
86+
{
87+
"id": "HP:0001260",
88+
"label": "Dysarthria",
89+
"type": "phenotype",
90+
"observed": "yes"
91+
},
92+
{
93+
"id": "HP:0001290",
94+
"label": "Generalized hypotonia",
95+
"type": "phenotype",
96+
"observed": "yes"
97+
},
98+
{
99+
"id": "HP:0001298",
100+
"label": "Encephalopathy",
101+
"type": "phenotype",
102+
"observed": "yes"
103+
},
104+
{
105+
"id": "HP:0002194",
106+
"label": "Delayed gross motor development",
107+
"type": "phenotype",
108+
"observed": "yes"
109+
},
110+
{
111+
"id": "HP:0002370",
112+
"label": "Poor coordination",
113+
"type": "phenotype",
114+
"observed": "yes"
115+
},
116+
{
117+
"id": "HP:0002425",
118+
"label": "Anarthria",
119+
"type": "phenotype",
120+
"observed": "yes"
121+
},
122+
{
123+
"id": "HP:0007018",
124+
"label": "Attention deficit hyperactivity disorder",
125+
"type": "phenotype",
126+
"observed": "yes"
127+
},
128+
{
129+
"id": "HP:0012758",
130+
"label": "Neurodevelopmental delay",
131+
"type": "phenotype",
132+
"observed": "yes"
133+
},
134+
{
135+
"id": "HP:0100702",
136+
"label": "Arachnoid cyst",
137+
"type": "phenotype",
138+
"observed": "yes"
139+
}
140+
],
141+
"genes": [
142+
{
143+
"gene": "DDX39B",
144+
"id": "ENSG00000198563",
145+
"strategy": [
146+
"sequencing"
147+
],
148+
"status": "candidate"
149+
},
150+
{
151+
"gene": "DLG4",
152+
"id": "ENSG00000132535",
153+
"strategy": [
154+
"sequencing"
155+
],
156+
"status": "candidate"
157+
}
158+
],
159+
"last_modified_by": "affoksinska"
160+
}

‎etc/fixtures/initial-seed/annotations-config.json‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -429,7 +429,7 @@
429429
"annotation_source_type": "forge",
430430
"base_string_cache": true,
431431
"base_string": "{ZEBRAFISH_SUMMARY_ALLIANCE_GENOME_CACHE}",
432-
"attribute": ".Zebrafish_Zebrafish_Information_Network_url | { Zebrafish_Alliance_Genome_Automated_Summary: .automatedGeneSynopsis }",
432+
"attribute": ".Zebrafish_Alliance_Genome_Automated_Summary | { Zebrafish_Alliance_Genome_Automated_Summary: .automatedGeneSynopsis }",
433433
"dependencies": [
434434
"ZEBRAFISH_SUMMARY_ALLIANCE_GENOME_CACHE"
435435
],
@@ -444,7 +444,7 @@
444444
"annotation_source_type": "forge",
445445
"base_string_cache": true,
446446
"base_string": "{ZEBRAFISH_SUMMARY_ALLIANCE_GENOME_CACHE}",
447-
"attribute": ".Zebrafish_Zebrafish_Information_Network_url | { Zebrafish_Alliance_Genome_ZFIN_Summary: .geneSynopsis }",
447+
"attribute": ".Zebrafish_Alliance_Genome_ZFIN_Summary | { Zebrafish_Alliance_Genome_ZFIN_Summary: .geneSynopsis }",
448448
"dependencies": [
449449
"ZEBRAFISH_SUMMARY_ALLIANCE_GENOME_CACHE"
450450
],

0 commit comments

Comments
 (0)