data¶
The study data of a model, collected from the study folders of PK-DB.
The studies of PK-DB are curated in a checkout of
pkdb_data: the folder studies
holds a folder per substance and in it a folder per study, with the digitized
data as hidden .tsv files next to the figures and tables they were read
from. A model keeps the subset of the studies it uses in its own data/
folder, so its simulations run without the checkout; collect_tsv_files
copies them there from the folder studies_dir() finds.
module-attribute
¶
The environment variable with the path of a checkout of pkdb_data.
Get the folder of the PK-DB studies, studies of a checkout of pkdb_data.
The checkout is the path of the environment variable PKDB_DATA; without
the variable it is ../pkdb_data relative to the working directory, i.e.
a checkout next to the repository a script runs in.
Returns:
| Type | Description |
|---|---|
Path
|
The absolute path of the folder |
Raises:
| Type | Description |
|---|---|
FileNotFoundError
|
if the folder does not exist; the message names the environment variable and the default location. |
Copy the data of the studies of a substance into the data folder of a model.
The data files of a study folder of pkdb_data are its hidden .tsv files
(.Boulton1996a_Fig1.tsv); the figures, the tables and the publication
are left behind. Every study folder of source_dir which passes
filter_study and has data files becomes a folder of the same name in
target_dir with copies of them, and every copy is reported on the
console.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
source_dir
|
Path
|
the folder of the studies of a substance, e.g.
|
required |
target_dir
|
Path
|
the data folder of the model, created if it does not exist (its parent has to). |
required |
filter_study
|
Callable[[str], bool] | None
|
decides by the name of a study folder whether the study is collected; all studies by default. |
None
|