diff --git a/components/content/RefseqDb.vue b/components/content/RefseqDb.vue
index 08ca0836885ee5a808d2cccdb5dd6a0ee4119728..91e0d266785346d91290ff0292c9e589d7830f62 100644
--- a/components/content/RefseqDb.vue
+++ b/components/content/RefseqDb.vue
@@ -25,29 +25,51 @@ onBeforeMount(async () => {
index: toValue(dbName), query: "", params: {
facets: ["*"],
filter: [],
- limit: 500000,
- sort: ["type:asc"]
+ page: 1,
+ hitsPerPage: 25,
+
}
})
autocompleteMeiliFacetsProps.value.facetDistribution = toValue(data)?.facetDistribution
- allHitsDb.value = toValue(data)?.hits
-
+ // allHitsDb.value = toValue(data)?.hits
+ const { data: taxo } = await useAsyncMeiliSearch({
+ index: toValue("refseqtaxo"), query: "", params: {
+ facets: ["*"],
+ filter: [],
+ page: 1,
+ hitsPerPage: 25,
+ }
+ })
+ taxonomyFacet.value = toValue(taxo)?.facetDistribution
})
-const allHitsDb = ref<Record<string, any>[] | undefined>(undefined)
+const taxonomyFacet = ref<Record<string, any> | undefined>(undefined)
+// const allHitsDb = ref<Record<string, any>[] | undefined>(undefined)
onMounted(async () => {
+
const { data } = await useAsyncMeiliSearch({
index: toValue(dbName), query: "", params: {
facets: ["*"],
filter: [],
- // page: 1,
- // hitsPerPage: 25,
- limit: 500000,
- sort: ["type:asc"]
+ page: 1,
+ hitsPerPage: 25,
+ // limit: 500000,
+ // sort: ["type:asc"]
}
})
+
autocompleteMeiliFacetsProps.value.facetDistribution = toValue(data)?.facetDistribution
- allHitsDb.value = toValue(data)?.hits
+ // allHitsDb.value = toValue(data)?.hits
+
+ const { data: taxo } = await useAsyncMeiliSearch({
+ index: toValue("refseqtaxo"), query: "", params: {
+ facets: ["*"],
+ filter: [],
+ page: 1,
+ hitsPerPage: 25,
+ }
+ })
+ taxonomyFacet.value = toValue(taxo)?.facetDistribution
})
@@ -104,12 +126,13 @@ const availableTaxo: Ref<string[]> = ref([
"genus",
"family",
"order",
+ "class",
"phylum",
"Superkingdom"
]);
const scaleTypes = ref<string[]>(['linear', 'sqrt', 'log', 'symlog'])
-const selectedTaxoRank = ref("Superkingdom");
+const selectedTaxoRank = ref<"species" | "genus" | "family" | "order" | "class" | "phylum" | "Superkingdom">("Superkingdom");
const headers = ref([
{
@@ -152,12 +175,25 @@ const computedWidth = computed(() => {
const allHits: Ref<Record<string, any> | undefined> = ref(undefined)
+
const pendingAllHits = ref(false)
async function getAllHits(params: { index: string, params: Record<string, any>, query: string }) {
+ if (!params?.params?.filter || params?.params?.filter?.length === 0) {
+ selectedTaxoRank.value = "Superkingdom"
+
+ }
if (params.index === toValue(dbName)) {
+
pendingAllHits.value = true
try {
- const { data, error } = await useAsyncMeiliSearch(params)
+ console.log(params.params.filter)
+ const { data, error } = await useAsyncMeiliSearch({
+ ...params,
+ params: {
+ ...params.params,
+ 'attributesToRetrieve': ['type', 'Assembly', ...toValue(availableTaxo)]
+ }
+ })
allHits.value = data.value
console.log(error.value)
} finally {
@@ -303,15 +339,16 @@ const binPlotGroup = computed(() => {
fill: {
label: `Normalize by ${selectedTaxoRank.value} clade`,
reduceIndex: function (I, X) {
- const toValAssemblyPerRank = toValue(assemblyPerRank)
- if (toValAssemblyPerRank?.size > 0) {
+ const toValTaxonomyFacet = toValue(taxonomyFacet)
+ if (toValTaxonomyFacet !== undefined) {
const clade = X[I[0]][selectedTaxoRank.value]
const system = X[I[0]].type
// Get the list of item for this group
const itemsPerGroup = d3.rollup(I.map(index => {
return X[index]
}), D => D.length, d => d.type, d => d.Assembly)
- const countForClade = toValAssemblyPerRank.get(clade).size
+ const countForClade = toValTaxonomyFacet[selectedTaxoRank.value][clade]
+ console.log(`${itemsPerGroup.get(system).size} / ${countForClade}`)
const frequency = (itemsPerGroup.get(system).size / countForClade) * 100
return frequency
}
@@ -349,15 +386,6 @@ const binPlotDataOptions = computed(() => {
} : null
})
-const assemblyPerRank = computed(() => {
- const toValueAllHits = toValue(allHitsDb)
-
- if (toValueAllHits && toValueAllHits?.length > 0) {
- return d3.rollup(toValueAllHits, D => D.length, d => d[toValue(selectedTaxoRank)], d => d.Assembly)
- }
-})
-
-
const scaleType = ref("linear")
const systemsDistributionPlot = ref<ComponentPublicInstance | null>(null)
diff --git a/data/refseq_res.csv b/data/refseq_res.csv
index 85812c477a9bac3da1201f81cff06a539ec0c2ec..becb696192d60bc89a646284da9d6d86ba120069 100644
--- a/data/refseq_res.csv
+++ b/data/refseq_res.csv
@@ -1,3 +1,3 @@
version https://git-lfs.github.com/spec/v1
-oid sha256:4801eea1e299738e8d01b233091f81404410799a6901da74b11131d12b390158
-size 73983918
+oid sha256:1a7d382a7f767718dc48aa49ae3dd9b0159fdffd96e48946c7a167bcbc516deb
+size 68772089
diff --git a/packages/df-wiki-cli/df_wiki_cli/meilisearch/__init__.py b/packages/df-wiki-cli/df_wiki_cli/meilisearch/__init__.py
index 2963d14df8773cba9b7dc759ec247fe984bdfca7..1111225625f07cbc4584ae571646350cbe00a998 100644
--- a/packages/df-wiki-cli/df_wiki_cli/meilisearch/__init__.py
+++ b/packages/df-wiki-cli/df_wiki_cli/meilisearch/__init__.py
@@ -78,6 +78,66 @@ class StrucutreStatistics(BaseModel):
Foldseek_name: Optional[str]
+def update_refseqtaxo(host: str, key: str, file: Path, document: str):
+ client = meilisearch.Client(host, key)
+ index = client.index(document.lower())
+ documents = []
+ with open(file, "r") as csvfile:
+ csvreader = csv.DictReader(csvfile)
+ assembly = {}
+ for row in csvreader:
+ assembly_id = row["Assembly"]
+ assembly[row["Assembly"]] = {
+ k: row[k]
+ for k in (
+ "Superkingdom",
+ "phylum",
+ "class",
+ "order",
+ "family",
+ "genus",
+ "species",
+ "Assembly",
+ )
+ if k in row
+ }
+ assembly[assembly_id]["Assembly"] = assembly[assembly_id]["Assembly"].split('.')[0]
+ for item in assembly.values():
+ documents.append(item)
+ tasks = index.add_documents_in_batches(documents, primary_key="Assembly")
+ print(tasks)
+ index.update_pagination_settings({"maxTotalHits": 1000000})
+ index.update_filterable_attributes(
+ body=[
+ "Superkingdom",
+ "phylum",
+ "class",
+ "order",
+ "family",
+ "genus",
+ "species",
+ "Assembly",
+ ]
+ )
+ index.update_sortable_attributes(
+ [
+ "Superkingdom",
+ "phylum",
+ "class",
+ "order",
+ "family",
+ "genus",
+ "species",
+ "Assembly",
+ ]
+ )
+ params = {
+ "maxValuesPerFacet": 1000000,
+ "sortFacetValuesBy": {"*": "count"},
+ }
+ index.update_faceting_settings(params)
+
+
def update_refseq(
host: str,
key: str,
@@ -104,10 +164,12 @@ def update_refseq(
index.update_filterable_attributes(
body=[
"replicon",
+ "Assembly",
"type",
"subtype",
"Superkingdom",
"phylum",
+ "class",
"order",
"family",
"genus",
@@ -117,10 +179,12 @@ def update_refseq(
index.update_sortable_attributes(
[
"replicon",
+ "Assembly",
"type",
"subtype",
"Superkingdom",
"phylum",
+ "class",
"order",
"family",
"genus",
diff --git a/packages/df-wiki-cli/df_wiki_cli/meilisearch/main.py b/packages/df-wiki-cli/df_wiki_cli/meilisearch/main.py
index e7e3037766ce72d268bfdae830e4e52de3d34b03..f32ac8c3af221457efe03522b7e0bdf206f0c610 100644
--- a/packages/df-wiki-cli/df_wiki_cli/meilisearch/main.py
+++ b/packages/df-wiki-cli/df_wiki_cli/meilisearch/main.py
@@ -2,7 +2,12 @@ import typer
import meilisearch
from typing_extensions import Annotated
from pathlib import Path
-from df_wiki_cli.meilisearch import update_refseq, update_structure, update_systems
+from df_wiki_cli.meilisearch import (
+ update_refseq,
+ update_structure,
+ update_systems,
+ update_refseqtaxo,
+)
from enum import Enum
from types import SimpleNamespace
from rich.console import Console
@@ -14,6 +19,7 @@ app = typer.Typer()
class Documents(str, Enum):
+ refseqtaxo = "refseqtaxo"
refseq = "refseq"
structure = "structure"
systems = "systems"
@@ -55,6 +61,8 @@ def update(
] = Documents.refseq,
content_type: Annotated[str, typer.Option(help="Content-Type header")] = "text/csv",
):
+ if document == "refseqtaxo":
+ update_refseqtaxo(ctx.obj.host, ctx.obj.key, file, document)
if document == "refseq":
update_refseq(ctx.obj.host, ctx.obj.key, file, document)
if document == "structure":