run computation when opening the project, not when creating it.

Check presence of files, and status of the encompassing task to know if computation is already running, or should be started.

Closes #110

jass/models/project.py

@@ -7,6 +7,7 @@ import abc
 import shutil
 from datetime import datetime
 from pathlib import Path
+from celery import states
 import json
 from typing import List, Optional, Union, Dict
 try:
@@ -38,6 +39,7 @@ from jass.models.worktable import (
     get_worktable_phenolist,
     create_worktable_file,
     create_genome_full_csv,
+    create_genome_full_csv_lock_file,
 )
 
 from jass.config import config
@@ -66,6 +68,14 @@ def call_with_tb(status_key):
     return inner_dec
 
 
+def get_project_update_progress_callback(project_id):
+    def __update_progress(progress: int):
+        p = load_project(project_id)
+        p.update_progress(progress)
+        p.save()
+    return __update_progress
+
+
 class ProjectStatusEnum(str, Enum):
     does_not_exist = "DOES_NOT_EXIST"
     creating = "CREATING"
@@ -86,6 +96,7 @@ class Project(BaseModel, abc.ABC):
     delayed_gen_csv_file: Optional[bool] = True
     status: Optional[Dict[str,ProjectStatusEnum]] = {}
     progress: Optional[int] = 0
+    celery_id: Optional[str] = None
 
     def get_hash(self):
         m = hashlib.md5()
@@ -124,6 +135,17 @@ class Project(BaseModel, abc.ABC):
     def create_id(self):
         return self.get_hash().hexdigest()
 
+    def has_computation_going_on(self):
+        if self.celery_id is None:
+            return False
+        from jass.tasks import celery
+        celery_task = celery.AsyncResult(self.celery_id)
+        print(self.celery_id, celery_task.status)
+        if celery_task.status in [states.FAILURE, states.SUCCESS, states.PENDING]:
+            # PENDING means "unknown task" for celery
+            return False
+        return True
+
     @classmethod
     def get_folder_path_from_id(cls, project_id):
         return os.path.join(config["PROJECTS_DIR"], f"project_{project_id}")
@@ -219,6 +241,27 @@ class Project(BaseModel, abc.ABC):
     def create_worktable_file(self):
         pass
 
+    def delete_large_files(self):
+        # delete the worktable file
+        project_hdf_path = self.get_worktable_path()
+        if os.path.exists(project_hdf_path):
+            os.remove(project_hdf_path)
+        # as a consequence, its creation will have to be redone, so set progress to 0 and remove is status.
+        self.progress = 0
+        try:
+            del self.status['worktable']
+        except KeyError:
+            # worktable not in status
+            pass
+        self.save()
+
+        if self.delayed_gen_csv_file:
+            # Delete the full csv file if it exists, and re-set the lock file indicating that it should be generated
+            create_genome_full_csv_lock_file(project_hdf_path)
+            csv_path = self.get_csv_path()
+            if os.path.exists(csv_path):
+                os.remove(csv_path)
+
     @call_with_tb('global_manhattan')
     def create_global_manhattan_plot(self):
         return create_global_plot(
@@ -258,8 +301,8 @@ class GlobalProject(Project):
             chunk_size=self.chunk_size,
             significance_treshold=self.significance_threshold,
             post_filtering=self.post_filtering,
-            delayed_gen_csv_file=self.delayed_gen_csv_file
-            ,callback_report= self.update_progress
+            delayed_gen_csv_file=self.delayed_gen_csv_file,
+            callback_report=get_project_update_progress_callback(self.id),
         )
 
 
@@ -296,11 +339,11 @@ class LocalProject(Project):
             chromosome=self.chromosome,
             pos_Start=self.start,
             pos_End=self.end,
-            callback_report= self.update_progress
+            callback_report=get_project_update_progress_callback(self.id),
         )
 
 
-def load_project(project_id):
+def load_project(project_id, flag_as_visited: bool = True):
     path = os.path.join(Project.get_folder_path_from_id(project_id), "meta.json")
     with open(path, "r") as fp:
         project = parse_raw_as(
@@ -310,7 +353,8 @@ def load_project(project_id):
             ],
             "".join(fp.readlines()),
         )
-        flag_project_as_visited(project_id)
+        if flag_as_visited:
+            flag_project_as_visited(project_id)
         return project