feat(server): added route to get user dynamic run status

apps/server/app.py

@@ -1,20 +1,17 @@
 from flask import Flask
 from flask_cors import CORS
 from flask_restful import Api
-from flask_sock import Sock
 from server.config import Config
 from server.resources.downloads import DownloadDynamicAssets
 from server.resources.generate_acpype import GenerateAcpypeCommands
 from server.resources.generate_apo import GenerateApoCommands
 from server.resources.generate_prodrg import GenerateProdrgCommands
 from server.resources.health import Health
 from server.resources.run import RunDynamic
-from server.utils.run_command import run_command
 
 app = Flask(__name__)
 app.config.from_object(Config)
 api = Api(app)
-sock = Sock(app)
 
 CORS(app)
 
@@ -34,19 +31,5 @@
 api.add_resource(Health, "/api/v1/health")
 
 
-@sock.route("/api/v1/run-status")
-# @requires_connection
-def run(ws):
-    """
-    Format expected:
-    data: {
-        dynamic_id: str
-    }
-    """
-    data = ws.receive()
-
-    ws.close(reason="success")
-
-
 if __name__ == "__main__":
     app.run(debug=True)

apps/server/package.json

@@ -5,7 +5,8 @@
   "scripts": {
     "dev": "poetry run flask run --reload",
     "padd": "poetry add",
-    "pinstall": "poetry install"
+    "pinstall": "poetry install",
+    "prm": "poetry remove"
   },
   "keywords": [],
   "author": "",

apps/server/pyproject.toml

@@ -10,7 +10,6 @@ python = "^3.10"
 flask = "^2.2.3"
 flask-restful = "^0.3.9"
 prisma = "^0.8.2"
-flask-sock = "^0.6.0"
 asyncio = "^3.4.3"
 flask-cors = "^3.0.10"
 

apps/server/server/resources/generate_apo/__init__.py

@@ -60,7 +60,7 @@ def post(self):
                     f'{gmx} grompp -f PME_em.mdp -c "{filename}_charged.gro" -p "{filename}.top" -o "{filename}_charged" -maxwarn 2\n',
                     f'{gmx} mdrun -v -s "{filename}_charged.tpr" -deffnm "{filename}_sd_em"\n',
                     f'echo \'10 0\' | {gmx} energy -f "{filename}_sd_em.edr" -o "{filename}_potentialsd.xvg"\n',
-                    f'{grace} -nxy "{filename}_potentialsd.xvg" -hdevice PNG -hardcopy -printfile "../graficos/{filename}_potentialsd.png"\n\n',
+                    f'{grace} -nxy "{filename}_potentialsd.xvg" -hdevice PNG -hardcopy -printfile "../figures/{filename}_potentialsd.png"\n\n',
                 ]
             )
 
@@ -70,34 +70,34 @@ def post(self):
                 f'{gmx} grompp -f PME_cg_em.mdp -c "{filename}_sd_em.gro" -p "{filename}.top" -o "{filename}_cg_em" -maxwarn 2\n',
                 f'{gmx} mdrun -v -s "{filename}_cg_em.tpr" -deffnm "{filename}_cg_em"\n',
                 f'echo \'10 0\' | {gmx} energy -f "{filename}_cg_em.edr" -o "{filename}_potentialcg.xvg"\n',
-                f'{grace} -nxy "{filename}_potentialcg.xvg" -hdevice PNG -hardcopy -printfile "../graficos/{filename}_potentialcg.png"\n\n',
+                f'{grace} -nxy "{filename}_potentialcg.xvg" -hdevice PNG -hardcopy -printfile "../figures/{filename}_potentialcg.png"\n\n',
                 "#equilibrationnvt\n",
                 f'{gmx} grompp -f nvt.mdp -c "{filename}_cg_em.gro" -r "{filename}_cg_em.gro" -p "{filename}.top" -o "{filename}_nvt.tpr" -maxwarn 2\n',
                 f'{gmx} mdrun -v -s "{filename}_nvt.tpr" -deffnm "{filename}_nvt"\n',
                 f'echo \'16 0\' | {gmx} energy -f "{filename}_nvt.edr" -o "{filename}_temperature_nvt.xvg"\n',
-                f'{grace} -nxy "{filename}_temperature_nvt.xvg" -hdevice PNG -hardcopy -printfile "../graficos/{filename}_temperature_nvt.png"\n\n',
+                f'{grace} -nxy "{filename}_temperature_nvt.xvg" -hdevice PNG -hardcopy -printfile "../figures/{filename}_temperature_nvt.png"\n\n',
                 "#equilibrationnpt\n",
                 f'{gmx} grompp -f npt.mdp -c "{filename}_nvt.gro" -r "{filename}_nvt.gro" -p "{filename}.top" -o "{filename}_npt.tpr" -maxwarn 2\n',
                 f'{gmx} mdrun -v -s "{filename}_npt.tpr" -deffnm "{filename}_npt"\n',
                 f'echo \'16 0\' | {gmx} energy -f "{filename}_npt.edr" -o "{filename}_temperature_npt.xvg"\n',
-                f'{grace} -nxy "{filename}_temperature_npt.xvg" -hdevice PNG -hardcopy -printfile "../graficos/{filename}_temperature_npt.png"\n\n',
+                f'{grace} -nxy "{filename}_temperature_npt.xvg" -hdevice PNG -hardcopy -printfile "../figures/{filename}_temperature_npt.png"\n\n',
                 "#productionmd\n",
                 f'{gmx} grompp -f md_pr.mdp -c "{filename}_npt.gro" -p "{filename}.top" -o "{filename}_pr" -maxwarn 2\n',
                 f'{gmx} mdrun -v -s "{filename}_pr.tpr" -deffnm "{filename}_pr"\n\n',
                 "#analyzemd\n",
                 f'echo \'1 1\' | {gmx} trjconv -s "{filename}_pr.tpr" -f "{filename}_pr.xtc" -o "{filename}_pr_PBC.xtc" -pbc mol -center\n',
                 f'echo \'4 4\' | {gmx} rms -s "{filename}_pr.tpr" -f "{filename}_pr_PBC.xtc" -o "{filename}_rmsd_prod.xvg" -tu ns\n',
-                f'{grace} -nxy "{filename}_rmsd_prod.xvg" -hdevice PNG -hardcopy -printfile "../graficos/{filename}_rmsd_prod.png"\n',
+                f'{grace} -nxy "{filename}_rmsd_prod.xvg" -hdevice PNG -hardcopy -printfile "../figures/{filename}_rmsd_prod.png"\n',
                 f'echo \'4 4\' | {gmx} rms -s "{filename}_charged.tpr" -f "{filename}_pr_PBC.xtc" -o "{filename}_rmsd_cris.xvg" -tu ns\n',
-                f'{grace} -nxy "{filename}_rmsd_cris.xvg" -hdevice PNG -hardcopy -printfile "../graficos/{filename}_rmsd_cris.png"\n',
-                f'{grace} -nxy "{filename}_rmsd_prod.xvg" "{filename}_rmsd_cris.xvg" -hdevice PNG -hardcopy -printfile "../graficos/{filename}_rmsd_prod_cris.png"\n',
+                f'{grace} -nxy "{filename}_rmsd_cris.xvg" -hdevice PNG -hardcopy -printfile "../figures/{filename}_rmsd_cris.png"\n',
+                f'{grace} -nxy "{filename}_rmsd_prod.xvg" "{filename}_rmsd_cris.xvg" -hdevice PNG -hardcopy -printfile "../figures/{filename}_rmsd_prod_cris.png"\n',
                 f'echo \'1\' | {gmx} gyrate -s "{filename}_pr.tpr" -f "{filename}_pr_PBC.xtc" -o "{filename}_gyrate.xvg"\n',
-                f'{grace} -nxy "{filename}_gyrate.xvg" -hdevice PNG -hardcopy -printfile "../graficos/{filename}_gyrate.png"\n',
+                f'{grace} -nxy "{filename}_gyrate.xvg" -hdevice PNG -hardcopy -printfile "../figures/{filename}_gyrate.png"\n',
                 f'echo \'1\' | {gmx} rmsf -s "{filename}_pr.tpr" -f "{filename}_pr_PBC.xtc" -o "{filename}_rmsf_residue.xvg" -res\n',
-                f'{grace} -nxy "{filename}_rmsf_residue.xvg" -hdevice PNG -hardcopy -printfile "../graficos/{filename}_rmsf_residue.png"\n',
+                f'{grace} -nxy "{filename}_rmsf_residue.xvg" -hdevice PNG -hardcopy -printfile "../figures/{filename}_rmsf_residue.png"\n',
                 f'echo \'1\' | {gmx} sasa -s "{filename}_pr.tpr" -f "{filename}_pr_PBC.xtc" -o "{filename}_solvent_accessible_surface.xvg" -or "{filename}_sas_residue.xvg"\n',
-                f'{grace} -nxy "{filename}_solvent_accessible_surface.xvg" -hdevice PNG -hardcopy -printfile "../graficos/{filename}_solvent_accessible_surface.png"\n',
-                f'{grace} -nxy "{filename}_sas_residue.xvg" -hdevice PNG -hardcopy -printfile "../graficos/{filename}_sas_residue.png"\n',
+                f'{grace} -nxy "{filename}_solvent_accessible_surface.xvg" -hdevice PNG -hardcopy -printfile "../figures/{filename}_solvent_accessible_surface.png"\n',
+                f'{grace} -nxy "{filename}_sas_residue.xvg" -hdevice PNG -hardcopy -printfile "../figures/{filename}_sas_residue.png"\n',
             ]
         )
 

apps/server/server/resources/run/__init__.py

@@ -1,7 +1,7 @@
 import threading
-import json
 import os
 import shutil
+from flask import request
 from flask_restful import Resource, reqparse
 from server.config import Config
 from server.utils.run_command import run_command
@@ -17,6 +17,9 @@ def post(self):
         # Get absolute path to run folder
         folder_run = os.path.abspath(args["folder_run"])
 
+        # Get absolute path to dynamic folder
+        folder = os.path.abspath(os.path.join(folder_run, ".."))
+
         # Get absolute path to the folder where our default MDP files are stored
         folder_mdp = os.path.abspath(Config.MDP_LOCATION_FOLDER)
 
@@ -29,13 +32,14 @@ def post(self):
             if os.path.isfile(file_path):
                 shutil.copy(file_path, folder_run)
 
-        file_log_path = os.path.join(folder_run, "logs", "gmx.log")
-        file_step_path = os.path.join(folder_run, "..", "steps.txt")
+        file_log_path = os.path.abspath(os.path.join(folder_run, "logs", "gmx.log"))
+        file_step_path = os.path.abspath(os.path.join(folder, "steps.txt"))
+        file_is_running = os.path.abspath(os.path.join(folder, "..", "is-running"))
 
         # UPDATE STATUS ON DB THAT `dynamic_id` is now running
 
         # Load commands file contents to  a variable
-        file_commands_path = os.path.join(folder_run, "..", "commands.txt")
+        file_commands_path = os.path.join(folder, "commands.txt")
         with open(file_commands_path, "r") as f:
             commands_file_content = f.readlines()
 
@@ -49,10 +53,13 @@ def run_commands():
             # Make our shell go to the run folder
             os.chdir(folder_run)
 
+            with open(file_is_running, "w") as f:
+                f.write(folder)
+
             # Iterate in our command list
             for command in commands:
                 if command[0] == "#":
-                    with open(file_step_path, "w+") as f:
+                    with open(file_step_path, "a+") as f:
                         f.write(f"{command}\n")
                 else:
                     (pid, rcode) = run_command(command, file_log_path)
@@ -64,20 +71,45 @@ def run_commands():
                         # UPDATE ON DB THAT EXECUTION FAILED
 
                         # SEND MAIL NOTIFYING DYNAMIC ERRORED
-                        return {"status": "errored"}
-                        # ws.close(reason="errored", message=command)
+                        with open(os.path.join(folder_run, "error"), "w") as f:
+                            f.writelines(f"errored at: {command}")
 
             # UPDATE ON DB THAT EXECUTION ENDED WITH SUCCESS
 
             # SEND EMAIL NOTIFYING DYNAMIC ENDED
-            # ws.close(reason="success")
-            return {
-                "status": "success",
-            }
+            with open(file_log_path, "a+") as f:
+                f.write("\n\nfinished")
+
+            if os.path.exists(file_is_running):
+                os.remove(file_is_running)
 
         # Start the command execution in a new thread
         thread = threading.Thread(target=run_commands)
         thread.start()
 
         # Return a response indicating that the command has started
         return {"status": "started"}
+
+    def get(self):
+        args = request.args
+
+        user_id = args["user_id"]
+
+        folder_user = os.path.abspath(os.path.join(Config.UPLOAD_FOLDER, user_id))
+
+        file_is_running = os.path.abspath(os.path.join(folder_user, "is-running"))
+
+        if os.path.exists(file_is_running):
+            with open(file_is_running, "r") as f:
+                folder = f.readline()
+
+            file_gmx_log = os.path.abspath(
+                os.path.join(folder, "run", "logs", "gmx.log")
+            )
+
+            with open(file_gmx_log, "r") as f:
+                log_lines = f.readlines()
+
+            return {"status": "running", "log": log_lines[-30:]}
+
+        return {"status": "running", "folder": args["folder"]}

apps/server/server/static/mdp/md_pr.mdp

@@ -1,7 +1,7 @@
 title		= OPLS Lysozyme MD simulation 
 ; Run parameters
 integrator	= md		; leap-frog integrator
-nsteps      = 1250000    ; 2 * 50000 = 1000 ps (1 ns) 
+nsteps      = 300   ;1250000    ; 2 * 50000 = 1000 ps (1 ns) 
 dt          = 0.002     ; 2 fs 
 ; Output control
 nstxout		        = 5000		; save coordinates every 10.0 ps

package.json

@@ -13,7 +13,6 @@
   "author": "",
   "license": "ISC",
   "devDependencies": {
-    "concurrently": "^8.0.1",
-    "prisma": "^4.12.0"
+    "concurrently": "^8.0.1"
   }
 }