From e70b3a91e41ebf93271a76c20bd83edd8017ef10 Mon Sep 17 00:00:00 2001
From: Remi PLANEL <rplanel@pasteur.fr>
Date: Fri, 12 Apr 2024 18:15:15 +0200
Subject: [PATCH] fix issue with refseqsanitized index
---
.gitlab-ci.yml | 2 +-
packages/df-wiki-cli/df_wiki_cli/meilisearch/main.py | 3 ++-
packages/df-wiki-cli/df_wiki_cli/meilisearch/update/main.py | 4 ++--
3 files changed, 5 insertions(+), 4 deletions(-)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index e31e3afe..5ad0b6ca 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -281,7 +281,7 @@ lint:
df-wiki-cli meilisearch
--host ${MEILI_HOST}
--key "${MEILI_MASTER_KEY}"
- index-update refseqsanitized index
+ index-update refseqsanitized sys_id
- >
df-wiki-cli
meilisearch
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 b7bbffdb..ddf75daf 100644
--- a/packages/df-wiki-cli/df_wiki_cli/meilisearch/main.py
+++ b/packages/df-wiki-cli/df_wiki_cli/meilisearch/main.py
@@ -52,7 +52,8 @@ def main(
def delete_all_documents(ctx: typer.Context, id: str):
client = meilisearch.Client(ctx.obj.host, ctx.obj.key)
index = client.index(id)
- index.delete_all_documents()
+ tasks = index.delete_all_documents()
+ console.print(tasks)
@app.command()
diff --git a/packages/df-wiki-cli/df_wiki_cli/meilisearch/update/main.py b/packages/df-wiki-cli/df_wiki_cli/meilisearch/update/main.py
index e23eae19..ef1e2c20 100644
--- a/packages/df-wiki-cli/df_wiki_cli/meilisearch/update/main.py
+++ b/packages/df-wiki-cli/df_wiki_cli/meilisearch/update/main.py
@@ -523,7 +523,7 @@ def split_on_comma(str_val: Optional[str]) -> Optional[List[str]]:
return None
-def update_refseq(client, document, file):
+def update_refseq(client, document, file, primary_key="sys_id"):
index = client.index(document.lower())
documents = []
with open(file, "r") as csvfile:
@@ -536,7 +536,7 @@ def update_refseq(client, document, file):
row["accession_in_sys"] = split_on_comma(row["accession_in_sys"])
doc = RefSeqCsv(**row)
documents.append(doc.model_dump(by_alias=True))
- tasks = index.add_documents_in_batches(documents, primary_key="sys_id")
+ tasks = index.add_documents_in_batches(documents, primary_key=primary_key)
for task in tasks:
console.print(task)
index.update_pagination_settings({"maxTotalHits": 1000000})
--
GitLab