Structures in analysis report not showing after clean

[sverhoeven]

Describe the bug
Structures in analyis report are not showing.

To Reproduce

1. Run the examples/docking-protein-protein/docking-protein-protein-full.cfg the recipe with 358f39f checked out.
2. Start web server on examples/docking-protein-protein/run1-full folder.
3. Open the examples/docking-protein-protein/run1-full/analysis/11_caprieval_analysis/report.html in a web browser.
4. Click download or view links of best structure

Expected behavior

I expected when I downloaded of viewrf astructure it would appear. However I got 404 not found errors.

Screenshots
If applicable, add screenshots to help explain your problem.

Configuration (optional - remove if not relevant)

• OS: [e.g. iOS]
• Version [e.g. 22]

Additional context (optional - remove if not relevant)
The examples/docking-protein-protein/run1-full/11_caprieval/capri_ss.tsv contains link to ../10_seletopclusts/cluster_1_model_1.pdb, but only examples/docking-protein-protein/run1-full/10_seletopclusts/cluster_1_model_1.pdb.gz exists.

[sverhoeven]

The problem always happened after cleaning, but with #706 implemented the problem now happens a lot more as cleaning is now done by default.

At

haddock3/src/haddock/clis/cli.py

Lines 179 to 181 in 358f39f

	if other_params["postprocess"]:
	workflow.postprocess()
	workflow.clean()

the clean is done after postprocess (command that generates report.html). So postprocess step does not know whether clean step will be done.

[mgiulini]

hi there, PR #706 indeed sets clean to true by default, with the aim to reduce the disk usage of haddock3. Three options to visualize structures:

• simply set clean to false at the beginning of the workflow
• we modify the clean option so that it does not compress PDB files

@amjjbonvin what do you say?

[sverhoeven]

I think cleaning is a good idea and compressed pdb file also work with the viewer.

In the webapp I added check whether pdb files are gzipped (i-VRESSE/haddock3-webapp@4cb98c5)

I could add a similar check in report.html

[mgiulini]

OK then, I misundestood the problem..it is not that the viewer cannot show compressed files, but rather a name issue in the tables! In that case yes, a simple check on the file name would be my favourite solution.

[amjjbonvin]

Sounds like the best solution

…

In the webapp I added check whether pdb files are gzipped ***@***.*** <i-VRESSE/haddock3-webapp@4cb98c5>) I could add a similar check in report.html

[amjjbonvin]

Would the viewer be able to load gzipped PDF files? PyMol can for example.

Currently also the download button does not work since it links to the pdb file and can not handle the pdb.gz files