BridgeDb loading issues

[DeniseSl22]

@mkutmon a BridgeDb file cannot be loaded if a bracket is in the name (or one of the parent folders).
For details see here.

pathvisio.log message: '(Het systeem kan het opgegeven bestand niet vinden)'

I will add a message on this issue in the FAQ on the website.

[egonw]

Some pointer where the error log is would be welcome too:

[DeniseSl22]

Some pointer where the error log is would be welcome too:

We actually have a few lines on that in the FAQ ;)

[egonw]

We actually have a few lines on that in the FAQ ;)

What I meant, that pointer should be in the GUI already.

[DeniseSl22]

Ah, got it. Let's write that up for PV 4 ;)

[traybug23]

Hi @DeniseSl22 ! I'm interested in devising a fix for this issue. I noticed that this issue is still prevelant for the newer version of Pathvisio. Are there any pointers or additional informations I need to know before I carry forward?

[egonw]

ping @mkutmon

[DeniseSl22]

Hi @traybug23 : thanks for picking this up! I think this was related to an error we saw on Windows; if you download a file twice, it automatically adds a '(1)' version number in the name to avoid duplicate names. However, our code cannot handle these characters at the moment in file names (it might also hold true for other symbols, but I did not check that).

The BridgeDb issue is for files loaded through a plugin (I'm looking for the source code, will paste the link here when I found it).

[DeniseSl22]

@traybug23 : code is available here: https://github.com/bridgedb/BridgeDbConfig

[traybug23]

ping @mkutmon
Hi! @egonw
I did ping her regarding this and am awaiting her reply.

[traybug23]

@traybug23 : code is available here: https://github.com/bridgedb/BridgeDbConfig

Thank you so much for sharing the code! I will look into the issue and try to understand how BridgeDb handles symbols such as (1) as it's common in windows to add that suffix when same file is downloaded twice. If possible, I will also run some tests to see if it holds true for other symbols as well.

[traybug23]

Hi @DeniseSl22 ! I have been working on this fix, basically i added a .toURI( ) encoding in PgdbParameterModel.java to read the brackets in filepath. To test if the fix is working now i tried building pathvisio4-ant, BridgeDb and BridgeDbConfig but the build was failing because the lib/ folder in pathvisio4-ant starts with org.bridgedb-3.0.18.jar and org.bridgedb.gui-3.0.18.jar, but the current BridgeDb build gives version 3.0.30. This version mismatch causes BridgeDbConfig to fail compilation with package org.bridgedb does not exist errors.

Is this a system error on my part or has this issue been prevalent for you too? Also, should I open a PR with the fix so that you can check the build issue and review it to see if the bracket read fix works?

[DeniseSl22]

Hi @traybug23 , thanks for your work (again)! I'll have to check this with @egonw : Is the maven build for PV4 working (so that the versions of BridgeDb don't have to be hardcoded, as I believe it is in ant)?

In the meantime, could you try to build the latest version of BridgeDb, and then manually copy in the required libraries, to see if your fixes are working as expected?

[traybug23]

Hi @traybug23 , thanks for your work (again)! I'll have to check this with @egonw : Is the maven build for PV4 working (so that the versions of BridgeDb don't have to be hardcoded, as I believe it is in ant)?

In the meantime, could you try to build the latest version of BridgeDb, and then manually copy in the required libraries, to see if your fixes are working as expected?

I am learning a lot while working on these fixes, you're welcome!

Regarding the issue, I did manually copy the libraries and build it, the problem is fixed now as you can see in the screenshot attached.
I have opened a pull request [https://github.com/bridgedb/BridgeDb/pull/260#issue-4122039111](Issue #211), I would be grateful if you can find the time to review it.

[traybug23]

Apart from that, I also noticed that the BridgeDbConfig plugin currently imports org.pathvisio.core.debug.Logger which doesn't exist in the pathvisio4 repository. The class is moved to org.pathvisio.libgpml.debug.Logger. This was causing a compilation error from my side while building the plugin in PathVisio4.
I updated the logger import in the following files:
BridgeDbConfigPlugin.java
BridgeDbConfigDlg.java
IdMapperDlg.java

This is only an import path change with no logic modifications whatsoever. I tested it by building the plugin in pathvisio4-ant and the plugin loads successfully. I have submitted a PR [https://github.com/bridgedb/BridgeDbConfig/pull/3#issue-4122201457](Import Logger for PathVisio4), I am looking forward to your feedback!