Merge pull request #215 from UtrechtUniversity/develop

v0.2.4

docs/source/faq.rst

@@ -33,3 +33,13 @@ add this to the path on the command line: `export PATH="${PATH}:/home/your_usern
 your shell to find the `ibridges` command. You would have to type the previous command every time you start a new shell, which can be inconvenient.
 To fix this permanently, add the command to your `.bashrc` or `.zshrc` file in your home directory at the end of the file
 (depending on your shell, type `echo ${SHELL}` to find out).
+
+
+**Help, I'm getting a "NetworkError" while trying to transfer (large) files**
+-----------------------------------------------------------------------------
+
+This error is most likely to happen if you try to transfer a large file. The default timeout for iBridges is 25000 seconds,
+which translates to roughly 7 hours. This should not cause issues during the actual transfer. However, if the calculation
+of the checksum takes more than 7 hours (if the iRODS server is busy for example, or the file is many terabytes), then 
+you will get a network error. The checksum itself should still be created. You can increase the timeout in your `irods_environment.json`
+file by adding a new entry with `"connection_timeout": 99999999999,`. 

ibridges/session.py

@@ -72,8 +72,7 @@ def __init__(self,
             raise TypeError(f"Error reading environment file '{irods_env_path}': "
                             f"expected dictionary, got {type(irods_env)}.")
 
-        if "connection_timeout" not in irods_env:
-            irods_env["connection_timeout"] = 25000
+        self.connection_timeout = irods_env.pop("connection_timeout", 25000)
 
         self._password = password
         self._irods_env: dict = irods_env
@@ -198,9 +197,11 @@ def close(self) -> None:
     def authenticate_using_password(self) -> iRODSSession:
         """Authenticate with the iRODS server using a password."""
         try:
-            irods_session = irods.session.iRODSSession(password=self._password,
-                                                             **self._irods_env,
-                                                       application_name=APP_NAME)
+            irods_session = irods.session.iRODSSession(
+                password=self._password,
+                **self._irods_env,
+                connection_timeout=self.connection_timeout,
+                application_name=APP_NAME)
             _ = irods_session.server_version
         except Exception as e:
             raise _translate_irods_error(e) from e
@@ -212,7 +213,8 @@ def authenticate_using_auth_file(self) -> iRODSSession:
         """Authenticate with an authentication file."""
         try:
             irods_session = irods.session.iRODSSession(
-                irods_env_file=self._irods_env_path, application_name=APP_NAME)
+                irods_env_file=self._irods_env_path, application_name=APP_NAME,
+                connection_timeout=self.connection_timeout)
             _ = irods_session.server_version
         except NonAnonymousLoginWithoutPassword as e:
             raise ValueError("No cached password found.") from e