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Update orthology association table #930

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merged 6 commits into from
Dec 18, 2024
Merged

Update orthology association table #930

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e6eef6a
Define columns for orthology section separately from the generic method
kevinschaper Dec 13, 2024
5320402
turn off sorting on ortholog column (it's a composite of two columns)
kevinschaper Dec 13, 2024
3e50071
for now, remove all of the sorting for orthologs. The ones that work …
kevinschaper Dec 13, 2024
7ac9401
remove 30% 5% 30% width formatting of first three columns from AppTable
kevinschaper Dec 13, 2024
f040d80
set key on has_evidence links to source.id
kevinschaper Dec 17, 2024
efcf884
removed unused index var in evidence column of ortholog table
kevinschaper Dec 18, 2024
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10 changes: 2 additions & 8 deletions backend/src/monarch_py/solr_cli.py
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Original file line number Diff line number Diff line change
Expand Up @@ -210,11 +210,7 @@ def multi_entity_associations(
] = None,
counterpart_category: Annotated[
Optional[List[str]],
typer.Option(
"--counterpart-category",
"-c",
help="A comma-separated list of counterpart categories"
),
typer.Option("--counterpart-category", "-c", help="A comma-separated list of counterpart categories"),
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This was autoformatting from make format

] = None,
limit: fields.LimitOption = 20,
offset: fields.OffsetOption = 0,
Expand Down Expand Up @@ -306,9 +302,7 @@ def histopheno(

@solr_app.command("association-counts")
def association_counts(
entity_id: Annotated[
str, typer.Argument(help="The entity to get association counts for")
],
entity_id: Annotated[str, typer.Argument(help="The entity to get association counts for")],
fmt: fields.FormatOption = fields.OutputFormat.json,
output: fields.OutputOption = None,
):
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autoformatting

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15 changes: 0 additions & 15 deletions frontend/src/components/AppTable.vue
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Expand Up @@ -454,21 +454,6 @@ const ariaSort = computed(() => {
text-transform: capitalize;
}

/* first th */
.th:nth-child(1) {
width: 30%;
}

/* second th */
.th:nth-child(2) {
width: 5%;
}

/* third th */
.th:nth-child(3) {
width: 30%;
}

/** body cells */
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This is where I might be causing trouble by altering potentially broader impact css, but I think I'm actually reducing the trouble that this overly broad css was causing. This PR is the first of many for defining the columns for each association type separately, and it doesn't make sense that we'll always want these widths. Plus, if you scan through Human Disease on this branch, most tables look better, in particular it gives as much space as possible to disease models.

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Yeah, we really need the new UI person to do a CSS review across the app but this looks good for now.

.td {
border-bottom: solid 2px $light-gray;
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78 changes: 74 additions & 4 deletions frontend/src/pages/node/AssociationsTable.vue
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Expand Up @@ -24,6 +24,31 @@
:total="associations.total"
@download="download"
>
<!-- ortholog -->
<template #ortholog="{ row }">
<AppNodeBadge
v-if="row.direction === AssociationDirectionEnum.outgoing"
:node="{
id: row.object,
name: row.object_label,
category: 'biolink:Gene',
info: row.object_taxon_label,
}"
:breadcrumbs="getBreadcrumbs(node, row, 'subject')"
/>

<AppNodeBadge
v-if="row.direction === AssociationDirectionEnum.incoming"
:node="{
id: row.subject,
name: row.subject_label,
category: 'biolink:Gene',
info: row.subject_taxon_label,
}"
:breadcrumbs="getBreadcrumbs(node, row, 'object')"
/>
</template>

<!-- subject -->
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how to display an ortholog cell

<template #subject="{ row }">
<AppNodeBadge
Expand Down Expand Up @@ -65,6 +90,15 @@
<span v-else class="empty">No info</span>
</template>

<template #has_evidence="{ row }">
<AppLink
v-for="(source, index) in row.has_evidence_links"
:key="index"
:to="source.url || ''"
>{{ source.id }}</AppLink
>
</template>

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how to display a has_evidence cell (borrowed from SectionAssociationDetails)

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You likely shouldn't be using index as a key here. If the table gets resorted, this may not be re-rendered. See the Vue documentation, and also #892 for a fix to a similar bug.

The key should uniquely identify what objcet this is rendering. I'm not totally familiar with this data structure, but I'm guessing that would be source.id.

For example, if I had the set of rows:

[
  { source: { id: 'a' }}, // index is 0
  { source: { id: 'b' }}, // index is 1
  { source: { id: 'c' }}, // index is 2
]

Vue would render if fine initially. But if I resorted those rows:

[
  { source: { id: 'c' }}, // index is 0
  { source: { id: 'b' }}, // index is 1
  { source: { id: 'a' }}, // index is 2
]

Vue would not know that it would need to re-render those rows, since the key of the elements never changes-- the first element always has index 0, the second index 1, and so on.

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fixed! thanks for catching that!

<!-- button to show details -->
<template #details="{ row }">
<AppButton text="Details" icon="info-circle" @click="openModal(row)" />
Expand Down Expand Up @@ -180,8 +214,46 @@ const search = ref("");

type Datum = keyof DirectionalAssociation;

/** Orholog columns */

const orthologColoumns = computed<Cols<Datum>>(() => {
return [
{
slot: "taxon",
key: "taxon" as Datum,
heading: "Taxon",
},
{
slot: "ortholog",
key: "ortholog" as Datum,
heading: "Ortholog",
},
{
slot: "has_evidence",
key: "has_evidence" as Datum,
heading: "Evidence",
},
{
slot: "primary_knowledge_source",
key: "primary_knowledge_source" as Datum,
heading: "Source",
},
{ slot: "divider" },
{
slot: "details",
key: "evidence_count",
heading: "Details",
align: "center",
},
];
});

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which columns should be shown for the ortholog section

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I really like how you are using this data structure.

/** table columns */
const cols = computed((): Cols<Datum> => {
if (props.category.id.includes("GeneToGeneHomology")) {
return orthologColoumns.value;
}

/** standard columns, always present */
const baseCols: Cols<Datum> = [
{
Expand Down Expand Up @@ -219,14 +291,12 @@ const cols = computed((): Cols<Datum> => {
let extraCols: Cols<Datum> = [];

/** taxon column. exists for many categories, so just add if any row has taxon. */
if (
props.category.id.includes("GeneToGeneHomology") ||
props.category.id.includes("Interaction")
)
if (props.category.id.includes("Interaction")) {
extraCols.push({
slot: "taxon",
heading: "Taxon",
});
}

if (
props.node.in_taxon_label == "Homo sapiens" &&
Expand Down
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