Python API¶

AMAD offers a python API to interact with user notebooks and their data directly from python scripts (or JupyterLab).

Installation¶

The API code (labcore.py) is freely available to all registered users, and is obtained by clicking the download button in the Dashboard/Account panel.

The API source code shoule be placed in the same folder as the python scripts that will use it in order to be importable. Alternatively, it can be placed in any folder included in the PYTHONPATH environment variable.

It is also necessary to download the SSL certificate from the Dashboard/Account panel and place it in the same folder as the python code.

Dependencies¶

The API requires the following python packages to be installed in your environment:

asd

Using the API¶

Once properly installed, it is straightforward to use the API by importing the labcore module and all its content. Here is an example python script that retrieves the list of user notebooks:

from labcore import *
import numpy

# setup the API
LabCore.SERVER = 'https://amad.aalto.fi'
LabCore.APITOKEN = '5fa2847501684136921855a6.1906e26a9c19c68717726f9780651092fdb8bb1f'

# this is only necessary if the file is not in the same folder as this script
# LabCore.CERT = '/path/to/certificate/labcore.pem'
#
# SSL certificate verification can be disabled with:
# LabCore.CERT = False
# but don't come crying to me when you get hacked!


# fetch list of notebooks
nbs = LabCore.notebook_list()

# print notebook titles
for nb in nbs:
        print("notebook:",nb['title'])

The important lines are:

from labcore import *: import all functions and objects from the API module
LabCore.SERVER = '...': tells the API the URL of AMAD server
LabCore.APITOKEN = '...': set the API token for this user

The API token can be requested from the Dashboard/Account panel and remains valid for 24 hours after it is last used. When a new token is obtained, just replace the string with the new token. If the token is expired or invalid, all the API functions will return an error.

Note

Issuing a new token will replace the existing one.

The token inlcudes the unique ID of the user, thus every notebook/data interaction done through the API is associated to the user.

Using the API with RSA keys¶

It is also possible to use the API with RSA keys that do not expire. First generate an RSA private key in the PKCS#1 format:

openssl genrsa -traditional -out id_api_private.pem 2048

and the corresponding public key:

openssl rsa -in id_api_private.pem -pubout -out id_api_public.pem

The public key should look like this:

Click the add key button in the Dashboard/Account panel and paste the public key in the text area. After uploading the public key, configure the API in your python script as follows:

from labcore import *

f = open('id_api_private.pem', 'rb')
LabCore.SetUserKey('USER ID HERE', f.read())
f.close()

The file to read is the private key corresponding to any of the public keys uploaded in the dashboard. The user ID string is also visible in the Dashboard/Account panel. After the calling labCore.SetUserKey, all API functions can be used as long as the corresponding public key remains in the database.

API Documentation¶

Here is an overview of the API functions.

Enumerators¶

EDataType (enum)¶

This is an Enum with all the basic data types. It masks integer values. The full list of data types can be found here.

Example:

print(int(EDataType.FILE))

EMetaType (enum)¶

This is an Enum for the metadata types. Possible values are:

EMetaTyp.TAG: simple metadata tag
EMetaTyp.VTAG: value-tag
EMetaTyp.ITAG: inventory tag

See Metadata Systems for more info.

Notebook Interactions¶

LabCore.notebook_list()¶

Returns the full list of notebook documents that the user can acces from the database.

A notebook document is a python dictionary, currently containing the following keys:

notebook document structure¶
key	value
_id	dictionary with the notebook ID
_id.$oid	hexadecimal notebook ID
title	notebook title

Example:

...

# get a list of notebooks
nbs = LabCore.notebook_list()

# print ID and title of each one
for nb in nbs:
        print("notebook[{}] title is:".format(nb['_id']['$oid'], nb['title']))

LabCore.MakeRecord(name, typ, data, units=”1”)¶

name: record name
typ: record type from the EDataType enum
data: the data payload
units: physical units, see Physical Quantities for list of choices

Returns a data record in the proper python dictionary format, with the given data.

Example:

# matrix of random distances
data = numpy.random.random((10,10))

# create a DATA2D record
record = LabCore.MakeRecord("distances", EDataType.DATA2D, data, units="m")

Note

This will not upload anything to the database. It only creates a properly formatted dictionary describing the record.

Metadata Interactions¶

LabCore.metadata_print() and LabCore.metadata_list()¶

Returns the list of all metadata tags in the platform. The metadata_print version also prints the metadata to the standard output in a nice format. The output is a complex structure of nested python dictionaries. At the first level the dictionary has three main keys, and the corresponding values are dictionaries of metadata tags for each of the main types (see Metadata Systems):

tags: simple metadata tags dictionary
kvps: dictionary of key-value pair metadata (also known as vtags)
itags: dictionary of inventory metadata

Each of the three main dictionaries uses the metadata tag ID as key.

Example:

# get the metadata
metadataDB = LabCore.metadata_print()

# this is a dictionary of only inventory tags
itags = metadataDB['itags']

# show details of a particular item tag
print(tags['6214b0d240c0d996fab705a5'])

Object Oriented API¶

labcore.Notebook¶

class labcore.Notebook(ID)¶

Creates a notebook object from the server’s notebook with given ID.

Parameters: ID (str) – hex ID of the notebook
Returns: Notebook object with the given ID, if found
Return type: labcore.Notebook
Variables: records – list of labcore.Record objects for all data records in the notebook

CreateCompositeRecord(master, records)¶

Uploads a composite record and its children to the notebook. The master and children records must be properly formatted dictionaries with the records information.

Parameters

master (dict) – master COMPOSITE record
records (list of dict) – list of children records for the COMPOSITE

Warning

The API does not check that the master and records are formatted correctly. It is up to the user to make sure the supplied data matches their record types.

Warning

It is better to let the API create proper master and records dictionary using dedicated parsers, e.g. Record.SPM_from_IBW.

Example:

from labcore import *

# get a notebook
nb = Notebook.Find_byID('60eed666f49103c93f6aa988')

# parse SPM data from an ibw 
master, records = Record.SPM_from_IBW('Mica_in_water.ibw', nameprefix='noisy')

# upload the whole composite into the notebook
nb.CreateCompositeRecord(master, records)

CreateRecord(name, rectype, data, units='1')¶

Creates a new data record and uploads it into the notebook

Parameters

name (str) – name of the new record to make
rectype (labcore.EDataType) – recrod type
data (variable) – the record data (type depends on rectype)
units (str) – physical units of the data (default is “1” for adimensional)

Returns

the new record object (without the data)

Return type

labcore.Record

Warning

The API does not check that the data is formatted correctly. It is up to the user to make sure the supplied data matches rectype.

Warning

The record name shall not contain special characters - !@$%^&*?=”’/

Example:

from labcore import *

# get a notebook
nb = Notebook.Find_byID('60eed666f49103c93f6aa988')

# create data for an array record (DATA1D)
data = [0,1,1,2,3,5,8,-12]

# make the record and save it in the notebook
rec = nb.CreateRecord("fribonacchy", EDataType.DATA1D, data, "1")

# print the UUID
print(rec.uuid)

Find()¶

Retrieves the notebook with given title from the server.

Parameters: title (str) – title of the notebook
Returns: Notebook object if found
Return type: labcore.Notebook

Example:

from labcore import *

nb = Notebook.Find('test notebook')

FindRecord(name)¶

Returns the object representing the data record with given name.

Parameters: name (str) – name of the record to find.
Returns: labcore.Record object with given name, or None if not found.
Return type: labcore.Record

Example:

from labcore import *

nb = Notebook.Find_byID('60eed666f49103c93f6aa988')
rec = nb.FindRecord('test array')
print(rec.uuid)

FindRecord_byID(uuid)¶

Returns the object representing the data record with given UUID.

Parameters: uuid (str) – UUID of the record to find.
Returns: labcore.Record object with given name, or None if not found.
Return type: labcore.Record

Example:

from labcore import *

nb = Notebook.Find_byID('60eed666f49103c93f6aa988')
rec = nb.FindRecord_byID('trolo-lol-olol')
print(rec.name)

Find_byID()¶

Retrieves the notebook with given ID from the server.

Parameters: ID (str) – hex ID of the notebook.
Returns: Notebook object if found.
Return type: labcore.Notebook

Example:

from labcore import *

nb = Notebook.Find_byID('60eed666f49103c93f6aa988')

FluidElement(uuid)¶

Returns the notebook fluid element with given uuid.

Raises an exception if the fluid element was not found.

Parameters: uuid (str) – uuid of the element to find.
Returns: Dictionary with the fluid element information.
Return type: dict

Example:

from labcore import *

nb = Notebook.Find('test notebook')

# we know the uuid corresponds to a table!
table = nb.FluidElement('ad788298-3fda8d4b0000000008528643c81ae5bd-55ca5e2d')

# print out the configuration of the table
print(table['config'])

FluidElements(uuidOnly=False)¶

Prints the list of fluid elements in the notebook and their uuid.

Parameters: uuidOnly (bool) – set True to only show referrable elements (tables, figures, …), default is False.

GetActiveTable(uuid)¶

Returns the active table with given uuid (or index). If the argument is integer, it will be interpreted as the index of the table in the list of all active tables (starting from 0). Raises an exception if the uuid/index is wrong.

Parameters: uuid (str or int) – uuid (or integer index) of the active table to find.
Returns: Active table object.
Return type: labcore.ActiveTable

Example:

from labcore import *

nb = Notebook.Find('test notebook')

# we know the uuid corresponds to an active table
table = nb.GetActiveTable('ad788298-3fda8d4b0000000008528643c81ae5bd-55ca5e2d')

# print out the configuration of the active table
print(table._src['config'])

GetMessages(printout=False, newfirst=False)¶

Returns the message log for this notebook. Each message is a dictionary with sender, timestamp and text.

Parameters

printout (bool) – If True prints the messages to the screen (default is False).
newfirst (bool) – If True sorts the messages from newest to oldest (default is False).

Returns

List of dictionary with the messages details.

Return type

list

Example:

from labcore import *

nb = Notebook.Find('test notebook')

messages = nb.GetMessages(printout=True, newfirst=True)

property ID¶: Notebook’s ID string, e.g. “60eed666f49103c93f6aa988”.

Records(withHidden=False)¶

Returns a List of data record objects in this notebook, optionally including hidden ones.

Parameters

withHidden (bool) – True if hidden records should be included, False (default) otherwise.
rectype – recrod type

Returns

the record object list

Return type

lits of labcore.Record

Warning

Adding/removing records to the output list will not have any effect on the server!

SendMessage(message, withEmail=False)¶

Send a message to all users on this notebook, optionally via email as well.

Note

Only users with explicit permission will get the email.

Parameters

message (str) – message text.
withEmail (bool) – set to True to also send the message via email (default is False).

Example:

from labcore import *

nb = Notebook.Find_byID('60eed666f49103c93f6aa988')

nb.SendMessage('Table 1 was updated with the latest MtG rare prices.', withEmail=True)

property records¶: List of data record objects in this notebook.

Warning

Adding/removing records to this list will not have any effect on the server!

Note

Hidden records will not be included in the list

property title¶: Notebook’s title.

labcore.ActiveTable¶

class labcore.ActiveTable(src, notebook)¶

Creates an active table object from the notebook source code.

Parameters

src (dict) – source code of the active table
notebook (labcore.Notebook) – Notebook object where the table is found

Returns

Interface to the active table

Return type

labcore.ActiveTable

AddColumn(title='', width=150, units='1')¶

Adds a column to the active table, with given title, width and units.

Parameters

title (str) – column name (default is “column-X”)
width (int) – column width (default is 150)
units (str) – column physical units (default is “1”)

Example:

from labcore import *

nb = Notebook.Find('test notebook')

# get the table
table = nb.GetActiveTable('ad788298-3fda8d4b0000000008528643c81ae5bd-55ca5e2d')
print(table.data())

table.AddColumn(title="BladeLength", units="cm", width=200)
print(table.data())

AddRow(title='')¶

Adds a row to the active table, with given title (ID column value).

Parameters: title (str) – row title (default is “”)

Example:

from labcore import *

nb = Notebook.Find('test notebook')

# get the table
table = nb.GetActiveTable('ad788298-3fda8d4b0000000008528643c81ae5bd-55ca5e2d')
print(table.data())

table.AddRow(title="Elm Street")
print(table.data())

GetColumnIDs()¶

Returns the list of column names.

Returns: list of column names
Return type: list

Example:

from labcore import *

nb = Notebook.Find('test notebook')

# get the table
table = nb.GetActiveTable('ad788298-3fda8d4b0000000008528643c81ae5bd-55ca5e2d')

columns = table.GetColumnIDs()
print(columns)

GetColumnMeta(column)¶

Get the metadata dictionary attached to a given column (0-based index). The dictionary has three keys (‘tags’, ‘kvps’, ‘itags’) for the three metadata types, and each of the associated values is a list of labcore.Metadata objects.

Parameters: column (int) – column number (starting from 0)
Returns: Metadata dictionary for the column
Return type: dict

Example:

from labcore import *

nb = Notebook.Find('test notebook')

# get the table
table = nb.GetActiveTable('ad788298-3fda8d4b0000000008528643c81ae5bd-55ca5e2d')

colmeta = table.GetColumnMeta(1)
print(colmeta)

GetColumnUnits()¶

Returns the list of column physical units.

Returns: list of column units
Return type: list

Example:

from labcore import *

nb = Notebook.Find('test notebook')

# get the table
table = nb.GetActiveTable('ad788298-3fda8d4b0000000008528643c81ae5bd-55ca5e2d')

colUnits = table.GetColumnUnits()
print(colUnits)

GetRowIDs()¶

Returns the list of row names.

Returns: list of row names
Return type: list

Example:

from labcore import *

nb = Notebook.Find('test notebook')

# get the table
table = nb.GetActiveTable('ad788298-3fda8d4b0000000008528643c81ae5bd-55ca5e2d')

rows = table.GetRowIDs()
print(rows)

GetRowMeta(row)¶

Get the metadata dictionary attached to a given row (0-based index). The dictionary has three keys (‘tags’, ‘kvps’, ‘itags’) for the three metadata types, and each of the associated values is a list of labcore.Metadata objects.

Parameters: row (int) – row number (starting from 0)
Returns: Metadata dictionary for the row
Return type: dict

Example:

from labcore import *

nb = Notebook.Find('test notebook')

# get the table
table = nb.GetActiveTable('ad788298-3fda8d4b0000000008528643c81ae5bd-55ca5e2d')

rowmeta = table.GetRowMeta(1)
print(rowmeta)

LockColumn(column, lock=True)¶

Sets the lock status of a column.

Parameters

column (int) – column number (starting from 0)
lock (bool) – lock status, default is True

Example:

from labcore import *

nb = Notebook.Find('test notebook')

# get the table
table = nb.GetActiveTable('ad788298-3fda8d4b0000000008528643c81ae5bd-55ca5e2d')
print(table.data())

# lock a column
table.LockColumn(2, True)

# the next line should raise an error since column 2 is locked
table.SetValue(1,2, "Freddy's coming for you")

LockRow(row, lock=True)¶

Sets the lock status of a row.

Parameters

row (int) – row number (starting from 0)
lock (bool) – lock status, default is True

Example:

from labcore import *

nb = Notebook.Find('test notebook')

# get the table
table = nb.GetActiveTable('ad788298-3fda8d4b0000000008528643c81ae5bd-55ca5e2d')
print(table.data())

# lock a row
table.LockRow(1, True)

# the next line should raise an error since row 1 is locked
table.SetValue(1,2, "Freddy's coming for you")

property Notebook¶: Parent Notebook object.

RemoveColumn(index)¶

Remove the column with given index from the active table.

Parameters: index (int) – column index, not 0

Example:

from labcore import *

nb = Notebook.Find('test notebook')

# get the table
table = nb.GetActiveTable('ad788298-3fda8d4b0000000008528643c81ae5bd-55ca5e2d')
print(table.data())

table.RemoveColumn(1)
print(table.data())

RemoveRow(index)¶

Remove the row with given index from the active table.

Parameters: index (int) – row index

Example:

from labcore import *

nb = Notebook.Find('test notebook')

# get the table
table = nb.GetActiveTable('ad788298-3fda8d4b0000000008528643c81ae5bd-55ca5e2d')
print(table.data())

table.RemoveRow(2)
print(table.data())

SetColumnMeta(column, metas)¶

Set the metadata dictionary attached to a given column (0-based index). The dictionary should have three keys (‘tags’, ‘kvps’, ‘itags’) for the three metadata types, and each of the associated values has to be a list of labcore.Metadata objects. Omitted keys will set the list of corresponding metadata type to empty.

..note:

The first column cannot be modified.

Parameters

column (int) – column number (starting from 0)
metas (dict) – metadata dictionary

Example:

from labcore import *

nb = Notebook.Find('test notebook')

# get the first table in the notebook
table = nb.GetActiveTable(0)

# get metadata tags from the database
tag = Metadata("b4d4557460fd00m", 'tag')
kvp = Metadata("57affedf4ff3der", 'kvp', value=1.23)

# combine into a dictionary
metadict = {'tags': ["b4d4557460fd00m"], 'kvps': [kvp]}

# set the metadata for the second column
table.SetColumnMeta(1, metadict)

SetData(data, ignoreLock=False)¶

Set the entire data table to the desired matrix.

Parameters

data (numpy 2D ndarray or list) – matrix (numpy or list), without the ID column
ignoreLock (bool) – True if the operation should ignore any row/column lock (default=False)

Example:

from labcore import *

nb = Notebook.Find('test notebook')

# get the table
table = nb.GetActiveTable('ad788298-3fda8d4b0000000008528643c81ae5bd-55ca5e2d')
print(table.data())

table.SetValue(1,2, "Freddy's coming for you")
table.SetValue(3,4, "better lock your door")
print(table.data())

SetRowMeta(row, metas)¶

Set the metadata dictionary attached to a given row (0-based index). The dictionary should have three keys (‘tags’, ‘kvps’, ‘itags’) for the three metadata types, and each of the associated values has to be a list of labcore.Metadata objects. Omitted keys will set the list of corresponding metadata type to empty.

Parameters

row (int) – row number (starting from 0)
metas (dict) – metadata dictionary

Example:

from labcore import *

nb = Notebook.Find('test notebook')

# get the first table in the notebook
table = nb.GetActiveTable(0)

# get metadata tags from the database
tag = Metadata("b4d4557460fd00m", 'tag')
kvp = Metadata("57affedf4ff3der", 'kvp', value=1.23)

# combine into a dictionary
metadict = {'tags': ["b4d4557460fd00m"], 'kvps': [kvp]}

# set the metadata for the first row
table.SetRowMeta(0, metadict)

SetValue(i, j, value)¶

Sets the value of the given ActiveTable cell. The cell is specified by i,j coordinates (start from 0). Since the ID column cannot be modified this way, the indexing for columns excludes the true first column (ID).

Note

Element ([i, 0]) is not the ID of the i-th row, but the data in the first data column for i-th row.

Parameters

i (int) – row number (starting from 0)
j (int) – column number (starting from 0)
value (str or number) – value to write in the cell, or None to clear it.

Example:

from labcore import *

nb = Notebook.Find('test notebook')

# get the table
table = nb.GetActiveTable('ad788298-3fda8d4b0000000008528643c81ae5bd-55ca5e2d')
print(table.data())

table.SetValue(1,2, "Freddy's coming for you")
table.SetValue(3,4, "better lock your door")
print(table.data())

SetupColumn(column, name=None, units=None)¶

Change the name and/or units of a column.

Parameters

column (int) – column index (0 being the first column after ID)
name (str) – new column name (optional)
units (str) – new column physical units (optional)

Example:

from labcore import *

nb = Notebook.Find('test notebook')

# get the table
table = nb.GetActiveTable('ad788298-3fda8d4b0000000008528643c81ae5bd-55ca5e2d')

table.SetupColumn(3, name="SnailSpeed", units="m/fortnight")
print(table.data())

SetupRow(row, name)¶

Change the name of a row.

Parameters

column (int) – row index
name (str) – new row name

Example:

from labcore import *

nb = Notebook.Find('test notebook')

# get the table
table = nb.GetActiveTable('ad788298-3fda8d4b0000000008528643c81ae5bd-55ca5e2d')

table.SetupRow(1, name="snail-1")
print(table.data())

property UUID¶: UUID of the active table.

data(withID=False)¶

Returns the data in the as a numpy array.

Parameters: withID (bool) – include the ID column in the output (default is False)
Returns: Table data.
Return type: numpy array

Example:

from labcore import *

nb = Notebook.Find('test notebook')

# we know the uuid corresponds to an active table
table = nb.GetActiveTable('ad788298-3fda8d4b0000000008528643c81ae5bd-55ca5e2d')

# print out the active table data (with the ID column)
data = table.data(withID=True)
print(data())

labcore.Record¶

class labcore.Record(notebook, record)¶

Represents a data record.

Delete()¶

Deletes this record from the notebook it belongs to.

..warn::: This will permanently delete the data!

Example:

from labcore import *

nb = Notebook.Find('test notebook')
rec = nb.FindRecord('test array')

rec.Delete()

GetData()¶

Downloads the actual data payload of this record and stores it in record.data

Example:

from labcore import *

nb = Notebook.Find('test notebook')
rec = nb.FindRecord('test array')

rec.GetData()
print(rec.data)

MetadataAdd(meta)¶

Adds a metadata element to this record, and save the change into the database. If the metadata is already present, prints a message without changing anything.

Parameters: meta (labcore.Metadata) – metadata object to attach

Example:

from labcore import *

nb = Notebook.Find('test notebook')
rec = nb.FindRecord('test array')

# create a key-value pair metadata tag
tag = Metadata('bad455000571dd1c34d18411', 'kvp', '30 celsius')

# add the tag - also saves on the server
rec.MetadataAdd(tag)

MetadataPrint()¶

Prints all metadata in this record.

Example:

from labcore import *

nb = Notebook.Find('test notebook')
rec = nb.FindRecord('test array')

# print metadata attached to record
rec.MetadataPrint()

MetadataRemove(meta)¶

Removes the given metadata element from this record, and save the change into the database. If the metadata is not present, prints a message without changing anything.

Parameters: meta (labcore.Metadata) – metadata object to remove

Example:

from labcore import *

nb = Notebook.Find('test notebook')
rec = nb.FindRecord('test array')

# create a key-value pair metadata tag
tag = Metadata('bad455000571dd1c34d18411', 'kvp')

# remove the tag - also saves on the server
rec.MetadataRemove(tag)

MetadataSave()¶

Saves the current state of metadata in this record into the database.

Example:

from labcore import *

nb = Notebook.Find('test notebook')
rec = nb.FindRecord('test array')

# create a key-value pair metadata tag
tag = Metadata('bad455000571dd1c34d18411', 'kvp', '30 celsius')

# set the list of key-value pairs
rec.kvps = [tag]

# save
rec.MetadataSave()

Rename(newName=None, newUnits=None)¶

Changes the record name and/or physical units.

Parameters

newName (labcore.Metadata) – metadata object to attach
newUnits (labcore.Metadata) – metadata object to attach

Example:

from labcore import *

nb = Notebook.Find('test notebook')
rec = nb.FindRecord('test array')

rec.Rename(newName='dis array', newUnits='m/s')

SPMCompare(target, parameters={})¶

Performs SPM image comparison (johnbot v4) between channels of SPM records.

Parameters

ref (labcore.Record) – DATA2D record with the reference channel
target (labcore.Record) – DATA2D record with the target channel
parameters (dict) – dictionary of calculation parameters

Returns

dictionary with comparison metrics results

Return type

dict

The parameters dictionary should have the following keys: * sigma [float]: stdv of the gaussian filter applied to FFT * kmin [float]: minimum k-space value to consider in the possible range (0-1) * kmax [float]: maximum k-space value to consider in the possible range (0-1) * angscans [int]: number of angular scans * angres [float]: resolution of the angular scans (in degrees)

The function returns a dictionary with the following elements: * PatternMismatch: mismatch factor between the image patterns (absolute error) * PatternMismatchPct: mismatch factor between the image patterns as percentage (relative error) * PowerMismatch’: mismatch between image contrast magnitudes * OffsetMismatch’: mismatch between image offsets

Example:

from labcore import *

# get the DATA2D records of two SPM image channels to compare
ref = ...
trg = ...

# compute mismatch metrics
results = Record.SPMCompare(ref,trg)

SPM_from_IBW(nameprefix='')¶

Creates an SPM record by parsing an ibw file. Returns the dictionary form of the master record and a list of children. The optional name prefix will be added to the record name, before the original file name.

Parameters

filename (string) – full path of the ibw file to parse
nameprefix (string) – custom prefix for the output record name

Warning

The nameprefix must not contain special characters - !@$%^&*?=”’/

Example:

from labcore import *

# get a notebook
nb = Notebook.Find_byID('60eed666f49103c93f6aa988')

# parse SPM data from an ibw 
master, records = Record.SPM_from_IBW('Mica_in_water.ibw', nameprefix='noisy')

# upload the whole composite into the notebook
nb.CreateCompositeRecord(master, records)

STRUCTURE_from_ASE()¶

Returns the data for a STRUCTURE record for the given ASE system instance.

Parameters: aseObject (ASE Atoms) – a valid ASE object representing an atomistic structure.
Returns: STRUCTURE record data field
Return type: dict

Example:

from labcore import *
import ase.io

# import an atomistic system with ASE
aseobj = ase.io.read('somemolecule.xyz')

# create LabCore data representation
data = Record.STRUCTURE_from_ASE(aseobj)


# add a new STRUCTURE record to a notebook
nb = Notebook.Find_byID('60eed666f49103c93f6aa988')

# make the record and save it in the notebook
rec = nb.CreateRecord("somemolecule", EDataType.STRUCTURE, data, "1")

UploadData()¶

Uploads the content of record.data to the server.

This will effectively overwrite the existing data.

Example:

from labcore import *

nb = Notebook.Find('test notebook')
rec = nb.FindRecord('test array')

# set the new data
rec.data = [1,2,3,4,5]

# upload to server
rec.UploadData()

property children¶: List of labcore.Record objects that are grouped into this record. If called on a record that is not of type COMPOSITE, the list is empty.

property masterRecord¶: labcore.Record object of the master COMPOSITE where the current record belongs. Returns None if called by a record that is not a child of a COMPOSITE.

property name¶: Record’s name.

property notebook¶: Reference to the labcore.Notebook object this record belongs to.

property type¶: Record’s type as labcore.EDataType enum.

property uuid¶: Record’s unique ID.

labcore.Metadata¶

class labcore.Metadata(ID, metaType, value=None)¶

Metadata tag.

Create a Metadata object. The corresponding tag with same ID must exist in the database.

Parameters

ID (str) – valid ID string of the metadata
metaType (str) – type of metadata [“tag”|”kvp”|”itag”]
value (str|int|float) – value of the tag (only for kvp type)

Example:

from labcore import *

# create a key-value pair metadata tag
tag = Metadata('bad455000571dd1c34d18411', 'kvp', "123 celsius")

property ID¶: ID string of this metadata tag.

ToString(withType=False)¶

Returns a string with the metadata details.

Parameters: withType (bool) – set to True to display the tag type (default False)
Returns: info string
Return type: str

from labcore import *

# create a key-value pair metadata tag
tag = Metadata('bad455000571dd1c34d18411', 'kvp', '30 celsius')

# print its string representation (including type)
print(tag.ToString(withType=True))

property info¶: Metadata description.

property name¶: Name of this metadata tag.

property type¶: Type of this metadata [“tag”|”kvp”|”itag”].

property value¶: Metadata value (only for key-value type).