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small polishing #13

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17 changes: 12 additions & 5 deletions docs/parser_plugins.md
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Original file line number Diff line number Diff line change
Expand Up @@ -22,7 +22,7 @@ In practice, however, parser developers have to manage discrepancies in semantic
This has lead to five distinct categories of responsibility for the developer to manage.
Here, they are ordered to match the parser's execution:

1. **file selection** - navigate the upload's folder structure and select the relevant files.
1. **file selection** - navigate the uploads folder structure and select the relevant files.
2. **source extraction** - read the files into Python. This step may already include some level of data field filtering.
3. **source to target** - map the data of interest with their counterparts in the target/NOMAD schema. This is where the bulk of the filtering happens.
4. **data mangling** - manipulate the data to match the target/NOMAD `Quantity`s' specification, e.g. dimensionality, shape. This may include computing derived properties not present in the original source files.
Expand Down Expand Up @@ -154,7 +154,7 @@ xml_entry_point = VasprunXMLEntryPoint(
)
```

`load` comes from the entry point system and should just return our parser (see below).
`load()` comes from the entry point system and should just return our parser (see below).
The entry point itself specifies _parser data_ and the directives.
There are three kinds of file aspects that can be targeted, all via _regular expressions_ (regex):

Expand All @@ -179,7 +179,7 @@ There are three kinds of file aspects that can be targeted, all via _regular exp
```
<!-- TODO double-check -->

#### Mainfile Interfacing
#### Interfacing with NOMAD base

Within the cascade, `MatchingParser`, acts as the connection point on the parser side.
It plays less of a role in manipulating the directives, and more so in defining the _interface_ &mdash;a formalization of mutually agreed upon behavior&mdash; back to the parser.
Expand Down Expand Up @@ -207,7 +207,7 @@ class VasprunXMLParser(MatchingParser):

### Notebooks
If you are using Jupyter Notebook, you can manipulate data in a head-on way without NOMAD base as an intermediary.
Note that this enntails providing the parsing input yourself, as well as manually triggering normalization.
Note that this entails providing the parsing input yourself, as well as manually triggering normalization.
A template setup looks something like:

```python
Expand Down Expand Up @@ -534,6 +534,13 @@ Since all NOMAD sections are convertible to `dict`, one can generate a `get` cha
...

class VasprunXMLParser(MatchingParser):
...
convert_xc: dict[str, str] = {
'--': 'GGA_XC_PBE',
'PE': 'GGA_XC_PBE',
...
}

def parse(
...
)
Expand Down Expand Up @@ -611,7 +618,7 @@ class VasprunXMLParser(MatchingParser):
self, mainfile: str, archive: EntryArchive, logger: BoundLogger,
child_archives: dict[str, EntryArchive] = None,
) -> None:
logger.info('VasprunXMLParser.parse', parameter=configuration.parameter)
... #logging
data_parser = MetainfoParser(annotation_key='xml', data_object=Simulation())
XMLParser(filepath=mainfile).convert(data_parser)
archive.data = data_parser.data_object
Expand Down