From 22a2e99608a27c1c5d4c974e0662e517e1bd520d Mon Sep 17 00:00:00 2001
From: Bryan Brancotte <bryan.brancotte@pasteur.fr>
Date: Mon, 30 Oct 2023 17:42:41 +0100
Subject: [PATCH] transmit initTable name when creating project
---
client/pages/phenotypes.vue | 7 ++++++-
jass/models/phenotype.py | 2 +-
jass/server.py | 2 +-
jass/tasks.py | 12 ++++++------
4 files changed, 14 insertions(+), 9 deletions(-)
diff --git a/client/pages/phenotypes.vue b/client/pages/phenotypes.vue
index c64e3c4d..16f0475c 100644
--- a/client/pages/phenotypes.vue
+++ b/client/pages/phenotypes.vue
@@ -87,7 +87,12 @@ export default {
},
runAnalysis(){
const { selectedRows, $axios } = this;
- const phenotypeIds = {phenotypeID: selectedRows.map(function(phenotype){return phenotype.id})};
+ const phenotypeIds = {
+ phenotypeID: selectedRows.map(function(phenotype){return phenotype.id}),
+ initTableName: "initTable.hdf5"
+ // phenotypeID: ["z_MAGIC_FAST-GLUCOSE", "z_MAGIC_FAST-INSULIN"],
+ // initTableName: "initTableTest.hdf5"
+ };
console.log("REQUEST POST")
console.log(phenotypeIds)
diff --git a/jass/models/phenotype.py b/jass/models/phenotype.py
index c99b7d4b..5abe2ec6 100644
--- a/jass/models/phenotype.py
+++ b/jass/models/phenotype.py
@@ -85,5 +85,5 @@ class ProjectNameModel(BaseModel):
raise ValueError(f"Prohibited char, only \"{_initTableNamePattern.pattern}\" allowed.")
return value
-class PhenotypeIdList(BaseModel):
+class PhenotypeIdList(ProjectNameModel, BaseModel):
phenotypeID: List[str] = []
diff --git a/jass/server.py b/jass/server.py
index da2feb99..9314435d 100644
--- a/jass/server.py
+++ b/jass/server.py
@@ -70,7 +70,7 @@ def inittable_meta():
def project_create(phenotype_id_list: PhenotypeIdList):
return create_project(
phenotype_id_list.phenotypeID,
- get_available_phenotypes(os.path.join(config["DATA_DIR"], "initTable.hdf5")),
+ init_table_name=phenotype_id_list.initTableName,
)
diff --git a/jass/tasks.py b/jass/tasks.py
index 25c96082..82e9b9d9 100644
--- a/jass/tasks.py
+++ b/jass/tasks.py
@@ -10,7 +10,7 @@ from flask import Flask
import jass.models.project
from jass.models.project import GlobalProject, Project, ensure_space_in_project_dir
-from jass.models.phenotype import Phenotype
+from jass.models.phenotype import Phenotype, get_available_phenotypes
from jass.config import config
@@ -155,22 +155,22 @@ def run_project_analysis_if_needed(project):
def create_project(
phenotype_ids: List[str],
- available_phenotypes: List[Phenotype],
chromosome: str = None,
start: str = None,
end: str = None,
+ init_table_name: str = None,
):
-
- available_phenotype_ids = [phenotype.id for phenotype in available_phenotypes]
+ init_table_path = os.path.join(config["DATA_DIR"], init_table_name)
+ available_phenotypes=get_available_phenotypes(init_table_path)
unavailable_requested_ids = set(phenotype_ids).difference(
- set(available_phenotype_ids)
+ set(phenotype.id for phenotype in available_phenotypes)
)
if len(unavailable_requested_ids) > 0:
raise HTTPException(status_code=404, detail=f"Phenotype IDs not found: {','.join(unavailable_requested_ids)}")
phenotypes = [
phenotype for phenotype in available_phenotypes if phenotype.id in phenotype_ids
]
- project = GlobalProject(phenotypes=phenotypes)
+ project = GlobalProject(phenotypes=phenotypes, init_table_path=init_table_path)
project.create(fail_if_exists=False)
ensure_space_in_project_dir(except_project_id=project.id)
--
GitLab