Repository: fractal-analytics-platform/fractal-client (language: python)

Issue:
Expose new endpoint for task collection
Same as https://github.com/fractal-analytics-platform/fractal-web/issues/517


Discussion / hints:
Most details are as in https://github.com/fractal-analytics-platform/fractal-web/issues/517#issuecomment-2210337149
Cmd: `fractal task collect-custom`

Fix patch:
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 0efabd3d4..f923fe30a 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -2,6 +2,7 @@
 
 # Unreleased
 
+* Add new command `task collect-custom` (\#667).
 * Update `poetry` version for development to 1.8.2.
 * Testing:
     * Update CI for fractal-server 2.1.0 compatibility (\#655).
diff --git a/fractal_client/cmd/__init__.py b/fractal_client/cmd/__init__.py
index ddfc271ff..2fc2842a7 100644
--- a/fractal_client/cmd/__init__.py
+++ b/fractal_client/cmd/__init__.py
@@ -21,6 +21,7 @@
 from ._task import get_task_list
 from ._task import patch_task
 from ._task import post_task
+from ._task import task_collect_custom
 from ._task import task_collect_pip
 from ._task import task_collection_check
 from ._user import user_edit
@@ -134,6 +135,17 @@ def task(
         ]
         function_kwargs = get_kwargs(parameters, kwargs)
         iface = task_collect_pip(client, batch=batch, **function_kwargs)
+    elif subcmd == "collect-custom":
+        parameters = [
+            "source",
+            "python_interpreter",
+            "manifest",
+            "version",
+            "package_name",
+            "package_root",
+        ]
+        function_kwargs = get_kwargs(parameters, kwargs)
+        iface = task_collect_custom(client, batch=batch, **function_kwargs)
     elif subcmd == "check-collection":
         parameters = ["state_id", "include_logs", "do_not_separate_logs"]
         function_kwargs = get_kwargs(parameters, kwargs)
diff --git a/fractal_client/cmd/_task.py b/fractal_client/cmd/_task.py
index 9b0558f4d..ce7979158 100644
--- a/fractal_client/cmd/_task.py
+++ b/fractal_client/cmd/_task.py
@@ -1,7 +1,9 @@
 import json
 import logging
 import sys
+from typing import Any
 from typing import Optional
+from urllib.request import urlopen
 
 from ..authclient import AuthClient
 from ..config import settings
@@ -61,6 +63,45 @@ def task_collect_pip(
         return Interface(retcode=0, data=state)
 
 
+def task_collect_custom(
+    client: AuthClient,
+    *,
+    source: str,
+    python_interpreter: str,
+    manifest: str,
+    version: Optional[str] = None,
+    package_name: Optional[str] = None,
+    package_root: Optional[str] = None,
+    batch: bool = False,
+) -> Interface:
+
+    with open(manifest, "r") as f:
+        manifest_dict = json.load(f)
+
+    task_collect = dict(
+        source=source,
+        python_interpreter=python_interpreter,
+        manifest=manifest_dict,
+    )
+    if version:
+        task_collect["version"] = version
+    if package_name:
+        task_collect["package_name"] = package_name
+    if package_root:
+        task_collect["package_root"] = package_root
+
+    res = client.post(
+        f"{settings.BASE_URL}/task/collect/custom/", json=task_collect
+    )
+
+    task_list = check_response(res, expected_status_code=201)
+    if batch:
+        task_ids = [str(task["id"]) for task in task_list]
+        return Interface(retcode=0, data=" ".join(task_ids))
+    else:
+        return Interface(retcode=0, data=task_list)
+
+
 def task_collection_check(
     client: AuthClient,
     *,
diff --git a/fractal_client/parser.py b/fractal_client/parser.py
index 83fa4290b..5026f51b2 100644
--- a/fractal_client/parser.py
+++ b/fractal_client/parser.py
@@ -14,6 +14,7 @@
 Zurich.
 """
 import argparse as ap
+from typing import Any
 
 
 parser_main = ap.ArgumentParser(
@@ -236,6 +237,49 @@
     ),
 )
 
+
+# task collect custom
+task_collect_custom_parser = task_subparsers.add_parser(
+    "collect-custom",
+    description="Collect all tasks from a custom Python interpreter.",
+    allow_abbrev=False,
+)
+task_collect_custom_parser.add_argument(
+    "source",
+    help="A common label identifying this package.",
+)
+task_collect_custom_parser.add_argument(
+    "python_interpreter",
+    help=(
+        "Absolute path to the Python interpreter to be used for running tasks."
+    ),
+)
+task_collect_custom_parser.add_argument(
+    "manifest", help="Local path of the Manifest of the Fractal task package."
+)
+task_collect_custom_parser.add_argument(
+    "--version",
+    help="Version of tasks to be collected.",
+)
+tasktask_collect_custom_pkg_name_or_root = (
+    task_collect_custom_parser.add_mutually_exclusive_group(required=True)
+)
+tasktask_collect_custom_pkg_name_or_root.add_argument(
+    "--package-name",
+    help=(
+        "Name of the package, as used in 'import <package_name>'; "
+        "this is then used to extract the package directory (package_root) "
+        "via 'importlib.util.find_spec <package_name>'."
+    ),
+)
+tasktask_collect_custom_pkg_name_or_root.add_argument(
+    "--package-root",
+    help=(
+        "The folder where the package is installed. If not provided, "
+        "it will be  automatically inferred based on 'package_name'."
+    ),
+)
+
 # task check-collection
 task_check_collection_parser = task_subparsers.add_parser(
     "check-collection",
diff --git a/poetry.lock b/poetry.lock
index d3271ceea..a1abed306 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -484,6 +484,34 @@ ssh = ["bcrypt (>=3.1.5)"]
 test = ["certifi", "pretend", "pytest (>=6.2.0)", "pytest-benchmark", "pytest-cov", "pytest-xdist"]
 test-randomorder = ["pytest-randomly"]
 
+[[package]]
+name = "decorator"
+version = "5.1.1"
+description = "Decorators for Humans"
+optional = false
+python-versions = ">=3.5"
+files = [
+    {file = "decorator-5.1.1-py3-none-any.whl", hash = "sha256:b8c3f85900b9dc423225913c5aace94729fe1fa9763b38939a95226f02d37186"},
+    {file = "decorator-5.1.1.tar.gz", hash = "sha256:637996211036b6385ef91435e4fae22989472f9d571faba8927ba8253acbc330"},
+]
+
+[[package]]
+name = "deprecated"
+version = "1.2.14"
+description = "Python @deprecated decorator to deprecate old python classes, functions or methods."
+optional = false
+python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
+files = [
+    {file = "Deprecated-1.2.14-py2.py3-none-any.whl", hash = "sha256:6fac8b097794a90302bdbb17b9b815e732d3c4720583ff1b198499d78470466c"},
+    {file = "Deprecated-1.2.14.tar.gz", hash = "sha256:e5323eb936458dccc2582dc6f9c322c852a775a27065ff2b0c4970b9d53d01b3"},
+]
+
+[package.dependencies]
+wrapt = ">=1.10,<2"
+
+[package.extras]
+dev = ["PyTest", "PyTest-Cov", "bump2version (<1)", "sphinx (<2)", "tox"]
+
 [[package]]
 name = "devtools"
 version = "0.12.2"
@@ -574,6 +602,26 @@ files = [
 [package.extras]
 tests = ["asttokens (>=2.1.0)", "coverage", "coverage-enable-subprocess", "ipython", "littleutils", "pytest", "rich"]
 
+[[package]]
+name = "fabric"
+version = "3.2.2"
+description = "High level SSH command execution"
+optional = false
+python-versions = "*"
+files = [
+    {file = "fabric-3.2.2-py3-none-any.whl", hash = "sha256:91c47c0be68b14936c88b34da8a1f55e5710fd28397dac5d4ff2e21558113a6f"},
+    {file = "fabric-3.2.2.tar.gz", hash = "sha256:8783ca42e3b0076f08b26901aac6b9d9b1f19c410074e7accfab902c184ff4a3"},
+]
+
+[package.dependencies]
+decorator = ">=5"
+deprecated = ">=1.2"
+invoke = ">=2.0"
+paramiko = ">=2.4"
+
+[package.extras]
+pytest = ["pytest (>=7)"]
+
 [[package]]
 name = "fastapi"
 version = "0.110.3"
@@ -637,7 +685,7 @@ typing = ["typing-extensions (>=4.8)"]
 
 [[package]]
 name = "fractal-server"
-version = "2.2.0"
+version = "2.3.0a0"
 description = "Server component of the Fractal analytics platform"
 optional = false
 python-versions = "^3.9"
@@ -650,6 +698,7 @@ alembic = "^1.13.1"
 bcrypt = "4.0.1"
 cloudpickle = ">=3.0.0,<3.1.0"
 clusterfutures = "^0.5"
+fabric = "^3.2.2"
 fastapi = "^0.110.0"
 fastapi-users = {version = "^12.1.0", extras = ["oauth"]}
 packaging = "^23.2"
@@ -669,7 +718,7 @@ postgres-psycopg-binary = ["psycopg[binary] (>=3.1.0,<4.0.0)"]
 type = "git"
 url = "https://github.com/fractal-analytics-platform/fractal-server.git"
 reference = "main"
-resolved_reference = "5917ea51946201b910ba25d255b29fb89a5794d0"
+resolved_reference = "d9cc7b873701581855965739555e88d5ccd70e7a"
 
 [[package]]
 name = "ghp-import"
@@ -898,6 +947,17 @@ files = [
     {file = "iniconfig-2.0.0.tar.gz", hash = "sha256:2d91e135bf72d31a410b17c16da610a82cb55f6b0477d1a902134b24a455b8b3"},
 ]
 
+[[package]]
+name = "invoke"
+version = "2.2.0"
+description = "Pythonic task execution"
+optional = false
+python-versions = ">=3.6"
+files = [
+    {file = "invoke-2.2.0-py3-none-any.whl", hash = "sha256:6ea924cc53d4f78e3d98bc436b08069a03077e6f85ad1ddaa8a116d7dad15820"},
+    {file = "invoke-2.2.0.tar.gz", hash = "sha256:ee6cbb101af1a859c7fe84f2a264c059020b0cb7fe3535f9424300ab568f6bd5"},
+]
+
 [[package]]
 name = "jinja2"
 version = "3.1.4"
@@ -1251,6 +1311,27 @@ files = [
     {file = "packaging-23.2.tar.gz", hash = "sha256:048fb0e9405036518eaaf48a55953c750c11e1a1b68e0dd1a9d62ed0c092cfc5"},
 ]
 
+[[package]]
+name = "paramiko"
+version = "3.4.0"
+description = "SSH2 protocol library"
+optional = false
+python-versions = ">=3.6"
+files = [
+    {file = "paramiko-3.4.0-py3-none-any.whl", hash = "sha256:43f0b51115a896f9c00f59618023484cb3a14b98bbceab43394a39c6739b7ee7"},
+    {file = "paramiko-3.4.0.tar.gz", hash = "sha256:aac08f26a31dc4dffd92821527d1682d99d52f9ef6851968114a8728f3c274d3"},
+]
+
+[package.dependencies]
+bcrypt = ">=3.2"
+cryptography = ">=3.3"
+pynacl = ">=1.5"
+
+[package.extras]
+all = ["gssapi (>=1.4.1)", "invoke (>=2.0)", "pyasn1 (>=0.1.7)", "pywin32 (>=2.1.8)"]
+gssapi = ["gssapi (>=1.4.1)", "pyasn1 (>=0.1.7)", "pywin32 (>=2.1.8)"]
+invoke = ["invoke (>=2.0)"]
+
 [[package]]
 name = "passlib"
 version = "1.7.4"
@@ -1495,6 +1576,32 @@ pyyaml = "*"
 [package.extras]
 extra = ["pygments (>=2.12)"]
 
+[[package]]
+name = "pynacl"
+version = "1.5.0"
+description = "Python binding to the Networking and Cryptography (NaCl) library"
+optional = false
+python-versions = ">=3.6"
+files = [
+    {file = "PyNaCl-1.5.0-cp36-abi3-macosx_10_10_universal2.whl", hash = "sha256:401002a4aaa07c9414132aaed7f6836ff98f59277a234704ff66878c2ee4a0d1"},
+    {file = "PyNaCl-1.5.0-cp36-abi3-manylinux_2_17_aarch64.manylinux2014_aarch64.manylinux_2_24_aarch64.whl", hash = "sha256:52cb72a79269189d4e0dc537556f4740f7f0a9ec41c1322598799b0bdad4ef92"},
+    {file = "PyNaCl-1.5.0-cp36-abi3-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:a36d4a9dda1f19ce6e03c9a784a2921a4b726b02e1c736600ca9c22029474394"},
+    {file = "PyNaCl-1.5.0-cp36-abi3-manylinux_2_17_x86_64.manylinux2014_x86_64.manylinux_2_24_x86_64.whl", hash = "sha256:0c84947a22519e013607c9be43706dd42513f9e6ae5d39d3613ca1e142fba44d"},
+    {file = "PyNaCl-1.5.0-cp36-abi3-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:06b8f6fa7f5de8d5d2f7573fe8c863c051225a27b61e6860fd047b1775807858"},
+    {file = "PyNaCl-1.5.0-cp36-abi3-musllinux_1_1_aarch64.whl", hash = "sha256:a422368fc821589c228f4c49438a368831cb5bbc0eab5ebe1d7fac9dded6567b"},
+    {file = "PyNaCl-1.5.0-cp36-abi3-musllinux_1_1_x86_64.whl", hash = "sha256:61f642bf2378713e2c2e1de73444a3778e5f0a38be6fee0fe532fe30060282ff"},
+    {file = "PyNaCl-1.5.0-cp36-abi3-win32.whl", hash = "sha256:e46dae94e34b085175f8abb3b0aaa7da40767865ac82c928eeb9e57e1ea8a543"},
+    {file = "PyNaCl-1.5.0-cp36-abi3-win_amd64.whl", hash = "sha256:20f42270d27e1b6a29f54032090b972d97f0a1b0948cc52392041ef7831fee93"},
+    {file = "PyNaCl-1.5.0.tar.gz", hash = "sha256:8ac7448f09ab85811607bdd21ec2464495ac8b7c66d146bf545b0f08fb9220ba"},
+]
+
+[package.dependencies]
+cffi = ">=1.4.1"
+
+[package.extras]
+docs = ["sphinx (>=1.6.5)", "sphinx-rtd-theme"]
+tests = ["hypothesis (>=3.27.0)", "pytest (>=3.2.1,!=3.3.0)"]
+
 [[package]]
 name = "pytest"
 version = "7.4.4"
@@ -1584,7 +1691,6 @@ files = [
     {file = "PyYAML-6.0.1-cp311-cp311-win_amd64.whl", hash = "sha256:bf07ee2fef7014951eeb99f56f39c9bb4af143d8aa3c21b1677805985307da34"},
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@@ -2032,6 +2138,85 @@ files = [
 [package.extras]
 watchmedo = ["PyYAML (>=3.10)"]
 
+[[package]]
+name = "wrapt"
+version = "1.16.0"
+description = "Module for decorators, wrappers and monkey patching."
+optional = false
+python-versions = ">=3.6"
+files = [
+    {file = "wrapt-1.16.0-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:ffa565331890b90056c01db69c0fe634a776f8019c143a5ae265f9c6bc4bd6d4"},
+    {file = "wrapt-1.16.0-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:e4fdb9275308292e880dcbeb12546df7f3e0f96c6b41197e0cf37d2826359020"},
+    {file = "wrapt-1.16.0-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:bb2dee3874a500de01c93d5c71415fcaef1d858370d405824783e7a8ef5db440"},
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+]
+
 [[package]]
 name = "zipp"
 version = "3.19.2"


Test patch:
diff --git a/tests/test_task.py b/tests/test_task.py
index f4e536e21..3a8cf5985 100644
--- a/tests/test_task.py
+++ b/tests/test_task.py
@@ -1,6 +1,8 @@
 import json
+import sys
 import time
 from pathlib import Path
+from urllib.request import urlopen
 from urllib.request import urlretrieve
 
 import pytest
@@ -438,3 +440,45 @@ def test_task_delete(
     res = invoke("task list")
     task_list = res.data
     assert len(task_list) == 0
+
+
+def test_task_collection_custom(register_user, tmp_path, invoke):
+    python_interpreter = sys.executable
+    package_name = "fractal-client"
+    manifest = str(tmp_path / "manifest.json")
+
+    # Download and write a valid Manifest
+    manifest_url = (
+        "https://github.com/fractal-analytics-platform/fractal-server/"
+        "raw/main/tests/v2/fractal_tasks_mock/src/fractal_tasks_mock/"
+        "__FRACTAL_MANIFEST__.json"
+    )
+    with urlopen(manifest_url) as f:
+        manifest_dict = json.loads(f.read())
+    with open(manifest, "w") as f:
+        json.dump(manifest_dict, f)
+
+    cmd = (
+        f"task collect-custom --package-name {package_name} "
+        f"source {python_interpreter} {manifest}"
+    )
+    res = invoke(cmd)
+    assert res.retcode == 0
+    assert isinstance(res.data, list)
+
+    cmd = (
+        "--batch task collect-custom --package-root /path --version 2 "
+        f"source2 {python_interpreter} {manifest}"
+    )
+    res = invoke(cmd)
+    assert res.retcode == 0
+    assert isinstance(res.data, str)
+
+    # test that '--package-root' and '--package-name' are mutually exclusive
+    cmd = (
+        "task collect-custom "
+        f"--package-root /path --package-name {package_name} "
+        f"source3 {python_interpreter} {manifest}"
+    )
+    with pytest.raises(SystemExit) as e:
+        res = invoke(cmd)