pyelabdata 0.1.7

pyelabdata provides functions for simple one-line access to data in eLabFTW

pyelabdata

pyelabdata provides functions for simple one-line access to data stored in eLabFTW via Python or Jupyter.

Examples

Examples for the use of pyelabdata can be found in the examples folder.

Functions

def connect(host: str, apikey: str):

Connects to the API interface of the eLabFTW server specified by the parameter host (e.g. https://yourserver.org/api/v2) using the given apikey.

def disconnect():

Disconnect from the eLabFTW server.

def list_experiments(searchstring: str='', tags=[]):

Retrieve a list of ids of all experiments that contain searchstring in the title, body or elabid and that match the tags specified in tags. All parameters are optional. If nothing is specified, all accessible experiments will be listed.

def open_experiment(expid: int, returndata: bool=False):

Open an experiment in eLabFTW using the id of the experiment. If returndata is True, the function returns a dictionary with the metadata of the experiment. All subsequent commands will operate on the opened experiment.

def close_experiment():

Close the current experiment. Subsequent commands will not further operate on the experiment.

def get_maintext(format: str='html', expid: int=None):

Retrieve the body text of the experiment.

All parameters are optional. If format is 'html', the content of body_html is returned, i.e. the body text in html format. Otherwise the content of body is returned, which depends on the format used in eLabFTW (markdown or html). expid is an integer number which identifies the eLabFTW experiment; if set to None, the currently opened experiment is used.

def get_table_data(tableidx: int=0, header: bool=True, 
                   datatype: str='np', expid: int=None):

In eLabFTW, tables can be defined in the body text of experiments. The data of such tables can be retrieved by using this function.

All parameters are optional. tableidx tells the function the return the data of the n^th table, where counting starts with n = 0. If header is true, the function assumes that the table contains columns of data where the first element (row) is the column heading. datatype may be either 'df' or 'np' (default). For 'df', a pandas dataframe representing the table data is returned, whereas for 'np' a dictionary of numpy arrays for each column is returned, in which the keys correspond to the column heading (in case of header = True). expid is an integer number which identifies the eLabFTW experiment; if set to None, the currently opened experiment is used.

def get_file_csv_data(filename: str, 
                      header: bool=True, sep: str=',', 
                      datatype: str='np', expid: int=None):

Get the data from csv files attached to eLabFTW experiments. filename is the name of the file stored in the experiment.

All other parameters are optional. sep is the column separator, by default a comma. The parameters header, datatype and expid have the same meaning as in get_table_data().

def upload_file(file: str, comment: str,
                replacefile: bool=True, expid: int=None):

Upload a file from local drives to an eLabFTW experiment. file is the filepath of the file to be uploaded, comment is a description of the file.

All other parameters are optional. If replacefile is true, an existing file with the same filename will be replaced. Otherwise, a new attachment with the same filename will be created. expid is an integer number which identifies the eLabFTW experiment; if set to None, the currently opened experiment is used.

def upload_image_from_figure(fig: Figure, filename: str, comment: str,
                             replacefile: bool=True, 
                             format: str='png', dpi='figure',
                             expid: int=None):

Upload an image of a matplotlib Figure (e.g. created by fig, ax = plt.subplots()) as attachment to an eLabFTW experiment. fig a matplotlib.figure.Figure object, filename the name of the image file to be uploaded, and comment is a description of the image.

All other parameters are optional. If replacefile is true, an existing file with the same filename will be replaced. Otherwise, a new attachment with the same filename will be created. format or dpi specify the file format or image resolution, respectively. They are passed to matplotlib's savefig() function. expid is an integer number which identifies the eLabFTW experiment; if set to None, the currently opened experiment is used.

def upload_csv_data(data, filename: str, comment: str,
                    replacefile: bool=True, index: bool=False,
                    expid: int=None):

Generate a csv file from a pandas dataframe or a dictionary of numpy arrays (column data) contained in data and upload it to an experiment on eLabFTW as csv file. comment is a description of the data.

All other parameters are optional. If replacefile is true, an existing file with the same filename will be replaced. Otherwise, a new attachment with the same filename will be created. If index is true, the line index of the dataframe is also stored to the file. expid is an integer number which identifies the eLabFTW experiment; if set to None, the currently opened experiment is used.

def upload_this_jupyternotebook(comment: str, replacefile: bool=True,
                                expid: int=None):

Saves and uploads the current jupyter notebook to an experiment on eLabFTW. comment is a description of the jupyter notebook.

All other parameters are optional. If replacefile is true, an existing file with the same filename will be replaced. Otherwise, a new attachment with the same filename will be created. expid is an integer number which identifies the eLabFTW experiment; if set to None, the currently opened experiment is used.