✨ Create or append descriptors to global IDs

d3b_api_client_cli/cli/__init__.py

@@ -7,6 +7,14 @@
 import click
 from d3b_api_client_cli.cli.dewrangle import *
 from d3b_api_client_cli.cli.postgres import *
+from d3b_api_client_cli.cli.faker import *
+
+
+@click.group()
+def faker():
+    """
+    Group of lower level CLI commands related to generating fake data
+    """
 
 
 @click.group()
@@ -35,6 +43,9 @@ def main():
     """
 
 
+# Fake data commands
+faker.add_command(generate_global_id_file)
+
 # Postgres API commands
 postgres.add_command(save_file_to_db)
 
@@ -57,7 +68,12 @@ def main():
 dewrangle.add_command(create_billing_group)
 dewrangle.add_command(delete_billing_group)
 dewrangle.add_command(read_billing_groups)
+dewrangle.add_command(upsert_global_descriptors)
+dewrangle.add_command(download_global_descriptors)
+dewrangle.add_command(upsert_and_download_global_descriptors)
+dewrangle.add_command(upsert_and_download_global_descriptor)
 
 # Add command groups to the root CLI
 main.add_command(dewrangle)
 main.add_command(postgres)
+main.add_command(faker)

d3b_api_client_cli/cli/dewrangle/__init__.py

@@ -10,3 +10,4 @@
 from d3b_api_client_cli.cli.dewrangle.volume_commands import *
 from d3b_api_client_cli.cli.dewrangle.job_commands import *
 from d3b_api_client_cli.cli.dewrangle.billing_group_commands import *
+from d3b_api_client_cli.cli.dewrangle.global_id_commands import *

d3b_api_client_cli/cli/dewrangle/global_id_commands.py

@@ -0,0 +1,285 @@
+"""
+All CLI commands related to creating, updating, and downloading global IDs
+in Dewrangle
+"""
+
+import os
+import logging
+import click
+
+from d3b_api_client_cli.config import log, FHIR_RESOURCE_TYPES
+from d3b_api_client_cli.dewrangle.global_id import GlobalIdDescriptorOptions
+from d3b_api_client_cli.dewrangle.global_id import (
+    upsert_global_descriptors as _upsert_global_descriptors,
+    download_global_descriptors as _download_global_descriptors,
+    upsert_and_download_global_descriptors as _upsert_and_download_global_descriptors,
+    upsert_and_download_global_descriptor as _upsert_and_download_global_descriptor,
+)
+
+logger = logging.getLogger(__name__)
+
+
+@click.command()
+@click.option(
+    "--output-filepath",
+    type=click.Path(exists=False, file_okay=True, dir_okay=False),
+    help="If provided, download the file to this path. This takes "
+    "precedence over the --output-dir option",
+)
+@click.option(
+    "--output-dir",
+    default=os.getcwd(),
+    type=click.Path(exists=True, file_okay=False, dir_okay=True),
+    help="If provided, download the file with the default file name into "
+    "this directory",
+)
+@click.option(
+    "--download-all",
+    is_flag=True,
+    help="What descriptor(s) for each global ID to download. Either download"
+    " all descriptors for each global ID or just the most recent",
+)
+@click.option(
+    "--study-global-id",
+    help="The global ID of the study in Dewrangle. You must provide either "
+    "the global ID of the study OR the GraphQL ID of the study but not both",
+)
+@click.option(
+    "--study-id",
+    help="The GraphQL ID of the study in Dewrangle. You must provide either "
+    "the global ID of the study OR the GraphQL ID of the study but not both",
+)
+@click.option(
+    "--global-id",
+    help="Global ID associated with this descriptor."
+    " If this is provided, and the descriptor is new, then Dewrangle"
+    " will append the descriptor to this global ID's descriptor list",
+)
+@click.option(
+    "--fhir-resource-type",
+    type=click.Choice([rt for rt in FHIR_RESOURCE_TYPES.keys()]),
+    required=True,
+)
+@click.option(
+    "--descriptor",
+    required=True,
+)
+def upsert_and_download_global_descriptor(
+    descriptor,
+    fhir_resource_type,
+    global_id,
+    study_id,
+    study_global_id,
+    download_all,
+    output_dir,
+    output_filepath,
+):
+    """
+    Send request to upsert one global ID descriptor in Dewrangle and
+    download the resulting global ID descriptors.
+
+    In order to create new global IDs provide:
+    descriptor, fhir-resource-type
+
+    In order to update existing global IDs:
+    descriptor, fhir-resource-type, global-id
+
+    \b
+    Arguments:
+      \b
+      input_filepath - Path to the file with global IDs and descriptors
+    """
+
+    log.init_logger()
+
+    if (not study_id) and (not study_global_id):
+        raise click.BadParameter(
+            "❌ You must provide either the study's global ID in Dewrangle OR "
+            "the study's GraphQL ID in Dewrangle"
+        )
+    return _upsert_and_download_global_descriptor(
+        descriptor,
+        fhir_resource_type,
+        global_id=global_id,
+        study_global_id=study_global_id,
+        dewrangle_study_id=study_id,
+        download_all=download_all,
+        output_dir=output_dir,
+        output_filepath=output_filepath,
+    )
+
+
+@click.command()
+@click.option(
+    "--output-filepath",
+    type=click.Path(exists=False, file_okay=True, dir_okay=False),
+    help="If provided, download the file to this path. This takes "
+    "precedence over the --output-dir option",
+)
+@click.option(
+    "--output-dir",
+    default=os.getcwd(),
+    type=click.Path(exists=True, file_okay=False, dir_okay=True),
+    help="If provided, download the file with the default file name into "
+    "this directory",
+)
+@click.option(
+    "--download-all",
+    is_flag=True,
+    help="What descriptor(s) for each global ID to download. Either download"
+    " all descriptors for each global ID or just the most recent",
+)
+@click.option(
+    "--study-global-id",
+    help="The global ID of the study in Dewrangle. You must provide either "
+    "the global ID of the study OR the GraphQL ID of the study but not both",
+)
+@click.option(
+    "--study-id",
+    help="The GraphQL ID of the study in Dewrangle. You must provide either "
+    "the global ID of the study OR the GraphQL ID of the study but not both",
+)
+@click.argument(
+    "input_filepath",
+    type=click.Path(exists=False, file_okay=True, dir_okay=False),
+)
+def upsert_and_download_global_descriptors(
+    input_filepath,
+    study_id,
+    study_global_id,
+    download_all,
+    output_dir,
+    output_filepath,
+):
+    """
+    Send request to upsert global ID descriptors in Dewrangle and
+    download the resulting global ID descriptors.
+
+    In order to create new global IDs provide a CSV file with the columns:
+    descriptor, fhirResourceType
+
+    In order to update existing global IDs provide a CSV file with the columns:
+    descriptor, fhirResourceType, globalId
+
+    \b
+    Arguments:
+      \b
+      input_filepath - Path to the file with global IDs and descriptors
+    """
+
+    log.init_logger()
+
+    if (not study_id) and (not study_global_id):
+        raise click.BadParameter(
+            "❌ You must provide either the study's global ID in Dewrangle OR "
+            "the study's GraphQL ID in Dewrangle"
+        )
+
+    return _upsert_and_download_global_descriptors(
+        input_filepath,
+        study_global_id=study_global_id,
+        dewrangle_study_id=study_id,
+        download_all=download_all,
+        output_dir=output_dir,
+        output_filepath=output_filepath,
+    )
+
+
+@click.command()
+@click.option(
+    "--study-global-id",
+    help="The global ID of the study in Dewrangle. You must provide either "
+    "the global ID of the study OR the GraphQL ID of the study but not both",
+)
+@click.option(
+    "--study-id",
+    help="The GraphQL ID of the study in Dewrangle. You must provide either "
+    "the global ID of the study OR the GraphQL ID of the study but not both",
+)
+@click.argument(
+    "filepath",
+    type=click.Path(exists=False, file_okay=True, dir_okay=False),
+)
+def upsert_global_descriptors(filepath, study_id, study_global_id):
+    """
+    Upsert global ID descriptors in Dewrangle for a study.
+
+    In order to create new global IDs provide a CSV file with the columns:
+    descriptor, fhirResourceType
+
+    In order to update existing global IDs provide a CSV file with the columns:
+    descriptor, fhirResourceType, globalId
+
+    \b
+    Arguments:
+      \b
+      filepath - Path to the file with global IDs and descriptors
+    """
+
+    log.init_logger()
+
+    if (not study_id) and (not study_global_id):
+        raise click.BadParameter(
+            "❌ You must provide either the study's global ID in Dewrangle OR "
+            "the study's GraphQL ID in Dewrangle"
+        )
+
+    return _upsert_global_descriptors(filepath, study_global_id, study_id)
+
+
+@click.command()
+@click.option(
+    "--output-dir",
+    default=os.getcwd(),
+    type=click.Path(exists=True, file_okay=False, dir_okay=True),
+    help="If provided, download the file with the default file name into "
+    "this directory",
+)
+@click.option(
+    "--download-all",
+    is_flag=True,
+    help="What descriptor(s) for each global ID to download. Either download"
+    " all descriptors for each global ID or just the most recent",
+)
+@click.option(
+    "--job-id", help="Dewrangle job id from the upsert_global_descriptors cmd"
+)
+@click.option(
+    "--study-global-id",
+    help="The global ID of the study in Dewrangle. You must provide either "
+    "the global ID of the study OR the GraphQL ID of the study but not both",
+)
+@click.option(
+    "--study-id",
+    help="The GraphQL ID of the study in Dewrangle. You must provide either "
+    "the global ID of the study OR the GraphQL ID of the study but not both",
+)
+@click.option(
+    "--filepath",
+    type=click.Path(exists=False, file_okay=True, dir_okay=False),
+    help="If provided, download the file to this filepath. This takes "
+    "precedence over --output-dir",
+)
+def download_global_descriptors(
+    filepath, study_id, study_global_id, job_id, download_all, output_dir
+):
+    """
+    Download global ID descriptors in Dewrangle for a study.
+    """
+
+    log.init_logger()
+
+    if (not study_id) and (not study_global_id):
+        raise click.BadParameter(
+            "❌ You must provide either the study's global ID in Dewrangle OR "
+            "the study's GraphQL ID in Dewrangle"
+        )
+
+    return _download_global_descriptors(
+        dewrangle_study_id=study_id,
+        study_global_id=study_global_id,
+        filepath=filepath,
+        job_id=job_id,
+        download_all=download_all,
+        output_dir=output_dir,
+    )

d3b_api_client_cli/cli/faker/__init__.py

@@ -0,0 +1,5 @@
+"""
+Package containing commands for fake data generation
+"""
+
+from d3b_api_client_cli.cli.faker.global_id_commands import *