From 007a8a469721e6e425a4a82d67d984f75fda452a Mon Sep 17 00:00:00 2001 From: De Date: Tue, 3 Sep 2024 15:40:22 +0200 Subject: [PATCH] BridgeDb loading issues @mkutmon update for FAQ to avoid issues loading BridgeDb files and more details on finding the error log --- faq.md | 10 +++++++++- 1 file changed, 9 insertions(+), 1 deletion(-) diff --git a/faq.md b/faq.md index 746c2d3..b432a45 100644 --- a/faq.md +++ b/faq.md @@ -193,7 +193,7 @@ Try clearing the Java webstart cache, you can find instructions [here](http://ww **2. Where can you find the log file?** You can find your pathvisio.log file in the local PathVisio directory: -* Windows: in your home directory, go into the hidden directory "AppData"- "Roaming" - "PathVisio" +* Windows: in your home directory, go into the hidden directory "AppData"- "Roaming" - "PathVisio" (you can also find this file using your file explorer, searching for 'pathvisio.log') * MacOS / Linux: in your home directory, go into the hidden directory ".PathVisio" **3. The installation does not work on Linux, what now?** @@ -210,3 +210,11 @@ chmod u+x deploy.sh ./pathvisio.sh ``` +**4. I cannot load a BridgeDb mapping file, 'failed to connect to database' error message** + +1. Check if your BridgeDb file is compatible with the version of PathVisio you are using (indicated on the [Download](https://data.bridgedb.org/gene_database/) page in the 'Tested with' column). +2. Try to load the file using the 'Data/Select Gene Database' button from the top menu (so not using the BridgeDb Plugin) +3. Check if your file name has special characters in them, for example round brackets '(' or ')', and remove these characters from the file name. +4. Check if one of the parent folders has special characters in them, and remove these characters from the folder name. +5. If the above does not work, check the pathviso.log file (see [here](https://github.com/PathVisio/pathvisio.github.io/edit/master/faq.md#193) how) to find a more detailed error message on what might be the cause of the problem. +6. Add an issue to the [BridgeDb GitHub](https://github.com/bridgedb/data/issues) repository including this detailed error message to get help.