Allow required property with default value to be absent

[sverhoeven]

Refs #154

Can be tested with

1. Add default: output to packages/haddock3_catalog/public/catalog/haddock3.easy.yaml:global.schema.properties.run_dir
2. yarn dev
3. open haddock3-download application on http://localhost:3000
4. Upload a workflow.cfg without run_dir key.
5. It should be loaded and valid.

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[sverhoeven]

I tried to use defaults but then every parameter with a default value is filled in the workflow.cfg file.

For example with the testing instructions and no-rundir.zip, I got

mode = 'local'
molecules = [
  'processed-A2A-2oob.pdb',
  'processed-B2B-2oob.pdb',
]

postprocess = true
clean = true
offline = false
ncores = 6
run_dir = 'output'
preprocess = false
batch_type = 'slurm'
queue_limit = 100
concat = 1

[topoaa]

delenph = true

[rigidbody]

ambig_fname = 'ambig.tbl'
sampling = 1000
randorien = true
elecflag = true

[caprieval]

irmsd = true
fnat = true
lrmsd = true
ilrmsd = true
dockq = true
irmsd_cutoff = 10
fnat_cutoff = 5
receptor_chain = 'A'
ligand_chains = [
  'B',
]

sortby = 'score'
sort_ascending = true
alignment_method = 'sequence'
clt_threshold = 4
allatoms = false

[seletop]

select = 200

['caprieval.2']

irmsd = true
fnat = true
lrmsd = true
ilrmsd = true
dockq = true
irmsd_cutoff = 10
fnat_cutoff = 5
receptor_chain = 'A'
ligand_chains = [
  'B',
]

sortby = 'score'
sort_ascending = true
alignment_method = 'sequence'
clt_threshold = 4
allatoms = false

[flexref]

ambig_fname = 'ambig.tbl'
dihedrals_on = false
ssdihed = 'none'
error_dih = 10
dnarest_on = false
elecflag = true
sinter_rigid_final = 0.001

['caprieval.3']

irmsd = true
fnat = true
lrmsd = true
ilrmsd = true
dockq = true
irmsd_cutoff = 10
fnat_cutoff = 5
receptor_chain = 'A'
ligand_chains = [
  'B',
]

sortby = 'score'
sort_ascending = true
alignment_method = 'sequence'
clt_threshold = 4
allatoms = false

[emref]

ambig_fname = 'ambig.tbl'
dihedrals_on = false
dihedrals_scale = 200
ssdihed = 'none'
error_dih = 10
dnarest_on = false
elecflag = true

['caprieval.4']

irmsd = true
fnat = true
lrmsd = true
ilrmsd = true
dockq = true
irmsd_cutoff = 10
fnat_cutoff = 5
receptor_chain = 'A'
ligand_chains = [
  'B',
]

sortby = 'score'
sort_ascending = true
alignment_method = 'sequence'
clt_threshold = 4
allatoms = false

[clustfcc]

plot_matrix = true
contact_distance_cutoff = 5
clust_cutoff = 0.6
min_population = 4
strictness = 0.75

[seletopclusts]

top_models = 4
top_cluster = 1000
sortby = 'score'

['caprieval.5']

irmsd = true
fnat = true
lrmsd = true
ilrmsd = true
dockq = true
irmsd_cutoff = 10
fnat_cutoff = 5
receptor_chain = 'A'
ligand_chains = [
  'B',
]

sortby = 'score'
sort_ascending = true
alignment_method = 'sequence'
clt_threshold = 4
allatoms = false

[contactmap]

ca_ca_dist_threshold = 9
shortest_dist_threshold = 4.5
color_ramp = 'Greys'
single_model_analysis = false
generate_heatmap = true
generate_chordchart = true
cluster_heatmap_datatype = 'shortest-cont-probability'
chordchart_datatype = 'shortest-dist'

This is not nice, as the user did not set most of those.

Setting the default value in the web app is not the way to go. The builder page in the app should be given a schema without run dir property, but validation on server side (that happens after the run_dir is set to output) could still validate with the prop.