feat: add "projects project-list" command

.github/workflows/main.yml

@@ -26,7 +26,7 @@ jobs:
       - name: Install Python
         uses: actions/setup-python@v2
         with:
-          python-version: "3.8"
+          python-version: "3.10"
 
       - name: Install dependencies
         run: |
@@ -52,7 +52,7 @@ jobs:
       - name: Install Python
         uses: actions/setup-python@v2
         with:
-          python-version: "3.8"
+          python-version: "3.10"
 
       - name: Install dependencies
         run: |
@@ -70,10 +70,9 @@ jobs:
     strategy:
       matrix:
         python-version:
-          - '3.8'
-          - '3.9'
           - '3.10'
           - '3.11'
+          - '3.12'
     needs: linting
     steps:
       - uses: actions/checkout@v2

setup.cfg

@@ -11,6 +11,7 @@ exclude =
     docs/
     varfish_cli/__init__.py
     versioneer.py
+    venv/
 
 ignore = E203, E266, E501, W503
 max-line-length = 80

setup.py

@@ -42,9 +42,9 @@ def parse_requirements(path):
         "Natural Language :: English",
         "Topic :: Scientific/Engineering :: Bio-Informatics",
         "Programming Language :: Python :: 3",
-        "Programming Language :: Python :: 3.8",
-        "Programming Language :: Python :: 3.9",
         "Programming Language :: Python :: 3.10",
+        "Programming Language :: Python :: 3.11",
+        "Programming Language :: Python :: 3.12",
     ],
     entry_points={"console_scripts": ("varfish-cli = varfish_cli.__main__:main",)},
     description="Command line interface client for VarFish Server.",

varfish_cli/__main__.py

@@ -13,6 +13,8 @@
 from varfish_cli.case import run as run_case
 from varfish_cli.case import setup_argparse as setup_argparse_case
 from varfish_cli.common import CommonConfig, run_nocmd
+from varfish_cli.projects import run as run_projects
+from varfish_cli.projects import setup_argparse as setup_argparse_projects
 from varfish_cli.varannos import run as run_varannos
 from varfish_cli.varannos import setup_argparse as setup_argparse_varannos
 
@@ -63,6 +65,7 @@ def setup_argparse():
     subparsers = parser.add_subparsers(dest="cmd")
 
     setup_argparse_case(subparsers.add_parser("case", help="Work with cases."))
+    setup_argparse_projects(subparsers.add_parser("projects", help="Work with projects."))
     setup_argparse_varannos(subparsers.add_parser("varannos", help="Work with varannos module."))
 
     return parser, subparsers
@@ -107,7 +110,7 @@ def main(argv=None):
     config = CommonConfig.create(args, toml_config)
 
     # Handle the actual command line.
-    cmds = {None: run_nocmd, "case": run_case, "varannos": run_varannos}
+    cmds = {None: run_nocmd, "case": run_case, "varannos": run_varannos, "projects": run_projects}
 
     res = cmds[args.cmd](
         config, toml_config, args, parser, subparsers.choices[args.cmd] if args.cmd else None

varfish_cli/api/__init__.py

@@ -2,4 +2,5 @@
 
 from varfish_cli.api.case import *  # noqa: F403, F401
 from varfish_cli.api.models import *  # noqa: F403, F401
+from varfish_cli.api.project import *  # noqa: F403, F401
 from varfish_cli.api.varannos import *  # noqa: F403, F401

varfish_cli/api/models.py

@@ -11,6 +11,36 @@
 import dateutil.parser
 
 
+@unique
+class ProjectType(Enum):
+    """Enumeration of possible project types."""
+
+    #: Container for other categories or projects but not primary data.
+    CATEGORY = "CATEGORY"
+    #: Project containing primary data but no other projects.
+    PROJECT = "PROJECT"
+
+
+@attr.s(frozen=True, auto_attribs=True)
+class Project:
+    #: The project identifier.
+    sodar_uuid: uuid.UUID
+    #: Parent category UUID, if any.
+    parent: typing.Optional[uuid.UUID]
+    #: Project title.
+    title: str
+    #: Project type.
+    type: ProjectType
+    #: Project description.
+    description: str
+    #: Markdown README string.
+    readme: str
+    #: Whether public guest access is allowed.
+    public_guest_access: bool
+    #: Whether the project has been archived.
+    archive: bool
+
+
 @attr.s(frozen=True, auto_attribs=True)
 class PedigreeMember:
     """Represent a pedigree member as returned by the VarFish API."""

varfish_cli/api/project.py

@@ -0,0 +1,30 @@
+"""Implementation of API operations on cases."""
+
+import typing
+
+from logzero import logger
+import requests
+
+from varfish_cli.api.models import CONVERTER, Project
+from varfish_cli.api.varannos import raise_for_status
+from varfish_cli.common import strip_trailing_slash
+
+ACCEPT_API_VARFISH = ""
+
+#: End point for listing projects.
+ENDPOINT_PROJECT_LIST = "/project/api/list"
+
+
+def project_list(
+    server_url: str,
+    api_token: str,
+    verify_ssl: bool = True,
+) -> typing.List[Project]:
+    """Listing of all projects that a user has access to."""
+    server_url = strip_trailing_slash(server_url)
+    endpoint = f"{server_url}{ENDPOINT_PROJECT_LIST}"
+    logger.debug("Sending GET request to end point %s", endpoint)
+    headers = {"Authorization": "Token %s" % api_token}
+    result = requests.get(endpoint, headers=headers, verify=verify_ssl)
+    raise_for_status(result)
+    return CONVERTER.structure(result.json(), typing.List[Project])

varfish_cli/projects/__init__.py

@@ -0,0 +1,74 @@
+"""Implementation of varfish-cli subcommand 'projects'."""
+
+import argparse
+import typing
+
+import attr
+
+from varfish_cli.common import CommonConfig, OutputFormat, run_nocmd
+from varfish_cli.projects.project_list import (
+    setup_argparse as setup_argparse_project_list,
+)
+
+
+@attr.s(frozen=True, auto_attribs=True)
+class ProjectsConfig:
+    """Configuration for the ``varfish-cli project`` command."""
+
+    #: Global configuration
+    global_config: CommonConfig
+
+    #: Path to output file
+    output_file: str = "-"
+
+    #: Output format
+    output_format: OutputFormat = OutputFormat.TABLE
+
+    #: delimiter for CSV output
+    output_delimiter: str = ","
+
+    #: Fields to use for output.
+    output_fields: typing.Optional[typing.List[str]] = []
+
+    @staticmethod
+    def create(args, global_config, toml_config=None):
+        _ = toml_config
+        return ProjectsConfig(
+            output_format=OutputFormat(args.output_format),
+            output_file=args.output_file,
+            output_delimiter=args.output_delimiter,
+            output_fields=args.output_fields.split(",") if args.output_fields else [],
+            global_config=global_config,
+        )
+
+
+def setup_argparse(parser: argparse.ArgumentParser) -> None:
+    """Main entry point for subcommand."""
+    of_choices = [o.value for o in OutputFormat]
+    of_default = OutputFormat.TABLE.value
+    parser.add_argument(
+        "--output-format",
+        help=f"Output format, one of {of_choices}, default: {of_default}",
+        choices=of_choices,
+        default=of_default,
+    )
+    parser.add_argument("--output-fields", help="Output fields if non-default ones")
+    parser.add_argument(
+        "--output-delimiter", help="Separator for CSV output, default: ','", default=","
+    )
+    parser.add_argument(
+        "--output-file", help="Path to file to write to, defaults to stdout", default="-"
+    )
+
+    subparsers = parser.add_subparsers(dest="projects_cmd")
+    setup_argparse_project_list(subparsers.add_parser("project-list", help="List project objects."))
+
+
+def run(config, toml_config, args, parser, subparser):
+    """Main entry point for project command."""
+    if not args.projects_cmd:  # pragma: nocover
+        return run_nocmd(config, args, parser, subparser)
+    else:
+        config = ProjectsConfig.create(args, config, toml_config)
+        print(args.projects_cmd)
+        return args.projects_cmd(config, toml_config, args, parser, subparser)

varfish_cli/projects/config.py

@@ -0,0 +1,52 @@
+import typing
+
+import attr
+
+from varfish_cli.common import CommonConfig, OutputFormat
+
+
+@attr.s(frozen=True, auto_attribs=True)
+class ProjectsConfig:
+    """Configuration for the ``varfish-cli project`` command."""
+
+    #: Global configuration
+    global_config: CommonConfig
+
+    #: Path to output file
+    output_file: str = "-"
+
+    #: Output format
+    output_format: OutputFormat = OutputFormat.TABLE
+
+    #: delimiter for CSV output
+    output_delimiter: str = ","
+
+    #: Fields to use for output.
+    output_fields: typing.Optional[typing.List[str]] = []
+
+    @staticmethod
+    def create(args, global_config, toml_config=None):
+        _ = toml_config
+        return ProjectsConfig(
+            output_format=OutputFormat(args.output_format),
+            output_file=args.output_file,
+            output_delimiter=args.output_delimiter,
+            output_fields=args.output_fields.split(",") if args.output_fields else [],
+            global_config=global_config,
+        )
+
+
+@attr.s(frozen=True, auto_attribs=True)
+class ProjectsListConfig:
+    """Configuration for the ``varfish-cli projects project-list`` command."""
+
+    #: Project configuration
+    projects_config: ProjectsConfig
+
+    @staticmethod
+    def create(args, projects_config, toml_config=None):
+        _ = args
+        _ = toml_config
+        return ProjectsListConfig(
+            projects_config=projects_config,
+        )

varfish_cli/projects/project_list.py

@@ -0,0 +1,72 @@
+"""Implementation of ``varfish-cli projects project-list``"""
+
+import argparse
+import sys
+import typing
+
+import attrs
+from logzero import logger
+
+from varfish_cli import api
+from varfish_cli.common import tabular_output, write_output
+from varfish_cli.projects.config import OutputFormat, ProjectsListConfig
+
+#: The default fields by output format.
+DEFAULT_FIELDS: typing.Dict[OutputFormat, typing.Optional[typing.Tuple[str]]] = {
+    OutputFormat.TABLE: (
+        "sodar_uuid",
+        "type",
+        "title",
+    ),
+    OutputFormat.CSV: None,
+    OutputFormat.JSON: None,
+}
+
+
+def setup_argparse(parser):
+    parser.add_argument("--hidden-cmd", dest="projects_cmd", default=run, help=argparse.SUPPRESS)
+
+
+def run(projects_config, toml_config, args, _parser, _subparser, file=sys.stdout):
+    """Run Project list command."""
+    projects_config = attrs.evolve(
+        projects_config,
+        output_fields=projects_config.output_fields
+        or DEFAULT_FIELDS.get(projects_config.output_format),
+    )
+    config = ProjectsListConfig.create(args, projects_config, toml_config)
+    logger.info("Configuration: %s", config)
+    logger.info("Listing Projects")
+    base_config = config.projects_config.global_config
+    res = api.project_list(
+        server_url=base_config.varfish_server_url,
+        api_token=base_config.varfish_api_token,
+        verify_ssl=config.projects_config.global_config.verify_ssl,
+    )
+
+    logger.info("Generating output")
+    header = (
+        projects_config.output_fields
+        if projects_config.output_fields
+        else [f.name for f in attrs.fields(api.Project)]
+    )
+    output = tabular_output(values=res, header=header)
+
+    logger.info("Writing output")
+    logger.info("==============")
+    if config.projects_config.output_file == "-":
+        write_output(
+            output,
+            sys.stdout,
+            config.projects_config.output_format,
+            config.projects_config.output_delimiter,
+        )
+    else:
+        with open(config.projects_config.output_file, "wt") as outputf:
+            write_output(
+                output,
+                outputf,
+                config.projects_config.output_format,
+                config.projects_config.output_delimiter,
+            )
+    logger.info("All done. Have a nice day!")