feat: download xtc, visual status of dynamic at home page, form valid…

…ation and more

app/blueprints/download/routes.py

@@ -8,71 +8,84 @@
 
 from app.config import Config
 from . import DownloadBlueprint
-from flask import render_template, make_response, request, send_file
+from flask import send_file
 from flask_babel import _
-from app import login_manager, login_required
+from app import login_required
 
-@DownloadBlueprint.route('/imgfiles/<filename>')
+@DownloadBlueprint.route('/downloads/graphics/<mode>/<protein>/<folder>')
 @login_required
-def imgsdownload(filename):
-    filename = filename.split('|')[1]
-    current_location = os.path.join(Config.UPLOAD_FOLDER, current_user.username, filename, 'graficos')
-    ziplocation = os.path.join(current_location, filename+'-graficos.zip')
+def imgsdownload(mode, protein, folder):
+    folder_path = os.path.join(Config.UPLOAD_FOLDER, current_user.username, mode, protein, folder)
+    folder_graphics_path = os.path.join(folder_path, 'graficos')
+
+    ziplocation = os.path.join(folder_graphics_path, f"{mode}-{protein}-{folder}-graphics.zip")
     zf = zipfile.ZipFile(ziplocation,'w')
 
     #move os arquivos .xvg para a pasta graficos.
-    directory_xvg = os.path.join(Config.UPLOAD_FOLDER, current_user.username, filename,'run')
+    directory_xvg = os.path.join(folder_path, 'run')
     for folder, subfolders, files in os.walk(directory_xvg):
         for file in files:
             if file.endswith('.xvg'):
-                file = directory_xvg +'/'+file 
-                shutil.move(file, current_location)
+                file = os.path.join(directory_xvg, file) 
+                shutil.move(file, folder_graphics_path)
 
-    for folder, subfolders, files in os.walk(current_location):
+    for folder, subfolders, files in os.walk(folder_graphics_path):
         for file in files:
             if not file.endswith('.zip'):
                 zf.write(os.path.join(folder, file), file, compress_type = zipfile.ZIP_DEFLATED)
     zf.close()
 
     return send_file(ziplocation, as_attachment=True)
 
-@DownloadBlueprint.route('/downloadmdpfiles')
+@DownloadBlueprint.route('/downloads/mdp')
 @login_required
 def downloadmdpfiles():
     ziplocation = os.path.join(Config.MDP_LOCATION_FOLDER, 'mdpfiles.zip')
 
     return send_file(ziplocation, as_attachment=True)
 
-@DownloadBlueprint.route('/dynamiccomandsdownload/<filename>')
+@DownloadBlueprint.route('/downloads/commands/<mode>/<protein>/<folder>')
 @login_required
-def dynamiccomandsdownload(filename):
-    filename = filename.split('|')[1]
-    os.chdir(Config.UPLOAD_FOLDER+'/'+current_user.username+'/'+filename)
+def dynamiccomandsdownload(mode, protein, folder):
+    folder_path = os.path.join(Config.UPLOAD_FOLDER, current_user.username, mode, protein, folder)
+    os.chdir(folder_path)
     files = glob.glob("*.txt")
     files.sort(key=os.path.getmtime)
-    file_comands = files[len(files)-1]
-    directory = Config.UPLOAD_FOLDER+'/'+current_user.username+'/'+filename+'/'+file_comands
-    return (send_file(directory, as_attachment=True))
+    commands = files[len(files) - 1]
+    directory = os.path.join(folder_path, commands)
+    return send_file(directory, as_attachment=True)
 
-@DownloadBlueprint.route('/download/<filename>')
+@DownloadBlueprint.route('/downloads/xtc/<mode>/<protein>/<folder>')
 @login_required
-def commandsdownload(filename):
-    filename = ast.literal_eval(filename)
-    return send_file('{}{}/{}/{}'.format(Config.UPLOAD_FOLDER,
-            current_user.username,filename["name"],filename["complete"]), as_attachment=True)
+def commandsdownload(mode, protein, folder):
+    folder_path = os.path.join(Config.UPLOAD_FOLDER, current_user.username, mode, protein, folder)
+    folder_run_path = os.path.join(folder_path, 'run')
+
+    ziplocation = os.path.join(folder_run_path, f"{mode}-{protein}-{folder}-xtc.zip")
+    zf = zipfile.ZipFile(ziplocation, 'w')
+
+    #move os arquivos .xvg para a pasta graficos.
+    for folder, subfolders, files in os.walk(folder_run_path):
+        for file in files:
+            if file.endswith('_PBC.xtc'):
+                zf.write(os.path.join(folder, file), file, compress_type=zipfile.ZIP_DEFLATED)
+
+    zf.close()
+
+    return send_file(ziplocation, as_attachment=True)
 
-@DownloadBlueprint.route('/downloadlogs/<filename>')
+@DownloadBlueprint.route('/downloads/logs/<mode>/<protein>/<folder>')
 @login_required
-def downloalogs(filename):
-    filename = filename.split('|')[1]
-    current_location = os.path.join(Config.UPLOAD_FOLDER, current_user.username, filename,'run','logs')
-    ziplocation = os.path.join(Config.UPLOAD_FOLDER, current_user.username, filename,'run','logs',filename+'-logs.zip')
+def downloalogs(mode, protein, folder):
+    folder_path = os.path.join(Config.UPLOAD_FOLDER, current_user.username, mode, protein, folder)
+    log_path = os.path.join(folder_path, 'run', 'logs')
+    ziplocation = os.path.join(log_path, f"{mode}-{protein}-{folder}-logs.zip")
     zf = zipfile.ZipFile(ziplocation,'w')
 
-    for folder, subfolders, files in os.walk(current_location):
+    for folder, subfolders, files in os.walk(log_path):
         for file in files:
-            if not file.endswith('.zip'):
-                zf.write(os.path.join(folder, file), file, compress_type = zipfile.ZIP_DEFLATED)
+            if file.endswith('.log'):
+                zf.write(os.path.join(folder, file), file, compress_type=zipfile.ZIP_DEFLATED)
 
     zf.close()
-    return (send_file(ziplocation, as_attachment=True))
+    return send_file(ziplocation, as_attachment=True)

app/blueprints/dynamic/executors/acpype.py

@@ -9,6 +9,8 @@ def execute(folder, CommandsFileName, username, filename, itpname, groname, mol)
         protein_name, _ = os.path.splitext(os.path.basename(filename))
         f.write(protein_name)
 
+    #
+
     #transferir os arquivos mdp necessarios para a execução
     RunFolder = os.path.join(folder, "run") #pasta q vai rodar
     SecureMdpFolder = os.path.join(os.path.expanduser('~'),Config.MDP_LOCATION_FOLDER)
@@ -21,17 +23,21 @@ def execute(folder, CommandsFileName, username, filename, itpname, groname, mol)
             shutil.copy(fullmdpname, RunFolder)
 
     # Use the `with` statement to open the file in 'x+' mode
-    with open(os.path.join(Config.UPLOAD_FOLDER, username, 'info_dynamics'), 'a') as f:
-        f.write(folder)
+    with open(os.path.join(Config.UPLOAD_FOLDER, username, 'info_dynamics'), 'a+') as f:
+        f.write(f"{folder}\n")
 
     with open(os.path.join(Config.UPLOAD_FOLDER, username, "log_dir"), "w") as f:
         f.write(os.path.join(folder, "run", "logs", f"gmx-commands.log"))
 
     #abrir arquivo
     with open(CommandsFileName) as f: #CODIGO PARA A PRODUÇÃO
         content = f.readlines()
-    lines = [line.rstrip('\n') for line in content if line is not '\n'] #cancela as linhas em branco do arquivo
+    lines = [line.rstrip('\n') for line in content if line is not '\n']
     linux_log_file_path = os.path.join(folder, "run", "logs", f"linux-commands.log")
+
+    with open(os.path.join(folder, 'status'), 'w') as f:
+        f.write(f"running\n")
+
     for l in lines:
         if l[0] == '#':
             WriteUserDynamics(l, username)
@@ -40,7 +46,10 @@ def execute(folder, CommandsFileName, username, filename, itpname, groname, mol)
             rcode = run_dynamics_command(l, os.path.join(folder, "run", "logs", f"gmx-commands.log"))
 
             if rcode != 0:
+                with open(os.path.join(folder, 'status'), 'w') as f:
+                    f.write(f"error: {l}\n")
                 os.remove(os.path.join(Config.UPLOAD_FOLDER, username, 'executing'))
+                os.remove(os.path.join(Config.UPLOAD_FOLDER, username, 'running_protein_name'))
                 os.remove(os.path.join(Config.UPLOAD_FOLDER, username, 'log_dir'))
                 return f"{l}"
 
@@ -98,8 +107,11 @@ def execute(folder, CommandsFileName, username, filename, itpname, groname, mol)
             with open(os.path.join(folder, "run", "logs", f"dynamic-log.log"), 'a') as f:
                 subprocess.call(comando_moleculetype, shell=True, stdin=f, stdout=f, stderr=f)
 
-
+    with open(os.path.join(folder, 'status'), 'w') as f:
+        f.write(f"success\n")
+
     os.remove(os.path.join(Config.UPLOAD_FOLDER, username, 'executing'))
+    os.remove(os.path.join(Config.UPLOAD_FOLDER, username, 'running_protein_name'))
     os.remove(os.path.join(Config.UPLOAD_FOLDER, username, 'log_dir'))
 
 

app/blueprints/dynamic/executors/apo.py

@@ -7,7 +7,7 @@ def execute(folder, CommandsFileName, username, filename):
     with open(os.path.join(Config.UPLOAD_FOLDER, username, 'running_protein_name'), 'w') as f:
         protein_name, _ = os.path.splitext(os.path.basename(filename))
         f.write(protein_name)
-    
+
     # transferir os arquivos mdp necessarios para a execução
     RunFolder = os.path.join(folder, 'run') # pasta q vai rodar
     SecureMdpFolder = os.path.join(os.path.expanduser('~'), Config.MDP_LOCATION_FOLDER)
@@ -20,8 +20,8 @@ def execute(folder, CommandsFileName, username, filename):
             shutil.copy(fullmdpname, RunFolder)
 
     # Use the `with` statement to open the file in 'x+' mode
-    with open(os.path.join(Config.UPLOAD_FOLDER, username, 'info_dynamics'), 'a') as f:
-        f.write(folder)
+    with open(os.path.join(Config.UPLOAD_FOLDER, username, 'info_dynamics'), 'a+') as f:
+        f.write(f"{folder}\n")
 
     with open(os.path.join(Config.UPLOAD_FOLDER, username, "log_dir"), "w") as f:
         f.write(os.path.join(folder, "run", "logs", f"dynamic-log.log"))
@@ -31,6 +31,9 @@ def execute(folder, CommandsFileName, username, filename):
         content = f.readlines()
     lines = [line.rstrip('\n') for line in content if line is not '\n'] #cancela as linhas em branco do arquivo
 
+    with open(os.path.join(folder, 'status'), 'w') as f:
+        f.write(f"running\n")
+
     for l in lines:
         if l[0] == '#':
             WriteUserDynamics(l, username)
@@ -39,10 +42,18 @@ def execute(folder, CommandsFileName, username, filename):
             rcode = run_dynamics_command(l, os.path.join(folder, "run", "logs", f"dynamic-log.log"))
 
             if rcode != 0:
+                with open(os.path.join(folder, 'status'), 'w') as f:
+                    f.write(f"error: {l}\n")
                 os.remove(os.path.join(Config.UPLOAD_FOLDER, username, 'executing'))
+                os.remove(os.path.join(Config.UPLOAD_FOLDER, username, 'running_protein_name'))
                 os.remove(os.path.join(Config.UPLOAD_FOLDER, username, 'log_dir'))
                 return f"{l}"
+
+    with open(os.path.join(folder, 'status'), 'w') as f:
+        f.write(f"success\n")
+
     os.remove(os.path.join(Config.UPLOAD_FOLDER, username, 'executing'))
+    os.remove(os.path.join(Config.UPLOAD_FOLDER, username, 'running_protein_name'))
     os.remove(os.path.join(Config.UPLOAD_FOLDER, username, 'log_dir'))
 
 def WriteUserDynamics(line, username):

app/blueprints/dynamic/executors/prodrg.py

@@ -9,7 +9,6 @@ def execute(folder, CommandsFileName, username, filename, itpname, groname, mol)
         protein_name, _ = os.path.splitext(os.path.basename(filename))
         f.write(protein_name)
 
-
     #transferir os arquivos mdp necessarios para a execução
     RunFolder = os.path.join(folder, "run") #pasta q vai rodar
     SecureMdpFolder = os.path.join(os.path.expanduser('~'),Config.MDP_LOCATION_FOLDER)
@@ -22,8 +21,8 @@ def execute(folder, CommandsFileName, username, filename, itpname, groname, mol)
             shutil.copy(fullmdpname, RunFolder)
 
     # Use the `with` statement to open the file in 'x+' mode
-    with open(os.path.join(Config.UPLOAD_FOLDER, username, 'info_dynamics'), 'a') as f:
-        f.write(folder)
+    with open(os.path.join(Config.UPLOAD_FOLDER, username, 'info_dynamics'), 'a+') as f:
+        f.write(f"{folder}\n")
 
     with open(os.path.join(Config.UPLOAD_FOLDER, username, "log_dir"), "w") as f:
         f.write(os.path.join(folder, "run", "logs", f"gmx-commands.log"))
@@ -33,6 +32,9 @@ def execute(folder, CommandsFileName, username, filename, itpname, groname, mol)
         content = f.readlines()
     lines = [line.rstrip('\n') for line in content if line is not '\n'] #cancela as linhas em branco do arquivo
 
+    with open(os.path.join(folder, 'status'), 'w') as f:
+        f.write(f"running\n")
+
     for l in lines:
         if l[0] == '#':
             WriteUserDynamics(l, username)
@@ -41,7 +43,10 @@ def execute(folder, CommandsFileName, username, filename, itpname, groname, mol)
             rcode = run_dynamics_command(l, os.path.join(folder, "run", "logs", f"gmx-commands.log"))
 
             if rcode != 0:
+                with open(os.path.join(folder, 'status'), 'w') as f:
+                    f.write(f"error: {l}\n")
                 os.remove(os.path.join(Config.UPLOAD_FOLDER, username, 'executing'))
+                os.remove(os.path.join(Config.UPLOAD_FOLDER, username, 'running_protein_name'))
                 os.remove(os.path.join(Config.UPLOAD_FOLDER, username, 'log_dir'))
                 return f"{l}"
 
@@ -119,7 +124,10 @@ def execute(folder, CommandsFileName, username, filename, itpname, groname, mol)
                 file_complx_gro[1] = ' {:>5}\n'.format(total)
                 file.write(''.join(file_complx_gro))
 
+    with open(os.path.join(folder, 'status'), 'w') as f:
+        f.write(f"success\n")
     os.remove(os.path.join(Config.UPLOAD_FOLDER, username, 'executing'))
+    os.remove(os.path.join(Config.UPLOAD_FOLDER, username, 'running_protein_name'))
     os.remove(os.path.join(Config.UPLOAD_FOLDER, username, 'log_dir'))
 
 

app/blueprints/dynamic/routes.py

@@ -91,7 +91,7 @@ def prodrg():
         filename, ext = os.path.splitext(os.path.basename(request.files.get('file').filename))
         fileitpname, ext1 = os.path.splitext(os.path.basename(request.files.get('fileitp').filename))
         filegroname, ext2 = os.path.splitext(os.path.basename(request.files.get('filegro').filename))
-        folder = f"{Config.UPLOAD_FOLDER}{current_user.username}/prodrg/{filename}_{fileitpname}_{filegroname}/{timestamp}/"
+        folder = os.path.join(Config.UPLOAD_FOLDER,current_user.username, 'prodrg', f"{filename}_{fileitpname}_{filegroname}", timestamp)
 
         CompleteFileName = prodrgGenerator.generate(
             folder,

app/blueprints/user/routes.py

@@ -1,27 +1,46 @@
-import datetime
 import dateutil.parser
 from app.config import Config
 from . import UserBlueprint
 from flask import render_template, make_response, request
 from flask_babel import _
 from flask_login import current_user, login_required
-from  app import login_manager
-
+from app import login_manager
+import os
 @UserBlueprint.route('/', methods=['GET'], endpoint='index')
 @login_required
 def index():
     try:
-        directory = Config.UPLOAD_FOLDER + '/' + current_user.username + '/info_dynamics'
-        info_dynamics = open(directory, 'r')
-        list_dynamics = info_dynamics.readlines()
-        info_dynamics.close()
+        directory = os.path.join(Config.UPLOAD_FOLDER, current_user.username, 'info_dynamics')
+        with open(directory, 'r') as f:
+            list_dynamics = f.readlines()
         dynamics = []
 
         for d in list_dynamics:
+            dsplit = d.strip().split('/')
+            date = dsplit[len(dsplit) - 1].replace('/', '')
+            protein = dsplit[len(dsplit) - 2].replace('/', '')
+            mode = dsplit[len(dsplit) - 3].replace('/', '')
+
+            status_path = os.path.join(d.replace('\n', ''), 'status')
+
+            print(status_path)
+            with open(status_path, 'r') as f:
+                line = f.readline()
+
+            print(line)
+
+            if 'error' in line:
+                status = line.replace('error: ', '').replace('\n', '')
+            else:
+                status = line.replace('\n', '')
+
+            print(status)
             obj = {
-                "date": dateutil.parser.isoparse(d.strip().split("|")[0]),
-                "protein": d.strip().split("|")[1],
-                "original": d
+                "folder": date,
+                "date": dateutil.parser.isoparse(date),
+                "protein": protein,
+                "mode": mode,
+                "status": status
             }
             dynamics.insert(0, obj)
 

app/static/css/custom.css

@@ -32,4 +32,8 @@ a {
 
 .order-9 {
   order: 9;
+}
+
+.-mt-3 {
+  margin-top: -0.75rem;
 }