ddipy

An Python package to obtain data from the Omics Discovery Index (OmicsDI. It uses the RESTful Web Services at OmicsDI WS for that purpose.

Installation

we need to install ddipy:

pip install ddipy

Examples

This example shows how retrieve details of one dataset by using the Python package ddipy.

from ddipy.dataset_client import DatasetClient
    
if __name__ == '__main__':
   client = DatasetClient()
   res = client.get_dataset_details("pride", "PXD000210", False)

This example shows a search for all the datasets for human.

from ddipy.dataset_client import DatasetClient
    
if __name__ == '__main__':
   client = DatasetClient()
   res = client.search("cancer human", "publication_date", "ascending")

This example shows a search for all the datasets for cancer human and loop over the pagination

from ddipy.dataset_client import DatasetClient
    
if __name__ == '__main__':
   client = DatasetClient()
   res = client.search("cancer human", "publication_date", "ascending", 1200, 30, 20)

This example is a query to retrieve all the datasets that reported the UniProt protein P21399 as identified.

from ddipy.dataset_client import DatasetClient

if __name__ == '__main__':
    client = DatasetClient()
    res = client.search("UNIPROT:P21399")

This example is a query to find all the datasets where the gene ENSG00000147251 is reported as differentially expressed.

from ddipy.dataset_client import DatasetClient

if __name__ == '__main__':
    client = DatasetClient()
    res = client.search("ENSEMBL:ENSG00000147251")

This example is a query to retrieve all databases recorded in OmicsDI

from ddipy.dataset_client import DatabaseClient

if __name__ == '__main__':
   client = DatabaseClient()
   res = client.get_database_all()

This example is retrieving JSON+LD for dataset page

from ddipy.dataset_client import SeoClient

if __name__ == '__main__':
    client = SeoClient()
    res = client.get_seo_dataset("pride", "PXD000210")

This example is retriveing JSON+LD for home page

from ddipy.dataset_client import SeoClient

if __name__ == '__main__':
    client = SeoClient()
    res = client.get_seo_home()

This example is a query for statistics about the number of datasets per Tissue

from ddipy.dataset_client import StatisticsClient

if __name__ == '__main__':
    client = StatisticsClient()
    res = client.get_statistics_tissues(20)

This example is a query for statistics about the number of datasets per dieases

from ddipy.dataset_client import StatisticsClient

if __name__ == '__main__':
    client = StatisticsClient()
    res = client.get_statistics_diseases(20)

This example for searching dictionary terms

from ddipy.dataset_client import TermClient

if __name__ == '__main__':
    client = TermClient()
    res = client.get_term_by_pattern("hom", 10)

This example for retrieving frequently terms from the repo

from ddipy.dataset_client import TermClient

if __name__ == '__main__':
    client = TermClient()
    res = client.get_term_by_pattern("pride", "description", 20)

Find out about us in our GitHub profiles:

Yasset Perez-Riverol
Pan Xu

When ddipy is installed correctly it should be available on your path through the command omicsdi. This command line interface makes it possible to list all the data links and download the data itself related to an accession number. The tool has one mandatory parameter 'accession number' and several options:

omicsdi_fetcher [OPTIONS] ACC_NUMBER

Option	Type	Description
--version	FLAG	Show the version and exit.
-d, --download	FLAG	Use this flag to download the files in the current directory or a specified output directory
-v, --verbose	FLAG	Use this flag to print identifiers and file extension along with the urls
-i, --input	LIST	This option allows you to download the a selection of the files based on comma separated list of identifiers
-o, --output	PATH	Output directory when downloading files (default: CWD)
-h, --help	FLAG	Show this message and exit.

Examples

A microarray dataset with ftp links:
```
omicsdi E-MTAB-5612
```
Downloading the microarray dataset with ftp links:
```
omicsdi E-MTAB-5612 -d
```
A BioModels dataset with https links and exposing identifiers for each file link:
```
omicsdi BIOMD0000000048 -v
```
Downloading a selection of the files belonging to an accession number based on a list of identifiers as input:
```
omicsdi BIOMD0000000048 -d -i "8b52492888, d3144265ac"
```

New comments from reviewers

After reviewing the codebase of https://github.com/OmicsDI/ddi-web-service/ it appears that there are almost no tests, but more importantly I did not found any trace of continuous integration. I can only recommend to enrich the tests, and enable it as you did for the clients, even though it might be harder due to the dependencies.
https://www.omicsdi.org/ws/dataset/pridr/PXD000210/ is now indicating that the database is missing but still uses a 500 while it should be a 404
In the python example of the client, providing a boolean argument while never indicating what it is add little to no information. Please either use named attribute, or remove it:

res=client.get_dataset_details(domain="pride", accession="PXD000210")
# or
res=client.get_dataset_details(domain="pride", accession="PXD000210", debug=True)

https://www.omicsdi.org/ws/database/blabla/picture fails with a 500 error and a NullPointerException, it should indicate that blabla database does not exists, and return a status_code of 404
In dataset_client.py search method refuse to not specify sortfield or order while API allows it. Client should not introduce such restriction without a reason. Here after a snippet where arguments are optional (but still must not be an empty string).

class DatasetClient:

    # (...)

    @staticmethod
    def search(query, sortfield=None, order=None, start=0, size=20, face_count=20):
        params = {
            "start": start,
            "size": size,
            "faceCount": face_count
        }
        if not query:
            raise BadRequest("missing parameter query", MISSING_PARAMETER, payload=None)
        else:
            params.update(query=query)
        if sortfield:
            params.update(sortfield=sortfield)
        if order:
            params.update(order=order)

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