Added ability to run jobs from flowcharts or previous jobs.

seamm_dashboard/jwt_patch.py

@@ -23,6 +23,12 @@
 
 
 def _decode_jwt_from_cookies(refresh):
+
+ try:
+ csrf_protect = config.csrf_protect
+ except AttributeError:
+ csrf_protect = config.cookie_csrf_protect
+
  if refresh:
  cookie_key = config.refresh_cookie_name
  csrf_header_key = config.refresh_csrf_header_name
@@ -37,7 +43,7 @@ def _decode_jwt_from_cookies(refresh):
  raise NoAuthorizationError('Missing cookie "{}"'.format(cookie_key))
 
  if (
- config.csrf_protect
+ csrf_protect
  and request.method in config.csrf_request_methods
  and current_app.config["JWT_CSRF_ACCESS_PATH"] in request.url
  ):

seamm_dashboard/results_dashboard.py

@@ -6,11 +6,15 @@
 def run():
  app = create_app()
 
+ # serve using waitress
  if "debug" in options:
  app.run(debug=True, use_reloader=True) 
  else: 
  # serve using waitress
- serve(app, port=options["port"])
+ if options["localhost"]:
+ serve(app, listen=f"localhost:{options['port']}", threads=12)
+ else:
+ serve(app, port=options["port"], threads=12)
 
 
 if __name__ == "__main__":

seamm_dashboard/routes/api/jobs.py

@@ -5,7 +5,6 @@
 import os
 import shutil
 from datetime import datetime, timezone
-import fasteners
 import json
 import logging
 from pathlib import Path
@@ -17,6 +16,7 @@
 from flask_jwt_extended import jwt_required, get_current_user
 
 from seamm_dashboard import db, datastore, options
+from seamm_dashboard.util import get_job_id
 from seamm_datastore.database.models import Job, Role
 from seamm_datastore.database.schema import JobSchema
 
@@ -80,62 +80,6 @@ def get_jobs(
  return jsonify(jobs), 200
 
 
-def get_job_id(filename):
- """Get the next job id from the given file.
-
- This uses the fasteners module to provide locking so that
- only one job at a time can access the file, so that the job
- ids are unique and monotonically increasing.
- """
-
- filename = os.path.expanduser(filename)
-
- lock_file = filename + ".lock"
- lock = fasteners.InterProcessLock(lock_file)
- locked = lock.acquire(blocking=True, timeout=5)
-
- if locked:
- if not os.path.isfile(filename):
- job_id = 1
- with open(filename, "w") as fd:
- fd.write("!MolSSI job_id 1.0\n")
- fd.write("1\n")
- lock.release()
- else:
- with open(filename, "r+") as fd:
- line = fd.readline()
- pos = fd.tell()
- if line == "":
- lock.release()
- raise EOFError("job_id file '{}' is empty".format(filename))
- line = line.strip()
- match = re.fullmatch(r"!MolSSI job_id ([0-9]+(?:\.[0-9]+)*)", line)
- if match is None:
- lock.release()
- raise RuntimeError(
- "The job_id file has an incorrect header: {}".format(line)
- )
- line = fd.readline()
- if line == "":
- lock.release()
- raise EOFError("job_id file '{}' is truncated".format(filename))
- try:
- job_id = int(line)
- except TypeError:
- raise TypeError(
- "The job_id in file '{}' is not an integer: {}".format(
- filename, line
- )
- )
- job_id += 1
- fd.seek(pos)
- fd.write("{:d}\n".format(job_id))
- else:
- raise RuntimeError("Could not lock the job_id file '{}'".format(filename))
-
- return job_id
-
-
 @jwt_required(optional=True)
 def add_job(body):
  """Add a new job to the queue.

seamm_dashboard/routes/jobs/forms.py

@@ -1,6 +1,7 @@
 from flask_wtf import FlaskForm
 from flask_wtf.file import FileField
-from wtforms import StringField, TextAreaField, SubmitField
+from wtforms import StringField, TextAreaField, SubmitField, SelectMultipleField
+
 
 from wtforms.validators import DataRequired, Length, Regexp
 
@@ -27,3 +28,8 @@ class ImportJob(FlaskForm):
  outfile = FileField("job_data.json File", validators=[DataRequired()])
  title = StringField("Job Title")
  submit = SubmitField("Import Job")
+
+
+class GetFlowchart(FlaskForm):
+ outfile = FileField("File (*.flow)", validators=[DataRequired()])
+ submit = SubmitField("Upload flowchart")