---
last_review: "2025-01-01"
last_reviewer: "-"
documented_code: [ ]
---

```{tags} explanation
```

# Other utilities in LinkAhead Advanced User Tools

:::{note}
This page has been migrated from the old documentation, and has not yet been fully revised.
There might be inconsistencies or errors when using with current LinkAhead versions.
:::
% TODO: Issue: https://gitlab.indiscale.com/caosdb/src/linkahead-docs/-/issues/93
% TODO: Create a tutorial, Split

## The table file importer

The LinkAhead Advanced user tools provide a generic
{py:class}`~caosadvancedtools.table_importer.TableImporter` class which reads different table file formats (at
the time of writing of this documentation, `.xls(x)`, `.csv`, and `.tsv`) and converts them into
{py:class}`pandas.DataFrame` objects. It provides helper functions for converting column values (e.g.,
converting the string values "yes" or "no" to `True` or `False`), checking the presence of
obligatory columns in a table and whether those have missing values, and datatype checks.

The base class {py:class}`~caosadvancedtools.table_importer.TableImporter` provides the general
verification methods, while each subclass like
{py:class}`~caosadvancedtools.table_importer.XLSXImporter` or
{py:class}`~caosadvancedtools.table_importer.CSVImporter` implements its own `read_file` function that is used
to convert a given table file into a {py:class}`pandas.DataFrame`.

### Empty fields in integer columns

Reading in table files that have integer-valued columns with missing data can result in datatype
contradictions (see the Pandas documentation
on [nullable integers](https://pandas.pydata.org/docs/user_guide/integer_na.html)) since the default
value for missing fields, `numpy.nan`, is a float. This is why from version 0.11 and above, the
`TableImporter` uses {py:class}`pandas.Int64Dtype` as the default datatype for all integer columns
which allows for empty fields while keeping all actual data integer-valued. This behavior can be
changed by initializing the `TableImporter` with `convert_int_to_nullable_int=False` in which case a
{py:class}`~caosadvancedtools.datainconsistency.DataInconsistencyError` is raised when an empty
field is encountered in a column with a non-nullable integer datatype.

## The loadfiles module and executable

For making files available to the LinkAhead server as File entities (see also the server's
[file server](/explanation/server/Fileserver.md) documentation), the LinkAhead Advanced User tools
provide the {py:mod}`~caosadvancedtools.loadFiles` module and a `linkahead-loadfiles` executable.
Both operate on a path as seen by the LinkAhead server (i.e., a path within the Docker container in
the typical LinkAhead Control setup) and can be further specified to exclude or exclude specific
files. In the typical setup, where a directory is mounted as an *extroot* into the Docker container
by LinkAhead control, running

```sh
linkahead-loadfiles /opt/caosdb/mnt/extroot
```

makes all files available. Execute

```sh
linkahead-loadfiles --help
```

for more information and examples.