From 33892d3a1f1fa48d252537beda03faeb66e25cc7 Mon Sep 17 00:00:00 2001
From: Remi PLANEL <rplanel@pasteur.fr>
Date: Thu, 25 Jan 2024 15:13:43 +0100
Subject: [PATCH] Update new refseq datatable
---
components/content/RefseqDb.vue | 12 ++++++++----
data/refseq_res.csv | 4 ++--
packages/df-wiki-cli/df_wiki_cli/content/main.py | 2 ++
.../df-wiki-cli/df_wiki_cli/meilisearch/__init__.py | 9 ++++++++-
4 files changed, 20 insertions(+), 7 deletions(-)
diff --git a/components/content/RefseqDb.vue b/components/content/RefseqDb.vue
index 4056d43c..be566e68 100644
--- a/components/content/RefseqDb.vue
+++ b/components/content/RefseqDb.vue
@@ -107,6 +107,8 @@ const scaleTypes = ref<string[]>(['linear', 'sqrt', 'log', 'symlog'])
const selectedTaxoRank = ref("Superkingdom");
const headers = ref([
+ { title: "Assembly", key: "Assembly" },
+
{ title: "Replicon", key: "replicon" },
{
title: "System",
@@ -474,14 +476,16 @@ async function downloadPng(component: ComponentPublicInstance | null, filename:
</CollapsibleChips>
</template>
<template #[`item.type`]="{ item }">
- <v-chip color="info" link size="small" :to="`/defense-systems/${item.type.toLowerCase()}`" target="_blank"> {{
- item.type }}
+ <v-chip color="info" link size="small" :to="`/defense-systems/${item.type.toLowerCase()}`"
+ target="_blank"> {{
+ item.type }}
</v-chip>
</template>
<template #[`item.subtype`]="{ item }">
- <v-chip color="info" link size="small" :to="`/defense-systems/${item.type.toLowerCase()}`" target="_blank"> {{
- item.subtype }}
+ <v-chip color="info" link size="small" :to="`/defense-systems/${item.type.toLowerCase()}`"
+ target="_blank"> {{
+ item.subtype }}
</v-chip>
</template>
</ServerDbTable>
diff --git a/data/refseq_res.csv b/data/refseq_res.csv
index 733fbf04..becb6961 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:f19dff4f92dd3ca79a66fe6835f71261b9a5264f3df176dd005490dd74aa552d
-size 64961046
+oid sha256:1a7d382a7f767718dc48aa49ae3dd9b0159fdffd96e48946c7a167bcbc516deb
+size 68772089
diff --git a/packages/df-wiki-cli/df_wiki_cli/content/main.py b/packages/df-wiki-cli/df_wiki_cli/content/main.py
index ee09705c..17b78657 100644
--- a/packages/df-wiki-cli/df_wiki_cli/content/main.py
+++ b/packages/df-wiki-cli/df_wiki_cli/content/main.py
@@ -270,6 +270,8 @@ def refseq(
writer = csv.DictWriter(out, fieldnames=fieldnames)
writer.writeheader()
for row in reader:
+ if row["sys_id"] == "":
+ row["sys_id"] = f'{row["Assembly"]}_{row["replicon"]}'
result = re.sub(r"^(\w+)\.\d+(_.*)$", r"\1\2", row["sys_id"])
console.print(f"[green]{row['sys_id']} -> {result}")
row["sys_id"] = result
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 3479787c..2963d14d 100644
--- a/packages/df-wiki-cli/df_wiki_cli/meilisearch/__init__.py
+++ b/packages/df-wiki-cli/df_wiki_cli/meilisearch/__init__.py
@@ -11,15 +11,22 @@ from rich.console import Console
console = Console()
+def emptyStringToNone(val: str) -> None | int:
+ if val == "":
+ return None
+ return int(float(val))
+
+
class RefSeqCsv(BaseModel):
sys_id: str
+ Assembly: str
replicon: str
type: str
subtype: str
sys_beg: str
sys_end: str
protein_in_syst: List[str]
- genes_count: int
+ genes_count: Annotated[int | None, BeforeValidator(emptyStringToNone)]
name_of_profiles_in_sys: List[str]
accession_in_sys: List[str]
Superkingdom: str
--
GitLab