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move to poetry
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@ypriverol
ypriverol committed Feb 8, 2025
1 parent 8e18940 commit e831657
Showing 1 changed file with 13 additions and 161 deletions.
174 changes: 13 additions & 161 deletions pridepy/pridepy.py
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Original file line number Diff line number Diff line change
Expand Up @@ -10,7 +10,6 @@
def main():
pass


@main.command(
"download-all-public-raw-files",
help="Download all public raw files from a given PRIDE public project",
Expand Down Expand Up @@ -272,69 +271,6 @@ def list_private_files(accession, user, password):
file_category = f["fileCategory"]["value"]
logging.info(f["fileName"] + "\t" + str(file_size) + " MB\t" + file_category)


@main.command()
@click.option(
"-k",
"--keyword",
required=False,
default="",
help="The entered word will be searched among the fields to fetch "
"matching pride. The structure of the keyword is : *:*",
)
@click.option(
"-f",
"--filter",
required=False,
help="Parameters to filter the search results. The structure of the "
"filter is: field1==value1, field2==value2. Example "
"accession==PRD000001",
)
@click.option(
"-ps",
"--page_size",
required=False,
default=100,
help="Number of results to fetch in a page",
)
@click.option(
"-p",
"--page",
required=False,
default=0,
help="Identifies which page of results to fetch",
)
@click.option(
"-sd",
"--sort_direction",
required=False,
default="DESC",
help="Sorting direction: ASC or DESC",
)
@click.option(
"-sf",
"--sort_fields",
required=False,
default="submission_date",
help="Field(s) for sorting the results on. Default for this "
"request is submission_date. More fields can be separated by "
"comma and passed. Example: submission_date,project_title",
)
def search_projects_by_keywords_and_filters(
keyword, filter, page_size, page, date_gap, sort_direction, sort_fields
):
"""
search public pride with keywords and filters
:return:
"""
project = Project()
logging.info(
project.search_by_keywords_and_filters(
keyword, filter, page_size, page, sort_direction, sort_fields
)
)


@main.command()
@click.option(
"-o",
Expand Down Expand Up @@ -372,115 +308,31 @@ def stream_files_metadata(accession, output_file):
files = Files()
asyncio.run(files.stream_all_files_metadata(output_file, accession))


@main.command()
@click.option(
"-ps",
"--page_size",
required=False,
default=100,
help="Number of results to fetch in a page",
)
@click.option(
"-p",
"--page",
required=False,
default=0,
help="Identifies which page of results to fetch",
)
@click.option(
"-sd",
"--sort_direction",
required=False,
default="DESC",
help="Sorting direction: ASC or DESC",
)
@click.option(
"-sc",
"--sort_conditions",
required=False,
default="projectAccession",
help="Field(s) for sorting the results on. Default for this "
"request is project_accession. More fields can be separated by "
"comma and passed. Example: submission_date,project_title",
)
def get_projects(page_size, page, sort_direction, sort_conditions):
"""
get paged projects
:return:
"""
project = Project()
logging.info(project.get_projects(page_size, page, sort_direction, sort_conditions))


@main.command()
@click.option("-a", "--accession", required=False, help="accession of the project")
def get_projects_by_accession(accession):
"""
get projects by accession
:return:
"""
project = Project()
logging.info(project.get_by_accession(accession))


@main.command()
@click.option("-a", "--accession", required=False, help="accession of the project")
def get_similar_projects_by_accession(accession):
"""
get similar projects by accession
:return:
"""
project = Project()
logging.info(project.get_similar_projects_by_accession(accession))


@main.command()
@click.option("-a", "--accession", required=True, help="accession of the project")
@click.option(
"-ps",
"--page_size",
required=False,
default=100,
help="Number of results to fetch in a page",
)
@click.option(
"-p",
"--page",
required=False,
default=0,
help="Identifies which page of results to fetch",
)
@click.option(
"-sd",
"--sort_direction",
required=False,
default="DESC",
help="Sorting direction: ASC or DESC",
)
@click.option(
"-sc",
"--sort_conditions",
"-k",
"--keyword",
required=False,
default="projectAccession",
help="Field(s) for sorting the results on. Default for this "
"request is project_accession. More fields can be separated by "
"comma and passed. Example: submission_date,project_title",
default="",
help="The entered word will be searched among the fields to fetch "
"matching pride. The structure of the keyword is : *:*",
)
def get_files_by_project_accession(
accession, filter, page_size, page, sort_direction, sort_conditions
def search_projects_by_keywords_and_filters(
keyword, filter, page_size, page, date_gap, sort_direction, sort_fields
):
"""
get files by project accession
:return:
TODO: @selva this function and command line should be reimplemented.
TODO: The idea is that the user can type a keyword or keywords and filters and get all the files projects in
TODO: JSON.
"""
project = Project()
logging.info(
project.get_files_by_accession(
accession, filter, page_size, page, sort_direction, sort_conditions
project.search_by_keywords_and_filters(
keyword, filter, page_size, page, sort_direction, sort_fields
)
)



if __name__ == "__main__":
main()

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