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[Python package](https://github.com/OmicsDI/ddipy) to obtain data from the Omics Discovery Index ([OmicsDI](http://www.omicsdi.org). It uses the RESTful Web Services at [OmicsDI WS](http://www.omicsdi.org/ws/) for that purpose.\n\n### Installation\n\nwe need to install `ddipy`:  \n\n```\npip install ddipy\n```\n\n### Examples  \n\nThis example shows how retrieve details of one dataset by using the Python package ddipy.\n\n```python\nfrom ddipy.dataset_client import DatasetClient\n    \nif __name__ == '__main__':\n   client = DatasetClient()\n   res = client.get_dataset_details(\"pride\", \"PXD000210\", False)\n   \n```\n        \nThis example shows a search for all the datasets for human.\n\n```python\nfrom ddipy.dataset_client import DatasetClient\n    \nif __name__ == '__main__':\n   client = DatasetClient()\n   res = client.search(\"cancer human\", \"publication_date\", \"ascending\")\n   \n```\n\nThis example shows a search for all the datasets for cancer human and loop over the pagination\n\n```python\nfrom ddipy.dataset_client import DatasetClient\n    \nif __name__ == '__main__':\n   client = DatasetClient()\n   res = client.search(\"cancer human\", \"publication_date\", \"ascending\", 1200, 30, 20)\n   \n```\n\nThis example is a query to retrieve all the datasets that reported the UniProt protein P21399 as identified.\n\n```python\nfrom ddipy.dataset_client import DatasetClient\n\nif __name__ == '__main__':\n    client = DatasetClient()\n    res = client.search(\"UNIPROT:P21399\")\n    \n```\n\nThis example is a query to find all the datasets where the gene ENSG00000147251 is reported as differentially expressed.\n\n```python\nfrom ddipy.dataset_client import DatasetClient\n\nif __name__ == '__main__':\n    client = DatasetClient()\n    res = client.search(\"ENSEMBL:ENSG00000147251\")\n    \n```\n\nThis example is a query to retrieve all databases recorded in OmicsDI\n\n```python\nfrom ddipy.dataset_client import DatabaseClient\n\nif __name__ == '__main__':\n   client = DatabaseClient()\n   res = client.get_database_all()\n```\n\n\nThis example is retrieving JSON+LD for dataset page\n\n```python\nfrom ddipy.dataset_client import SeoClient\n\nif __name__ == '__main__':\n    client = SeoClient()\n    res = client.get_seo_dataset(\"pride\", \"PXD000210\")\n```\n\nThis example is  retriveing JSON+LD for home page\n\n```python\nfrom ddipy.dataset_client import SeoClient\n\nif __name__ == '__main__':\n    client = SeoClient()\n    res = client.get_seo_home()\n```\n\nThis example is a query for statistics about the number of datasets per Tissue\n\n```python\nfrom ddipy.dataset_client import StatisticsClient\n\nif __name__ == '__main__':\n    client = StatisticsClient()\n    res = client.get_statistics_tissues(20)\n```\n\nThis example is a query for statistics about the number of datasets per dieases\n\n```python\nfrom ddipy.dataset_client import StatisticsClient\n\nif __name__ == '__main__':\n    client = StatisticsClient()\n    res = client.get_statistics_diseases(20)\n```\n\nThis example for searching dictionary terms\n\n```python\nfrom ddipy.dataset_client import TermClient\n\nif __name__ == '__main__':\n    client = TermClient()\n    res = client.get_term_by_pattern(\"hom\", 10)\n```\n\nThis example for retrieving frequently terms from the repo\n\n```python\nfrom ddipy.dataset_client import TermClient\n\nif __name__ == '__main__':\n    client = TermClient()\n    res = client.get_term_by_pattern(\"pride\", \"description\", 20)\n```\n\n\nFind out about us in our GitHub profiles:\n\n[Yasset Perez-Riverol](https://github.com/ypriverol)  \n[Pan Xu](https://github.com/hll3939092)\n\n\n### CLI for downloading files\n\nWhen 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:\n\n```\nomicsdi_fetcher [OPTIONS] ACC_NUMBER\n```\n\n| Option           | Type | Description                                                                                                  |\n|------------------|------|--------------------------------------------------------------------------------------------------------------|\n|   --version      | FLAG | Show the version and exit.                                                                                   |\n|   -d, --download | FLAG | Use this flag to download the files in the current directory or a specified output directory                 |\n|   -v, --verbose  | FLAG | Use this flag to print identifiers and file extension along with the urls                                    |\n|   -i, --input    | LIST | This option allows you to download the a selection of the files based on comma separated list of identifiers |\n|   -o, --output   | PATH | Output directory when downloading files (default: CWD)                                                       |\n|   -h, --help     | FLAG | Show this message and exit.                                                                                  |\n\n#### Examples\n\n- A microarray dataset with ftp links:\n    ```\n    omicsdi E-MTAB-5612\n    ```\n- Downloading the microarray dataset with ftp links:\n    ```\n    omicsdi E-MTAB-5612 -d\n    ```\n- A BioModels dataset with https links and exposing identifiers for each file link:\n    ```\n    omicsdi BIOMD0000000048 -v\n    ```\n\n- Downloading a selection of the files belonging to an accession number based on a list of identifiers as input:\n    ```\n    omicsdi BIOMD0000000048 -d -i \"8b52492888, d3144265ac\"\n    ```\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fomicsdi%2Fddipy","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fomicsdi%2Fddipy","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fomicsdi%2Fddipy/lists"}