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Can't read connection string from web.config

I have the following in my web.config located at the root of my project:
<configuration>
<connectionStrings>
<clear />
<add name="Default" providerName="System.Data.SqlClient" connectionString="Server=tcp:whoops;Encrypt=True;TrustServerCertificate=False;Connection Timeout=3000;" />
</connectionStrings>
<appSettings>
<add key="ConnectionString" value="test"/>
</appSettings>
....
I read from Startup.cs (this is an asp.net core web app):
string connection = ConfigurationManager.ConnectionStrings["Default"].ConnectionString;
However when I break on this, ConfigurationManager.ConnectionStrings and ConfigurationManager.AppSettings are empty (well, the first has some default connection string that is not the one in web.config).
What's going on here?

You will have to migrate the config to the new file appsettings.json
https://learn.microsoft.com/en-us/aspnet/core/migration/configuration?view=aspnetcore-2.1

Not saying this is how you should do it, but you can do the following...
In ASP.Net Core 2.2, you should be able to add an XML configuration to IConfigurationBuilder using
configBuilder.AddXmlFile("app.config");
Contents is pretty much the same as above...
<?xml version="1.0" encoding="utf-8"?>
<configuration>
<connectionStrings configSource="connectionStrings.config" />
<appSettings>
<add key="Test" value="TestValue" />
</appSettings>
</configuration>
You should then be able to access AppSettings/ConnectionStrings using...
ConfigurationManager.ConnectionStrings
ConfigurationManager.AppSettings.AllKeys
{string[1]}
[0]: "Test"
ConfigurationManager.AppSettings.Get("Test")
"TestValue"

Updating a config file adds additional config sections

My goal is to programatically update a .config file belonging to another application.
I start off with a simple config file that looks like this...
<?xml version="1.0" encoding="utf-8" ?>
<configuration>
<connectionStrings>
<add name="Test1" connectionString="data source=.\SQLEXPRESS;Integrated Security=SSPI;AttachDBFilename=|DataDirectory|aspnetdb.mdf;User Instance=true" providerName="System.Data.SqlClient"/>
</connectionStrings>
</configuration>
I then run my code to update the connection string named Test1 and rename it to Test2...
var configMap = new ExeConfigurationFileMap() { ExeConfigFilename = #"test\app.config" };
var externalConfiguration = ConfigurationManager.OpenMappedExeConfiguration(configMap, ConfigurationUserLevel.None);
externalConfiguration.ConnectionStrings.ConnectionStrings[1].Name = "Test2";
externalConfiguration.Save(ConfigurationSaveMode.Minimal, true);
This saves the configuration file, but now looking at the file you will see some other data has been added to it...
ConfigurationSaveMode.Minimal
<?xml version="1.0" encoding="utf-8" ?>
<configuration>
<connectionStrings>
<add name="Test2" connectionString="data source=.\SQLEXPRESS;Integrated Security=SSPI;AttachDBFilename=|DataDirectory|aspnetdb.mdf;User Instance=true"
providerName="System.Data.SqlClient" />
</connectionStrings>
<system.web>
<trust level="Full" />
<webControls clientScriptsLocation="/aspnet_client/{0}/{1}/" />
</system.web>
</configuration>
ConfigurationSaveMode.Modified
Using the Modified setting I get even more "stuff"...
<configuration>
<appSettings />
<configProtectedData />
<system.diagnostics />
<system.windows.forms />
<uri />
<connectionStrings>
<add name="Test2" connectionString="data source=.\SQLEXPRESS;Integrated Security=SSPI;AttachDBFilename=|DataDirectory|aspnetdb.mdf;User Instance=true"
providerName="System.Data.SqlClient" />
</connectionStrings>
<system.net>
<authenticationModules />
<connectionManagement />
<defaultProxy />
...snip...
What is this data and where has it come from? More importantly how can I stop it from being written into my file?

Try changing the ConfigurationSaveMode from
ConfigurationSaveMode.Minimal
to
ConfigurationSaveMode.Modified
Modified only saves the properties that you have changed.
From MSDN:
Full
Causes all properties to be written to the configuration file. This is useful mostly for creating information configuration files or moving configuration values from one machine to another.
Minimal
Causes only properties that differ from inherited values to be written to the configuration file.
Modified
Causes only modified properties to be written to the configuration file, even when the value is the same as the inherited value.

The way I have solved this was to set the Machine Configuration File to be the same as my EXE Configuration file, this way the .net Configuration object does not see that there is any difference between Machine and EXE when it is saving.
For example:
var fm = new ExeConfigurationFileMap();
fm.MachineConfigFilename = fm.ExeConfigFilename = #"C:\dude.config";
var c = ConfigurationManager.OpenMappedExeConfiguration(fm, ConfigurationUserLevel.None);
// Do Stuff
c.Save(ConfigurationSaveMode.Minimal, true);
This way you should not get the section in your config file upon save.

Is there anything wrong with ConfigurationManager in C#?

I read many topics related to configuration manager but could not resolve the issue. I just want to read the connection string as well some appsetting keys from a CLASS LIBRARY in the web application.
I have reference to System.Configuration Class.
This is my code:
using System.Configuration;
...
string constr = ConfigurationManager.ConnectionStrings["cbuddydb"].ConnectionString;
string strUserName = ConfigurationManager.AppSettings["username"];
string strPwd = ConfigurationManager.AppSettings["password"];
But it seems reading from a different config file. not from the web.config in my project. Because the value read is wrong.
My web.config is below:
<configuration>
<system.web>
<compilation debug="true" targetFramework="4.0" />
</system.web>
<system.data>
<connectionStrings>
<clear />
<add name="cbuddydb" connectionstring=
"Driver={MySQL ODBC 5.1 Driver};Server=localhost;Database=myDataBase;Persist Security Info=True;
User=#username;Password=#password;Option=3" providerName="MySql.Data.MySqlClient" password=""/>
</connectionStrings>
<appSettings >
<clear />
<add key="username" value ="6/0RUNnSmUBsbdNoCg+9Sw=="/>
<add key="password" value =""/>
</appSettings>
</system.data>
</configuration>

The reason for this is because of configuration file inheritance. The connection string at index 0 may not be in your config file, but it may have been inherited from machine.config etc. Have a look at ASP.Net config file hierarchy and inheritance: http://msdn.microsoft.com/en-us/library/ms178685.aspx
You could clear the inherited connection strings by specifying the following in your web.config
<connectionStrings>
<clear />
<add name=”MyConnString” connectionString=“Whatever“ />
</connectionStrings>
EDIT: In your config, place your connectionStrings and appSettings tags directly below the configuration element. They should not be within the system.data element. They are direct children of the configuration element. And remove the extra password attribute after the providerName. I can't validate your connection string, since I don't know how you're using it.
<configuration>
<connectionStrings>
<clear />
<add name="cbuddydb" connectionString=
"Driver={MySQL ODBC 5.1 Driver};Server=localhost;Database=myDataBase;Persist Security Info=True;
User=#username;Password=#password;Option=3" providerName="MySql.Data.MySqlClient"/>
</connectionStrings>
<appSettings >
<add key="username" value ="6/0RUNnSmUBsbdNoCg+9Sw=="/>
<add key="password" value =""/>
</appSettings>
<system.data>
....
You should consider encrypting sensitive information in your config file, like passwords.

update app.config file programmatically with ConfigurationManager.OpenExeConfiguration(ConfigurationUserLevel.None);

update app.config file programmatically with
Configuration config =
ConfigurationManager.OpenExeConfiguration(ConfigurationUserLevel.None);
this is my xml
<configuration>
<configSections>
<section name="nhibernateSettings" type="ProjectBase.Data.OpenSessionInViewSection, ProjectBase.Data" />
</configSections>
<appSettings>
<add key="NHibernateConfigPath" value="D:\PROJEKTI\crawler\WebCrawlerSuite\ViaMura.Web\NHibernate.config" />
<!--<add key="NHibernateConfigPath" value="C:\_ZAGON\ViaMura\CurrencyApp\at\NHibernate.config" />-->
<add key="ClientSettingsProvider.ServiceUri" value="" />
</appSettings>
<connectionStrings>
<add name="connectionString" connectionString="Integrated Security=SSPI;Persist Security Info=False;Initial Catalog=Viamura_at;Data Source=.\SQL2008" providerName="System.Data.SqlClient" />
<!--<add name="connectionString" connectionString="server=193.37.152.24\SQL2008;User Id=DBUser;password=Lualah8991;database=Viamura_at" providerName="System.Data.SqlClient" />-->
</connectionStrings>
<nhibernateSettings>
<!-- List every session factory that will be needed; transaction management and closing sessions
will be managed with the open-session-in-view module -->
<sessionFactories>
<clearFactories />
<sessionFactory name="WebCrawlerFactory" factoryConfigPath="D:\PROJEKTI\crawler\WebCrawlerSuite\ViaMura.Web\NHibernate.config" isTransactional="true" />
<!--<sessionFactory name="WebCrawlerFactory" factoryConfigPath="C:\_ZAGON\ViaMura\CurrencyApp\at\NHibernate.config" isTransactional="true" />-->
</sessionFactories>
</nhibernateSettings>
how can I programmatically edit WebCrawlerFactory? I am using
Configuration config =
ConfigurationManager.OpenExeConfiguration(ConfigurationUserLevel.None);

You can use the following code:
private void UpdateConfig(string key, string value, string fileName)
{
var configFile = ConfigurationManager.OpenExeConfiguration(fileName);
configFile.AppSettings.Settings[key].Value = value;
configFile.Save();
}
Where: fileName is the full path + application name (c:\project\application.exe)
In your case, change the AppSetting by Sections:
configFile.Sections["nhibernateSettings"]

The ProjectBase.Data.OpenSessionInViewSection indicates that there is already a custom config section defined that will allow access to the config settings. It may, however be protected or internal to NHibernate.
See if you can reference that class to access the settings.
You could also create a custom configuration section yourself, however it would cause NHibernate to be improperly configured since it would not be able to load the config section properly.
see How to: Create Custom Configuration Sections Using ConfigurationSection

Can we declare variables in the 'app.config' file?

I have a form which needs to get connected to SQL Server, and I have a drop down for selecting the list of databases and perform operations like primary key checking, etc.
But presently my connection string looks like this:
SqlConnection sConnection = new SqlConnection("Server=192.168.10.3;DataBase=GoalPlanNew;User Id=gp;Password=gp");
But apart from the given database, I need to take it variable, so that I can connect it to the database I select from the dropdown.
How can I do this?

Hmm you can declare your variables like this
<appSettings>
<add key="SmtpServerHost" value="********" />
<add key="SmtpServerPort" value="25" />
<add key="SmtpServerUserName" value="******" />
<add key="SmtpServerPassword" value="*****" />
</appSettings>
and read like
string smtpHost = ConfigurationManager.AppSettings["SmtpServerHost"];
int smtpPort = Convert.ToInt32(ConfigurationManager.AppSettings["SmtpServerHost"]);

I think he wants a "semi constant":
Web.Config
<?xml version='1.0' encoding='utf-8'?>
<configuration>
<connectionStrings>
<add name="YourName" providerName="System.Data.ProviderName" connectionString="Data Source={0}; Initial Catalog=myDataBase; User Id=myUsername; Password=myPassword;" />
</connectionStrings>
</configuration>
CS file
String Servername = "Test";
String ConnectionString = String.Format(ConfigurationManager.ConnectionStrings["YourName"].ConnectionString, ServerName);

you can use the connectionStrings tag in the app.config configuration. You can add as many as you want (giving them each a separate key) and then retrieve them
example app.config xml (set providerName to a valid provider, for example System.Data.SqlClient, and the appropriate connection string) :
<?xml version='1.0' encoding='utf-8'?>
<configuration>
<connectionStrings>
<clear />
<add name="firstDb"
providerName="System.Data.ProviderName"
connectionString="Valid Connection String;" />
<add name="secondDb"
providerName="System.Data.ProviderName"
connectionString="Valid Connection String;" />
</connectionStrings>
</configuration>
example on getting them and listing them (in your case, you would create the appropriate items in the dropdown and set the values) :
ConnectionStringSettingsCollection settings =
ConfigurationManager.ConnectionStrings;
if (settings != null)
{
foreach(ConnectionStringSettings cs in settings)
{
Console.WriteLine(cs.Name);
Console.WriteLine(cs.ProviderName);
Console.WriteLine(cs.ConnectionString);
}
}

You could use the AppSettings section. Read here for an example.