Feature/sof 4154

[csadorf]

No description provided.

[timurbazhirov]

(1) We should declare parameters and output in docstring
(2) Nit: docstring format is different than elsewhere in the code

[timurbazhirov]

Some ideas/questions:

1. Isolate instance into a JSON template configurable with parameters and use it here
2. add functions for parsing lattice, basis separately to increase modularity

[csadorf]

Could you elaborate on point 1? Do you mean to have a static file as a template or a template within the code? Where would that template be configured?

[csadorf]

From discussion: Store static template.

Consider: creating object from esse schema with https://github.com/cwacek/python-jsonschema-objects

[csadorf]

Tried using python-jsonschema-objects, however the following minimal example fails:

import esse
import python_jsonschema_objects as pjs

ES = esse.ESSE()
SCHEMA_MATERIAL = ES.get_schema_by_id('material')
builder = pjs.ObjectBuilder(SCHEMA_MATERIAL)
ns = builder.build_classes()

It's possible that I'm using it wrong, but at this point, I'll just move on and use a static template instead.

[timurbazhirov]

Let's log the event here, pls, to avoid a silent loophole

[csadorf]

I did not like this either, but followed this pattern:

express/express/parsers/formats/xml.py

Lines 20 to 22 in a8a9cd2

	except:
	# safely ignore broken xml file
	pass

[triplepoint]

In general, I really like this code. It's clean and concise without being dense and obscure. Good job.

[triplepoint]

I don't know enough about the context here; is this workable? If nothing else, maybe some commentary here about why this is acceptable?

[csadorf]

I don't think so, but I am also not sure how else to integrate this with existing patterns.

[csadorf]

Decision: Actually implement as function that returns value from initial_structure_strings().

[timurbazhirov]

What I meant is:

• inside the template below - materials.json (should be called material.json btw) we can add template variables, for example { ID }, or { LATTICE_VECTOR_A } like:

{
    "_id": "{{ ID }}"
    "lattice": {
       "vectors": {
        { "a": "{{ LATTICE_VECTOR_A }}" ...
   ...
}

• then, when we want to generate the instance from it we read text, render it and load:

json.loads(Template.render(template, ID=export_data['uuid'], LATTICE_VECTORS_A=attributes['cell'][0]
...)
 

[csadorf]

I've applied that change in 7aa402b and 3e19d11 .

[timurbazhirov]

Also - when we upload the job information to our database online, the ID is likely to be reset, especially if it's a duplicate. We could add a tag to store the original AiiDA ids there. With MP materials we retain them as mp-137, for example. So tags: ["aiida-<UUID>"] could be a good start.

[csadorf]

I applied that change in 3c01bbb .

[csadorf]

I've cycled the base to trigger the correct representation of this PR on GitHub.