Python client for EdelweissData
Project description
This python client library allows easy access to Edelweiss Data servers.
Table of Contents
Overview
The core concept of Edelweiss Data is that of a Dataset. A Dataset is a single table of data (usually originating from a csv file) and carries the following additional pieces of information:
- a schema describing the structure of the tabular data (data types, explanatory text for each column etc)
- a human readable description text (markdown formatted - like the readme of a repository on github)
- a metadata json structure (of arbitrary complexity - this can be used to store things like author information, instrument settings used to generate the data, ...).
Datasets are versioned through a processes called publishing. Once a version of a dataset is published, it is "frozen" and becomes immutable. Any change to it has to be done by creating a new version. Users of Edelweiss Data will always see the version history of a dataset and be able to ask for the latest version or specific earlier version.
Datasets can be public or access restricted. Public datasets can be accessed without any access restrictions. To access restricted datasets or to upload/edit your own dataset OpenIDConnect/OAuth is used - in the python client this process is done by calling the authenticate method on the Api instance that triggers a web based login at the end of which a token is confirmed.
When retrieving the tabular data of a dataset, the data can be filtered and ordered and only specific columns requested - this makes request for subsets of data much faster than if all filtering happened only on the client. Conditions for filtering and ordering are created by constructing QueryExpression instances using classmethods on the QueryExpression class to create specific Expressions. You can access the data either in it's raw form (as json data) or, more conveniently, as a Pandas Dataframe.
Just like the tabular data of one particular dataset can be retrieved as a Pandas DataFrame, you can also query for datasets using the same filtering and ordering capabilities - i.e. you can retrieve a DataFrame where each row represents a Dataset with it's name, description and optionally metadata and schema (not including the data though).
When you are searching for Datasets, a lot of the interesting information that you may want to filter by is hidden in the metadata (e.g. maybe most of your datasets have a metadata field "Species" at the top level of the metadata json that indicates from what kind of animal cells the data in this dataset originate from). To make such filtering easy, our Datasets query function take an optional list of "column mappings" that allow you to specify a JsonPath expression to extract a field from the metadata and include it with a given name in the resulting DataFrame. In the Species example, you could pass the list of column mappings [("Species from Metadata", "$.Species")] and the resulting DataFrame would contain an additional column "Species from Metadata" and for every row the result of evaluating the JsonPath $.Species would be included in this column and you could filter on it using conditions to e.g. only retrieve Datasets where the Species is set to "Mouse".
Edelweiss Data servers provide a rich User Interface as well that let's you visually browse and filter datasets and the data (and associated information) of each dataset. This UI is built to integrate nicely with the python client. The DataExplorer that is used to explore a dataset has a button in the upper right corner to generate the python code to get the exact same filtering and ordering you see in the UI into a Pandas DataFrame using the Edelweiss Data library for your convenience.
Getting started
Requirements
Python 3.6+
Installation
pip install edelweiss_data
Common use cases
Initialization
You interact with the Edelweiss Data API mainly via the API class of the edelweiss_data python library. Import it, point it at the Edelweiss Data instance you want to interact with and instantiate it like this:
from edelweiss_data import API, QueryExpression as Q
# Set this to the url of the Edelweiss Data server you want to interact with
edelweiss_api_url = 'https://api.develop.edelweiss.douglasconnect.com'
api = API(edelweiss_api_url)
Authentication
Some operations in Edelweiss Data are accessible without authentication (e.g. retrieving public datasets). For others (e.g. to create datasets), you need to be authenticated. Authentication is done with the authenticate call. Be aware that this call is currently built for interactive use like in a Jupyter environment - it will block execution for a up to a few minutes while it waits for you to log in to your account and confirm the access to the API on your behalf. Once accepted the python client will store the authentication token so that you will not have to enter it again for a few days (the token is stored in your home directory in the .edelweiss directory).
api.authenticate()
Create a new dataset
Creating and publishing a new dataset form a csv file can be done in one quick operation like so:
metadata = {"metadata-dummy-string": "string value", "metadata-dummy-number": 42.0}
with open ('FILENAME') as f:
dataset = api.create_published_dataset_from_csv_file("DATASETNAME", f, metadata)
This creates a new dataset form the file FILENAME with the name DATASETNAME. A trivial example metadata is used here as well.
When creating and publishing datasets like this you don't have a lot of control over details of the schema or to set a more elaborate dataset description. If you need more control, you can create a dataset like so:
datafile = '../../tests/Serialization/data/small1.csv'
name = 'My dataset'
schemafile = None # if none, schema will be inferred below
metadata = None # dict object that will be serialized to json or None
metadatafile = None # path to the metadata file or None
description = "This is a *markdown* description that can use [hyperlinks](https://edelweissconnect.com)"
dataset1 = api.create_in_progress_dataset(name)
print('DATASET:', dataset1)
try:
with open(datafile) as f:
dataset1.upload_data(f)
if schemafile is not None:
print('uploading schema from file ...')
with open(schemafile) as f:
dataset1.upload_schema_file(f)
else:
print('inferring schema from file ...')
dataset1.infer_schema()
if metadata is not None:
print('uploading metadata ...')
dataset1.upload_metadata(metadata)
elif metadatafile is not None:
print('uploading metadata from file ...')
with open(metadatafile) as f:
dataset1.upload_metadata_file(f)
dataset1.set_description(description)
published_dataset = dataset1.publish('My first commit')
print('DATASET published:',published_dataset)
except requests.HTTPError as err:
print('not published: ', err.response.text)
Filter and retrieve data
The tabular data of an individual dataset can be retrieved into a pandas dataframe easily like this:
dataframe = dataset.get_data()
You can also filter and order data with QueryExpressions, often aliased to Q in the import statement. In the following example we assume the data to have a column "Species" which we want to filter to the value "Mouse" with fuzzy text matching and "Chemical name" which we want to order by ascending:
dataframe = dataset.get_data(condition=Q.fuzzy_search(Q.column("Species"), "Mouse"), order_by=[Q.column("Chemical name")])
In this example you can see how to do a chemical substructure search so that only molecules with the fragment "CC=O" are returned and the results are sorted descending by similarity to the molecule "C(C(CO)(CO)N)O". Chemical similarity for ordering is calculated using the rdkit library using tanimoto distance between rdkit fingerprints (other fingerprints or distance metrics could be supported in the future)
dataframe = dataset.get_data(condition=Q.substructure_search("CC=O", Q.column("SMILES")), order_by=[Q.tanimoto_similarity("C(C(CO)(CO)N)O", Q.column("SMILES"))], ascending=False)
Search for datasets
To just retrieve a pandas dataframe with all published datasets that you are allowed to see use get_published_datasets(). This will return a pandas dataframe with a multiindex of the dataset id and version and then a single object column for the dataset class instance. This class instance can be used to retrieve e.g. the name property of the dataset or it can be used to retrieve the data for this dataset by calling the .get_data() method or similar operations.
datasets = api.get_published_datasets()
dataset = datasets.iloc[0].dataset
print("Found {} datasets. The name of the first is: ".format(len(datasets), dataset.name))
To retrieve a single dataset by index value rather than based on numerical position use the pandas multiindex functionality passing in tuples:
datasetid = '49fd99ee-ec6f-44df-a8cd-73f0f8bbcd76' # example dataset ID
version = 1
dataset = datasets.loc[(datasetid, version)]
Just like above with data you can use QueryExpressions to filter to only find datasets matching certain predicates. Below we filter on datasets that have the string "LTKB" somewhere in them (name etc)
datasets_filter = Q.search_anywhere("LTKB")
datasets = api.get_published_datasets(condition=datasets_filter)
Since very often the most interesting filter and sort critieria will be in the metadata (which is a Json of arbitrary structure), the Api gives you a way to add additional columns by extracting pieces from the metadata json with JsonPath expressions. Below we attempt to treat the metadata json of each dataset as an object with a key "Species" and if it is present we extract it and map it into the "Species from metadata json" column:
columns = [("Species from metadata json", "$.Species")]
datasets = api.get_published_datasets(columns=columns)
The result of such a query will always be a column containing lists of results as the jsonpath query could return not just a single primitive value or null or an object but also json arrays. Working with columns that contain lists in Pandas can be a bit awkward as some operations like filtering default to operating on series instead of individual cells. For cases like these, working with the Pandas apply method usually makes things easier - e.g. if you want to extract the first element if any from the above column this an easy way to do it that also extends well to more complex operations:
datasets['first_species_or_none'] = datasets.apply(lambda row: row['Species from metadata json'][0] if len(row['Species from metadata json']) > 0 else None, axis=1)
Delete a dataset
To delete a dataset and all versions call delete_all_versions:
dataset.delete_all_versions()
API reference
API
The central interaction point with EdelweissData. You instantiate this class with the base url of the
EdelweissData server you want to interact with. The init method will verify that the server is reachable and speaks a compatible API version, then you can use instance methods to interact with the API server.
add_dataset_group_permission
Add a group to a dataset
dataset_id : the id of the dataset
group : the Group to add
add_dataset_user_permission
Add a user to a dataset
dataset_id : the id of the dataset
user : the User to add
authenticate
change_dataset_visibility
Set if the dataset should be public or access protected when published
dataset_id : the id of the dataset
is_public : boolean to indicate if the dataset should be public
create_in_progress_dataset
Creates a new in-progress dataset on the server and returns it.
Returns: The InProgressDataset that was created.
name : the name of the dataset to create
create_in_progress_dataset_from_csv_file
Creates a new in-progress dataset from a CSV file on the server.
Returns: the updated dataset
name : the name of the dataset
file : opened text file to read the csv data from
metadata : dict of the metadata to store as json together with the dataset
create_published_dataset_from_csv_file
Creates a new published dataset from a CSV file on the server.
Returns: the published dataset
name : the name of the dataset
file : opened text file to read the csv data from
metadata : dict of the metadata to store as json together with the dataset
changelog : Publishing message to store for the first version
delete
Sends a DELETE request to a server.
Returns: dict with the JSON response.
route : route to which the request will be sent
get
Sends a GET request to a server.
Returns: dict with the JSON response.
route : route to which the request will be sent
json : dict with the JSON body to send
get_dataset_permissions
Get the permissions for the given dataset id
Returns: the DatasetPermissions instance for this dataset
dataset_id : the id of the dataset
get_in_progress_dataset
Returns an in-progress datasets with a given id.
Returns: an InProgressDataset
id : the id of the dataset to retrieve
get_in_progress_datasets
Returns a list of all in-progress datasets you are allowed to access (needs authentication).
Returns: a list of InProgressDatasets
limit : Number of datasets to retrieve - if None (default) it will retrieve all.
offset : Starting offset from which to retrieve the datasets
get_published_dataset
Returns a published dataset with a given id and version.
Returns: the PublishedDataset
id : id of the dataset to retrieve
version : version of the dataset to retrieve. Defaults to LATEST if none specified.
get_published_dataset_aggregations
Returns aggregation buckets and their sizes for each column.
Returns: aggregations as a Series with an index of buckets and terms, for example bucket term organ liver 10 kidney 20 species mouse 5 elephant 30
columns : same as in self.get_published_datasets
condition : same as in self.get_published_datasets
aggregation_filters : same as in self.get_published_datasets
get_published_dataset_versions
Returns all published versions of dataset with a given id.
Returns: a list of dicts containing id, version and name for each version of the dataset
id : id of the dataset
get_published_datasets
Returns a dataframe of all published datasets that match query.
Returns: a dataframe indexed by the id and version, which in addition to user-specified columns, contains a column with a PublishedDataset object for each dataset. Unless included explicitly, description, schema, and metadata are omitted from the datasets and the corresponding attributes are set to None. On the first access to any of the missing attributes of a given dataset, all three them are fetched from the server and set to the actual values, resulting in a single request for each dataset. If there are many datasets for which the attributes are required, it makes sense to include the content in the bulk request.
columns : a list of pairs (column_name, json_path) describing the name of the new column to generate and which jsonpath to use to extract the values from the metadata to fill this column.
condition : a QueryExpression object limiting the fetched datasets.
include_description : a boolean specifying if the datasets in the response should include the description
include_schema : a boolean specifying if the datasets in the response should include the schema
include_metadata : a boolean specifying if the datasets in the response should include the metadata
aggregation_filters : a dict limiting the fetched datasets to ones where column values fall into one of the selected aggregation buckets. For example, using the dict {'organ': ['liver', 'kidney'], 'species': ['mouse', 'elephant']} would return the datasets where both organ is either liver or kidney, AND species is either mouse or elephant.
limit : the number of rows to return. Returns all rows if set to None (default).
offset : the initial offset (default 0).
order_by : a list of QueryExpression objects by which to order the resulting datasets.
ascending : a boolean or list of booleans to select the ordering. If the single boolean is True (the default), the list is ascending according to order_by, if False, it is descending. If given as a list, it must be of the same length as the order_by list, and the order is the ascending/descending for each particular component.
dataset_column_name : the name of the dataframe column in which the corresponding PublishedDataset objects are available.
latest_only : a boolean specifying whether to return only the latest version of each dataset
get_raw_datasets
Get the published datasets. Unlike the more high-level get_published_datasets this method
does not create a dataframe but returns the raw list of dicts representing the json response. Unless explicity included the fields schema, metadata and description will not be included in the response.
Returns: The published datasets as a list of dicts (raw json response)
columns : a list of pairs (column_name, json_path) describing columns in the dataframe.
condition : a QueryExpression object limiting the fetched datasets.
include_description : a boolean specifying if the datasets in the response should include the description
include_schema : a boolean specifying if the datasets in the response should include the schema
include_metadata : a boolean specifying if the datasets in the response should include the metadata
aggregation_filters : a dict limiting the fetched datasets to ones where column values fall into one of the selected aggregation buckets. For example, using the dict {'organ': ['liver', 'kidney'], 'species': ['mouse', 'elephant']} would return the datasets where both organ is either liver or kidney, AND species is either mouse or elephant.
limit : the number of rows to return (default 100). Returns all rows if set to None.
offset : the initial offset (default 0).
order_by : a list of QueryExpression objects by which to order the resulting datasets.
ascending : a boolean or list of booleans to select the ordering. If the single boolean is True (the default), the list is ascending according to order_by, if False, it is descending. If given as a list, it must be of the same length as the order_by list, and the order is the ascending/descending for each particular component.
dataset_column_name : the name of the dataframe column in which the corresponding PublishedDataset objects are available.
latest_only : a boolean specifying whether to return only the latest version of each dataset
oidc_config
Returns the OpenID Connect configuration.
openapi
Returns the OpenAPI definition of the entire EdelweissData REST API.
Returns: The OpenAPI definition as a dict
openapi_documents
Returns a list of all dataset specific openapi descriptions (i.e. one openapi document for each dataset with the
precise Json Schema of the particular datasets data endpoint).
Returns: A list of url strings at which to retrieve the openapi.json documents for the documents
post
Sends a POST request to a server.
Returns: dict with the JSON response.
route : route to which the request will be sent
json : dict with the JSON body to send
post_raw
Sends a POST request with a given body to a server.
Returns: dict with the JSON response.
route : route to which the request will be sent
body : raw body to send (a bytes object or a string that will be encoded as UTF-8)
remove_dataset_group_permission
Remove a group from a dataset
dataset_id : the id of the dataset
name : the name of the group to remove
remove_dataset_user_permission
Remove a user from a dataset
dataset_id : the id of the dataset
user : the email of the user to remove
upload
Uploads a POST request that uploads files to a server.
Returns: dict with the JSON response.
route : route to which the request will be sent
files : a dictionary of files in which the keys are filenames and corresponding values are file objects
DatasetPermissions
The permission information for a dataset. A list of users (email + flag if they can write), groups (name + flag if they can write) and
an is_public field that indicates whether unauthenticated users can see this dataset when published.
Group
decode
encode
User
decode
encode
decode
encode
InProgressDataset
InProgressDataset - datasets that are not yet published and for which data can be uploaded, the schema modified, metadata changed etc.
copy_from
Copies all content from a PublishedDataset to this InProgressDataset. Useful to create new versions. See also set_data_source for
a more lightweight operation if you don't need to change the data or schema structure.
decode
delete
Deletes the InProgressDataset
encode
get_permissions
infer_schema
Triggers schema inference from uploaded data (this creates a schema on the server and sets it on the InProgressDataset)
publish
Attempts to publish the dataset. This means that a new version of a PublishedDataset will be created (and returned by this call)
and this InProgressDataset is no longer useable.
sample
Retrieve a list of lists representing a sample of the tabular data of this dataset. This
includes only a sample (e.g. the first N rows) of the data so that they can be displayed to a user as an example or similar.
set_data_source
Set the data source for an in-progress dataset. This allows you to efficiently re-use the data of a PublishedDataset
to create a new dataset without re-uploading the data. It is also useful if you want to create a new version of a PublishedDataset to fix a mistake in the metadata or description.
dataset : the PublishedDataset to copy data from when publishing
set_description
Set the description of the dataset. The description is assumed to be markdown formatted text, similar to a Github README.md
upload_data
Upload tabular data (a CSV file)
data : An open text file containing the csv data to upload
upload_metadata
Upload metadata (as a dict, not a file).
schema : The metadata to upload
upload_metadata_file
Upload a metadata file (an open text file containing the metadata in Json form).
file : The open text file to upload the metadata from
upload_schema
Upload a Schema (an instance of the class, not a file).
schema : The schema to upload
upload_schema_file
Upload a schema file (an open text file containing the schema in Json form).
file : The open text file to upload the schema from
PublishedDataset
Represents a published dataset
decode
delete_all_versions
Deletes all versions of a published dataset
encode
get_data
Gets the (tabular) data of a PublishedDataset as a pandas Dataframe. The data can be filtered so that only required columns or rows
are retrieved.
Returns: A pandas DataFrame with the tabular data
columns : a list of column names that should appear in the result. If None, all columns are included.
condition : a QueryExpression object limiting the fetched datasets.
aggregation_filters : a dict limiting the fetched datasets to ones where column values fall into one of the selected aggregation buckets. For example, using the dict {'organ': ['liver', 'kidney'], 'species': ['mouse', 'elephant']} would return the datasets where both organ is either liver or kidney, AND species is either mouse or elephant.
limit : the number of rows to return. Returns all rows if set to None (default).
offset : the initial offset (default 0).
order_by : a list of QueryExpression objects by which to order the resulting datasets.
ascending : a boolean or list of booleans to select the ordering. If the single boolean is True (the default), the list is ascending according to order_by, if False, it is descending. If given as a list, it must be of the same length as the order_by list, and the order is the ascending/descending for each particular component.
get_data_aggregations
Returns aggregation buckets and their sizes for each column.
Returns: aggregations as a Series with an index of buckets and terms, for example bucket term organ liver 10 kidney 20 species mouse 5 elephant 30
columns : a list of column names that should appear in the result. If None, all columns are included.
condition : a QueryExpression object limiting the fetched datasets.
aggregation_filters : a dict limiting the fetched datasets to ones where column values fall into one of the selected aggregation buckets. For example, using the dict {'organ': ['liver', 'kidney'], 'species': ['mouse', 'elephant']} would return the datasets where both organ is either liver or kidney, AND species is either mouse or elephant.
get_permissions
Returns the Permissions object of this PublishedDataset
get_raw_data
Gets the raw tabular data JSON response for a PublishedDataset. The data can be filtered so that only required columns or rows
are retrieved.
Returns: A dict representing the JSON response
columns : a list of column names that should appear in the result. If None, all columns are included.
condition : a QueryExpression object limiting the fetched datasets.
aggregation_filters : a dict limiting the fetched datasets to ones where column values fall into one of the selected aggregation buckets. For example, using the dict {'organ': ['liver', 'kidney'], 'species': ['mouse', 'elephant']} would return the datasets where both organ is either liver or kidney, AND species is either mouse or elephant.
limit : the number of rows to return. Returns all rows if set to None (default).
offset : the initial offset (default 0).
order_by : a list of QueryExpression objects by which to order the resulting datasets.
ascending : a boolean or list of booleans to select the ordering. If the single boolean is True (the default), the list is ascending according to order_by, if False, it is descending. If given as a list, it must be of the same length as the order_by list, and the order is the ascending/descending for each particular component.
new_version
Create a new version of this PublishedDataset. This will create and return a new InProgressDataset
that can be filled with content by uploading new files or copying data from a PublishedDataset
Returns: The InProgressDataset
openapi
Returns a OpenAPI descriptions for the data endpoint of this PublishedDataset, taking the schema
and thus the precise JSON structure of the response into account.
Returns: A dict respresenting the JSON decoded OpenAPI document
QueryExpression
Used to create filters or expressions to order records by. Use the classmethods on this
class to create instances, e.g. QueryExpression.fuzzySearch(QueryExpression.column("species"), "Monkey")
cast
Creates a Cast expression. This attempts to convert one datatype into another.
expr : The expression to cast
data_type : The datatype to cast to
column
Constructs a Column expression.
column_name : the name of the column
contained_in
Creates a ContainedIn expression. Tests if an expression is contained in an element. Often used
to check if columns of an Array datatype are contained in a value.
expr : The expression to search for
element : The element to search in
contains
Creates a Contains expression. Tests if an expression contains an element. Often used
to check if columns of an Array datatype contain a value.
expr : The expression to search in
element : The element to search for
decode
encode
exact_search
Constructs an ExactSearch expression. Only rows where the expr expression exactly matches the term will be returned. This can be used
to match exact substrings or exact numerical values
expr : the search expression to evaluate (often a column QueryExpression)
term : the search term
fuzzy_search
Constructs a FuzzySearch expression. Only rows where the expr expression fuzzy-matches the term will be returned. Fuzzy-matching
uses trigram indexing to match slightly different spellings.
expr : the search expression to evaluate (often a column QueryExpression)
term : the search term
search_anywhere
Constructs a SearchAnywhere expression. Only rows will be returned that contain the search term in one of their text-like columns.
term : The string to search for in all text-like columns.
substructure_search
Constructs a SubstructureSearch expression that uses chemical substructure testing. Only rows where the chemical substructure is contained in
the chemical superstructure are returned.
substructure : the substructure to search (often a SMILES string constant value)
superstructure : the search term (often a Column of datatype SMILES)
system_column
Constructs a SystemColumn expression. SystemColumns are special columns maintained by EdelweissData.
The following SystemColumns are available: name (text): the name of a dataset created (text/datetime): the timestamp the dataset was created at version: (int): the version number of the dataset
column_name : the name of the column
tanimoto_similarity
Calculates the tanimoto distance between two molecular fingerprints.
left : the left argument. Often a SMILES string constant value or Column of datatype SMILES.
right : the right argument. Often a SMILES string constant value or Column of datatype SMILES.
Schema
The schema of the dataset describing the columns (name, description, datatype, rdf predicate, ...)
Column
The schema data of one column. This tells EdelweissData the name of the column, the datatype to use, how to handle missing values, ...
decode
encode
decode
encode
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