I think it works, just need access to the couchdb

setup.py

@@ -5,7 +5,7 @@
 
 setuptools.setup(
     name = 'appia',
-    version = '7.1.2',
+    version = '7.2.0',
     author = 'Rich Posert',
     author_email = '[email protected]',
     description = 'Chromatography processing made easy',
@@ -16,14 +16,13 @@
         'License :: OSI Approved :: MIT License'
     ],
     package_dir = {'': 'src'},
-    package_data={'appia': ['processors/flow_rates.json', 'plotters/manual_plot_FPLC.R', 'plotters/manual_plot_HPLC.R']},
+    package_data={'appia': ['plotters/manual_plot_FPLC.R', 'plotters/manual_plot_HPLC.R']},
     include_package_data=True,
     packages = setuptools.find_packages(where = 'src'),
     python_requires = ">=3.6",
     install_requires = [
         'couchdb',
         'pandas',
-        'slack',
         'plotly',
         'kaleido'
     ],

src/appia/appia.py

@@ -1,7 +1,6 @@
 #!/usr/bin/env python3
 import argparse
 import logging
-import sys
 
 from appia.parsers.process_parser import parser as process_parser
 from appia.parsers.database_parser import parser as db_parser

src/appia/parsers/database_parser.py

@@ -1,13 +1,10 @@
 import argparse
 import os
-from appia.processors.database import Database, Config
 from appia.processors.core import three_column_print
 
 def main(args):
-    if args.config == 'env':
-        db = Database(Config())
-    else:
-        db = Database(Config(args.config))
+
+    from appia.processors.database import db
 
     if args.list or args.check_versions:
         list = db.update_experiment_list()
@@ -50,11 +47,6 @@ def main(args):
     add_help=False
 )
 parser.set_defaults(func = main)
-parser.add_argument(
-    'config',
-    help = 'Config JSON file',
-    type = str
-)
 parser.add_argument(
     '-l', '--list',
     help = 'Print list of all experiments in database',

src/appia/parsers/process_parser.py

@@ -4,11 +4,11 @@
 import logging
 import shutil
 from appia.processors import hplc, fplc, experiment, core
-from appia.processors.database import Database, Config
 from appia.plotters import auto_plot
 from appia.processors.gui import user_input
 
 def main(args):
+    from appia.processors.database import db
     file_list = core.get_files(args.files)
     logging.debug(file_list)
 
@@ -146,31 +146,10 @@ def main(args):
                 os.path.join(out_dir, f'{exp.id}_manual-plot-FPLC.R')
             )
 
-    if args.config:
-        if args.config == 'env':
-            db = Database(Config())
-        else:
-            db = Database(Config(args.config))
-
+    if args.database:
         exp.reduce_hplc(args.reduce)
         db.upload_experiment(exp, args.overwrite)
 
-    if args.post_to_slack:
-        config = Config(args.post_to_slack)
-
-        if config.slack:
-            from processors import slackbot
-
-            client = slackbot.get_client(config)
-
-            if client is not None:
-                slackbot.send_graphs(
-                    config,
-                    client,
-                    os.path.join(out_dir, 'fsec_traces.pdf')
-                )
-
-
 parser = argparse.ArgumentParser(
     description = 'Process chromatography data',
     add_help = False    
@@ -205,12 +184,6 @@ def main(args):
 	nargs = '?',
     const = 'plotters'
 )
-file_io.add_argument(
-	'-s', '--post-to-slack',
-	help = "Send completed plots to Slack. Need a config JSON with slack token and channel.",
-	nargs = '?',
-    const = os.path.join(os.path.dirname(os.path.realpath(__file__)), '..', 'config.json')
-)
 
 process_args = parser.add_argument_group('Processing Options')
 process_args.add_argument(
@@ -260,10 +233,8 @@ def main(args):
 )
 web_up.add_argument(
     '-d', '--database',
-    help = '''Upload experiment to couchdb. Optionally, provide config file location. Default config location is "config.json" in appia directory. Enter "env" to use environment variables instead.''',
-    dest = 'config',
-    nargs = '?',
-    const = os.path.join(os.path.dirname(os.path.realpath(__file__)), '..', 'config.json')
+    help = '''Upload experiment to couchdb. Must have set your parameters using `appia database`.''',
+    action = 'store_true'
 )
 web_up.add_argument(
     '--overwrite',

src/appia/parsers/user_settings.py

@@ -19,19 +19,24 @@ def save_settings(self):
         with open(self.settings_path, 'w') as f:
             json.dump(self._user_settings, f)
 
-    @property
-    def flow_rates(self) -> dict:
+    def access_private_property(self, propname:str, not_found = None):
         try:
-            return self._user_settings['flow_rates']
+            return self._user_settings[propname]
         except KeyError:
-            return {}
+            return not_found
+
+    # Flow rates --------------------------------------------------------
+
+    @property
+    def flow_rates(self) -> dict:
+        return self.access_private_property('flow_rates', {})
 
     @flow_rates.setter
     def flow_rates(self, new_flow_rates:dict):
         if isinstance(new_flow_rates, dict):
             self._user_settings['flow_rates'] = new_flow_rates
         else:
-            raise TypeError
+            raise TypeError(f'Flow rates must be a dict, not a {type(new_flow_rates)}')
 
     def delete_flow_rate(self, method_name):
         del self._user_settings['flow_rates'][method_name]
@@ -49,4 +54,53 @@ def check_flow_rate(self, method_name:str):
         elif len(matches) > 1:
             logging.warning(f'More than one match for {method_name}')
 
-        return None
+        return None
+
+    # Database -------------------------------------------------------------
+
+    @property
+    def database_host(self):
+        return self.access_private_property('database_host')
+
+    @database_host.setter
+    def database_host(self, hostname:str):
+        if isinstance(hostname, str):
+            self._user_settings['database_host'] = hostname
+        else:
+            raise TypeError(f'Hostname must be a string, not a {type(hostname)}')
+
+    @property
+    def database_port(self):
+        return self.access_private_property('database_port', '5984')
+
+    @database_port.setter
+    def database_port(self, port:int):
+        if isinstance(port, int):
+            self._user_settings['database_port'] = str(port)
+        else:
+            raise TypeError(f'Port must be an integer, not a {type(port)}')
+
+    @property
+    def database_user(self):
+        return self.access_private_property('database_username')
+
+    @database_user.setter
+    def database_user(self, username:str):
+        if isinstance(username, str):
+            self._user_settings['database_username'] = username
+        else:
+            raise TypeError(f'Username must be a strong, not a {type(username)}')
+
+    @property
+    def database_password(self):
+        return self.access_private_property('database_password')
+
+    @database_password.setter
+    def database_password(self, password:str):
+        if isinstance(password, str):
+            self._user_settings['database_password'] = password
+        else:
+            raise TypeError(f'Password must be a string, not a {type(password)}')
+
+
+appia_settings = AppiaSettings()

src/appia/parsers/utilities_parser.py

@@ -2,11 +2,9 @@
 import os
 import shutil
 import logging
-import json
-from appia.parsers.user_settings import AppiaSettings
+from appia.parsers.user_settings import appia_settings
 
 def main(args):
-    user_settings = AppiaSettings()
 
     if args.copy_manual is not None:
         script_location = os.path.normpath(os.path.join(os.path.dirname(os.path.realpath(__file__)), '..'))
@@ -30,19 +28,42 @@ def main(args):
                 logging.error('Bad flow rate. Give as --flow-rate {name} {mL/min number}')
                 raise TypeError
 
-        user_settings.update_flow_rates(new_flow_rates)
-        user_settings.save_settings()
+        appia_settings.update_flow_rates(new_flow_rates)
+        appia_settings.save_settings()
 
     if args.list_flow_rates:
         print('User specified flow rates:')
-        for method, fr in user_settings.flow_rates.items():
+        for method, fr in appia_settings.flow_rates.items():
             print(f' {method + ":":>20} {fr}')
 
     if args.delete_flow_rate:
         for fr_key in args.delete_flow_rate:
-            user_settings.delete_flow_rate(fr_key)
+            appia_settings.delete_flow_rate(fr_key)
 
-        user_settings.save_settings()
+        appia_settings.save_settings()
+
+    if args.database_setup:
+        print("Setting up database. To leave any of these settings unchanged, leave them blank.")
+
+        new_settings = {}
+        new_settings['database_host'] = input('Database host (something like blah.domain.edu): ')
+        new_settings['database_user'] = input('Database username. (You set this during the docker installation): ')
+        new_settings['database_password'] = input('Database password. (You set this during the docker installation): ')
+        port = input("Database port number. (If you don't know, it's the default so leave it blank): ")
+        new_settings['database_port'] = port if len(port) == 0 else int(port)
+
+        for setting, value in new_settings.items():
+            logging.debug(f'Setting {setting} is {value}')
+            if isinstance(value, int) or len(value) > 0:
+                setattr(appia_settings, setting, value)
+
+        appia_settings.save_settings()
+
+    if args.check_database_login:
+        print('Host:', appia_settings.database_host)
+        print('Username:', appia_settings.database_user)
+        print('Password:', appia_settings.database_password)
+        print('Port:', appia_settings.database_port)
 
 
 parser = argparse.ArgumentParser(
@@ -72,4 +93,14 @@ def main(args):
     '--delete-flow-rate',
     help = 'Remove a flow rate from user settings. Give the method names. Can give multiple method names.',
     nargs='+'
+)
+parser.add_argument(
+    '--database-setup',
+    help = 'Set database access parameters',
+    action = 'store_true'
+)
+parser.add_argument(
+    '--check-database-login',
+    help = 'Print login info to the terminal',
+    action = 'store_true'
 )

src/appia/processors/database.py

@@ -1,51 +1,23 @@
 import couchdb
 import logging
 import pandas as pd
-import os
 import sys
 from appia.processors.experiment import Experiment
-import json
-
-class Config:
-    def __init__(self, config_file = None) -> None:
-
-        if config_file is None:
-            try:
-                self.cuser = os.environ['COUCHDB_USERNAME']
-                self.cpass = os.environ['COUCHDB_PASSWORD']
-                self.chost = os.environ['COUCHDB_HOST']
-            except KeyError:
-                logging.error('Provide a config file or set $COUCHDB_USERNAME, $COUCHDB_PASSWORD, $COUCHDB_HOST')
-                sys.exit(1)
-        else:
-            with open(config_file) as conf:
-                config = json.load(conf)
-
-            try:
-                self.cuser = config['user']
-                self.cpass = config['password']
-                self.chost = config['host']
-                self.couch = True
-            except KeyError:
-                logging.warning('Config missing information to connect to CouchDB')
-                self.couch = False
-
-            try:
-                self.slack_token = config['token']
-                self.slack_channel = config['chromatography_channel']
-                self.slack = True
-            except KeyError:
-                logging.warning('Config missing information for Slack bot')
-                self.slack = False
-
-    def __repr__(self) -> str:
-        return f'config object for host {self.chost}'
+from appia.parsers.user_settings import appia_settings
 
 class Database:
-    def __init__(self, config) -> None:
-        self.config = config
+    def __init__(self) -> None:
         self.version = 4
-        couchserver = couchdb.Server(f'http://{config.cuser}:{config.cpass}@{config.chost}:5984')
+        username = appia_settings.database_user
+        password = appia_settings.database_password
+        hostname = appia_settings.database_host
+        port = appia_settings.database_port
+
+        if any([x is None for x in [username, password, hostname, port]]):
+            logging.error('You have not set your database login information. Please run `appia utils --database-setup`')
+            sys.exit(10)
+
+        couchserver = couchdb.Server(f'http://{username}:{password}@{hostname}:{port}')
 
         dbname = 'traces'
         if dbname in couchserver:
@@ -54,7 +26,7 @@ def __init__(self, config) -> None:
             self.db = couchserver.create(dbname)
 
     def __repr__(self) -> str:
-        return f'CouchDB at {self.config.chost}'
+        return f'CouchDB at {appia_settings.database_host}'
 
     def update_experiment_list(self):
         return [x['id'] for x in self.db.view('_all_docs')]
@@ -146,9 +118,11 @@ def upload_experiment(self, exp, overwrite = False):
             self.db.save(doc)
 
     def migrate(self):
-        if input(f'To migrate database hosted at {self.config.chost}, type: I have backed up my db\n').lower() == 'i have backed up my db':
+        if input(f'To migrate database hosted at {appia_settings.database_host}, type: I have backed up my db\n').lower() == 'i have backed up my db':
             for exp_name in self.update_experiment_list():
                 exp = self.pull_experiment(exp_name)
                 self.upload_experiment(exp, overwrite=True)
         else:
             logging.warning('Back up your database before migrating it.')
+
+db = Database()