From 1d64718b4611588def9943a9dda1720cc9a6f3e1 Mon Sep 17 00:00:00 2001
From: Bryan Brancotte <bryan.brancotte@pasteur.fr>
Date: Tue, 24 May 2022 13:49:59 +0200
Subject: [PATCH] dump metadata in a celery task, backend serve the content of
the metadata file
---
client/pages/projects/_id.vue | 2 +-
jass/models/project.py | 17 +++++++++++++++++
jass/server.py | 2 +-
jass/tasks.py | 9 +++++++++
4 files changed, 28 insertions(+), 2 deletions(-)
diff --git a/client/pages/projects/_id.vue b/client/pages/projects/_id.vue
index 7597a417..e84c19ac 100644
--- a/client/pages/projects/_id.vue
+++ b/client/pages/projects/_id.vue
@@ -598,7 +598,7 @@ methods:{
this.sharedUrl = "http://"+window.location.host + "/projects/" + this.project.id;
console.log(this.project.id);
this.status=result.status;
- if(result.status.worktable ==="READY" && ! this.isready){
+ if(result.status.metadata ==="READY" && ! this.isready){
await this.$axios.$get('/projects/'+this.project.id+"/gencov").then((async function (result2) {
this.gencov = result2;
diff --git a/jass/models/project.py b/jass/models/project.py
index 88bc7762..c118a9bb 100644
--- a/jass/models/project.py
+++ b/jass/models/project.py
@@ -218,6 +218,12 @@ class Project(BaseModel, abc.ABC):
def get_project_summary_statistics(self):
return get_worktable_summary(self.get_worktable_path())
+ def get_metadata_file_path(self):
+ """
+ Get the path of the metadata json file
+ """
+ return os.path.join(self.get_folder_path(), "metadata.json")
+
def get_project_nsnps(self):
return get_inittable_meta(self.get_worktable_path())
@@ -270,6 +276,11 @@ class Project(BaseModel, abc.ABC):
if filename.endswith(".png"):
os.remove(os.path.join(self.get_folder_path(), filename))
have_removed_file = True
+ try:
+ os.remove(self.get_metadata_file_path())
+ have_removed_file = True
+ except FileNotFoundError:
+ pass
return have_removed_file
@call_with_tb('global_manhattan')
@@ -296,6 +307,12 @@ class Project(BaseModel, abc.ABC):
def create_csv_file(self):
return create_genome_full_csv(self.get_worktable_path(), self.get_csv_path())
+ @call_with_tb('metadata')
+ def create_project_metadata_file(self):
+ with open(self.get_metadata_file_path(), 'w') as f:
+ f.write(json.dumps(self.get_project_nsnps()))
+ print("------ metadata -----")
+
class GlobalProject(Project):
@call_with_tb('worktable')
diff --git a/jass/server.py b/jass/server.py
index b1aa22e4..b040ffd6 100644
--- a/jass/server.py
+++ b/jass/server.py
@@ -106,7 +106,7 @@ def project_gencov_view(project_id: str):
@app.get("/api/projects/{project_id}/metadata")
def project_metadata(project_id: str):
- return load_project(project_id=project_id).get_project_nsnps()
+ return FileResponse(load_project(project_id=project_id).get_metadata_file_path())
@app.get("/api/projects/{project_id}/globalmanhattan")
diff --git a/jass/tasks.py b/jass/tasks.py
index 90e8f769..41e2a7a6 100644
--- a/jass/tasks.py
+++ b/jass/tasks.py
@@ -79,6 +79,12 @@ def create_project_csv_file(project_id):
return project.create_csv_file()
+@celery.task
+def create_project_metadata_file(project_id):
+ project = GlobalProject.load(project_id)
+ return project.create_project_metadata_file()
+
+
@celery.task
def dummy_task():
print("This task to nothing, but help the chain to have a valid status")
@@ -124,6 +130,9 @@ def run_project_analysis_if_needed(project):
if project.get_csv_path() and not os.path.exists(project.get_csv_path()):
post_worktable_tasks.append(create_project_csv_file.si(project.id))
+ if project.get_metadata_file_path() and not os.path.exists(project.get_metadata_file_path()):
+ post_worktable_tasks.append(create_project_metadata_file.si(project.id))
+
if len(tasks) + len(post_worktable_tasks) == 0:
return
main_wf = chain(
--
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