empd_admin.common module¶

Data

`DATADIR`	Path to the local directory of the cloned EMPD2/EMPD-data repository.
`DATA_LOCKFILE`	Lock file to lock the repository `DATADIR`.
`NUMERIC_COLS`	Columns in the EMPD-data metadata sheet that hold numeric values

Functions

`dump_empd_meta`(meta[, fname])	Dump the EMPD meta data to a file
`get_empd_master_repo`()	Get the repository to the data directory and download it if necessary
`get_psql_scripts`()	The path to the postgres scripts in the EMPD-data repository
`get_test_dir`()	The path to the tests directory in the data directory
`lock_empd_master`()	Lock the data repository
`read_empd_meta`([fname, addokexcept])	Read an EMPD-data metadata file into a pandas DataFrame
`wait_for_empd_master`([timeout])	Wait until the data repository is available

empd_admin.common.DATADIR = '/opt/empd-data'¶: Path to the local directory of the cloned EMPD2/EMPD-data repository. The path can be set through the EMPDDATA environment variable. Otherwise, it is assumed to be '$HOME/.local/share/EMPD-data'

empd_admin.common.DATA_LOCKFILE = '/var/lib/postgresql/cloning_master.lock'¶: Lock file to lock the repository DATADIR. By default, this is at '$HOME/cloning_master.lock' and is used by the lock_empd_master() and wait_for_empd_master() functions.

empd_admin.common.NUMERIC_COLS = ['Latitude', 'Longitude', 'Elevation', 'AreaOfSite', 'AgeBP', 'count', 'percentage']¶: Columns in the EMPD-data metadata sheet that hold numeric values

empd_admin.common.dump_empd_meta(meta, fname=None, **kwargs)¶

Dump the EMPD meta data to a file

This function dumps the meta data of the EMPD to a file with some standard formatting

Parameters

meta (pandas.DataFrame) – The dataframe holding the meta data (see read_empd_meta())
fname (str) – The filename where to save it (see pandas.DataFrame.to_csv())
**kwargs – Any other argument that is parsed to the pandas.DataFrame.to_csv() function

Examples

Read the EMPD meta file and dump it again:

from empd_admin.common import read_empd_meta, dump_empd_meta
meta = read_empd_meta('EMPD-data/meta.tsv')
dump_empd_meta(meta, 'EMPD-data/meta.tsv')

empd_admin.common.get_empd_master_repo()¶

Get the repository to the data directory and download it if necessary

This function returns a git.Repo instance for the DATADIR.

Returns: The local repository of the EMPD-data. If necessary, it has been cloned from https://github.com/EMPD2/EMPD-data.git.
Return type: git.Repo

empd_admin.common.get_psql_scripts()¶

The path to the postgres scripts in the EMPD-data repository

Returns: The path to the postgres scripts of the data repository
Return type: str

See also

get_empd_master_repo(): To get the data repository

empd_admin.common.lock_empd_master()¶

Lock the data repository

This will lock the data repository and blocks any access to it. The locking is done through a lock file (usually in '$HOME/cloning_master.lock', see the DATA_LOCKFILE).

Use this function as a context manager, i.e. such as:

with lock_empd_master():
    # now the repository is locked
    do_something()
# now it is not locked anymore

empd_admin.common.read_empd_meta(fname=None, addokexcept=True)¶

Read an EMPD-data metadata file into a pandas DataFrame

This function is the same as pandas.read_csv() but it also ensures the correct dtype for the various columns.

Parameters: fname (str) – The path to the (tab-delimited) meta data file. If None, it will default to the meta data in the DATADIR, i.e. DATADIR + '/meta.tsv'
Returns: The given fname as a data frame. The index column will be the SampleName column in fname.
Return type: pandas.DataFrame

Examples

Read the meta data of the EMPD-data repository:

import git
from empd_admin.common import read_empd_meta
git.Repo.clone_from('https://github.com/EMPD2/EMPD-data.git')
meta = read_empd_meta('EMPD-data/meta.tsv')