lyprox.patients.models.Dataset

class documentation

class Dataset(loggers.ModelLoggerMixin, models.Model):

A collection of patients, usually importet from a CSV file in a GitHub repo.

When created, this model fetches the CSV file from the GitHub repo and adds the Patient entries to the database. It also creates the realted Tumor and Diagnose entries.

Class	`Meta`	Undocumented
Static Method	`get_institution`	Return the institution that provided the dataset.
Method	`__str__`	Undocumented
Method	`check_integrity`	Check whether the dataset is still consistent with the GitHub repo.
Method	`compute_fields`	Dynamically compute fields from the GitHub repository.
Method	`delete`	Delete the model instance from the database.
Method	`fetch_dataframe`	Return the dataset as a pandas DataFrame.
Method	`fetch_file`	Return the GitHub file object.
Method	`fetch_readme`	Return the README.md file of the dataset as a string.
Method	`fetch_repo`	Return the GitHub repository object.
Method	`import_csv_to_db`	Import the dataset from the CSV file into the database.
Method	`lock`	Lock the dataset, so that it cannot be edited anymore.
Method	`save`	Save the model instance to the database.
Method	`unlock`	Unlock the dataset, so that it can be edited again.
Instance Variable	`data_path`	Path to the CSV file containing the patient data inside the git repo.
Instance Variable	`data_sha`	SHA of the CSV file in the GitHub repo.
Instance Variable	`date_created`	Date and time when the dataset was created.
Instance Variable	`git_repo_name`	Name of the GitHub repository that contains the dataset.
Instance Variable	`git_repo_owner`	Owner of the GitHub repository that contains the dataset.
Instance Variable	`institution`	The institution that provided the dataset.
Instance Variable	`is_locked`	Whether the dataset is locked or not. Locked datasets cannot be edited.
Instance Variable	`is_outdated`	Whether the data file has been updated since the last import.
Instance Variable	`is_public`	Whether the dataset is public or not. Public datasets can be viewed by everyone.
Instance Variable	`revision`	Git revision in which to search for the data. E.g., a commit hash, or tag.
Property	`data_url`	Return the URL of the data file in the GitHub repository.
Property	`git_repo_id`	Return the ID of the GitHub repository.
Property	`git_repo_url`	Return the URL of the GitHub repository.
Property	`name`	Return the name of the dataset.
Property	`patient_count`	Return the number of patients in the dataset.
Instance Variable	`_dataframe`	Undocumented
Instance Variable	`_file`	Undocumented
Instance Variable	`_readme`	Undocumented
Instance Variable	`_repo`	Undocumented

@staticmethod
def get_institution(table, fallback): ¶

Return the institution that provided the dataset.

Parameters
table:`pd.DataFrame`	Undocumented
fallback:`Institution`	Undocumented
Returns
`Institution`	Undocumented

def __str__(self): ¶

Undocumented

def check_integrity(self): ¶

Check whether the dataset is still consistent with the GitHub repo.

def compute_fields(self, git_repo_url, revision, data_path, user_institution, **_kwargs): ¶

Dynamically compute fields from the GitHub repository.

Parameters
git_repo_url:`str`	Undocumented
revision:`str`	Undocumented
data_path:`str`	Undocumented
user_institution:`Institution`	Undocumented
**_kwargs	Undocumented

def delete(self, *args, override=False, **kwargs): ¶

overrides lyprox.loggers.ModelLoggerMixin.delete

Delete the model instance from the database.

Rise an error if the dataset is locked and override is not set to True.

Parameters
*args	Undocumented
override:`bool`	Undocumented
**kwargs	Undocumented

def fetch_dataframe(self): ¶

Return the dataset as a pandas DataFrame.

Returns
`pd.DataFrame`	Undocumented

def fetch_file(self): ¶

Return the GitHub file object.

def fetch_readme(self): ¶

Return the README.md file of the dataset as a string.

Returns
`str`	Undocumented

def fetch_repo(self): ¶

Return the GitHub repository object.

def import_csv_to_db(self): ¶

Import the dataset from the CSV file into the database.

This method lock the dataset right afterwards to prevent editing the uploaded patients.

def lock(self): ¶

Lock the dataset, so that it cannot be edited anymore.

def save(self, *args, override=False, **kwargs): ¶

overrides lyprox.loggers.ModelLoggerMixin.save

Save the model instance to the database.

Rise an error if the dataset is locked and override is not set to True.

Parameters
*args	Undocumented
override:`bool`	Undocumented
**kwargs	Undocumented

def unlock(self): ¶

Unlock the dataset, so that it can be edited again.

data_path = ¶

Path to the CSV file containing the patient data inside the git repo.

data_sha = ¶

SHA of the CSV file in the GitHub repo.

date_created = ¶

Date and time when the dataset was created.

git_repo_name = ¶

Name of the GitHub repository that contains the dataset.

git_repo_owner = ¶

Owner of the GitHub repository that contains the dataset.

institution = ¶

The institution that provided the dataset.

is_locked: bool = ¶

Whether the dataset is locked or not. Locked datasets cannot be edited.

is_outdated: bool = ¶

Whether the data file has been updated since the last import.

is_public = ¶

Whether the dataset is public or not. Public datasets can be viewed by everyone.

revision = ¶

Git revision in which to search for the data. E.g., a commit hash, or tag.

@property
data_url = ¶

Return the URL of the data file in the GitHub repository.

@property
git_repo_id = ¶

Return the ID of the GitHub repository.

@property
git_repo_url = ¶

Return the URL of the GitHub repository.

@property
name = ¶

Return the name of the dataset.

@property
patient_count: int = ¶

Return the number of patients in the dataset.

_dataframe = ¶

Undocumented

_file = ¶

Undocumented

_readme = ¶

Undocumented

_repo = ¶

Undocumented