From 97d9a3486290787e1c10c67c6ef13c2087ad2f59 Mon Sep 17 00:00:00 2001 From: wd400 Date: Thu, 7 Mar 2024 16:35:58 +0100 Subject: [PATCH] Update Docker Compose files and fix code issues --- dev/scripts/reinit_db.sh | 6 +- services/base/AutoDiscServer/Dockerfile | 6 +- services/base/AutoDiscServer/flask_app/app.py | 5 +- .../experiments/experiments_handler.py | 5 +- .../systems/ExponentialMixture.py | 3 - .../libs/auto_disc/ExperimentPipeline.py | 2 + .../auto_disc/utils/expose_config/defaults.py | 2 - .../leafintegrations/expedb_locators.py | 5 +- .../tests/test_expedb_locators.py | 11 +- .../libs/debug_libs/debug.ipynb | 90 + services/base/AutoDiscServer/libs/poetry.lock | 1695 ++++++++++------- services/base/ExpeDB/API/Dockerfile | 9 +- services/base/ExpeDB/API/flask_app/app.py | 19 +- services/base/docker-compose-gpu.override.yml | 2 +- services/base/docker-compose.yml | 6 +- services/dev/sample.env | 2 +- 16 files changed, 1108 insertions(+), 760 deletions(-) create mode 100644 services/base/AutoDiscServer/libs/debug_libs/debug.ipynb diff --git a/dev/scripts/reinit_db.sh b/dev/scripts/reinit_db.sh index a727fe71..ad218465 100755 --- a/dev/scripts/reinit_db.sh +++ b/dev/scripts/reinit_db.sh @@ -1,10 +1,10 @@ #!/usr/bin/env bash echo "Removing AppDB/saved_data..." -rm -rf ../../services/AppDB/saved_data; +rm -rf ../../services/base/AppDB/saved_data; echo "Removing ExpeDB/saved_data..." -rm -rf ../../services/ExpeDB/saved_data; +rm -rf ../../services/base/ExpeDB/saved_data; echo "Removing JupyterLab/Notebooks/Experiments..." -find ../../services/JupyterLab/Notebooks/Experiments -type d ! -name '.*' -mindepth 1 -exec rm -rf {} +; +find ../../services/base/JupyterLab/Notebooks/Experiments -mindepth 1 -type d ! -name '.*' -exec rm -rf {} +; echo "Done!" diff --git a/services/base/AutoDiscServer/Dockerfile b/services/base/AutoDiscServer/Dockerfile index e0ce4a37..074bb9d8 100644 --- a/services/base/AutoDiscServer/Dockerfile +++ b/services/base/AutoDiscServer/Dockerfile @@ -41,12 +41,12 @@ RUN ln -s /etc/nginx/sites-available/flask /etc/nginx/sites-enabled/flask # AutoDiscServer dependency resolution # TODO: convert to poetry package -COPY flask_app/app.py /usr/src/services/flask_app/app.py +#COPY flask_app/app.py /usr/src/services/flask_app/app.py COPY flask_app/requirements.txt /usr/src/services/flask_app/requirements.txt RUN pip install -r /usr/src/services/flask_app/requirements.txt # stage app -COPY flask_app/ /usr/src/services/flask_app/ +#COPY flask_app/ /usr/src/services/flask_app/ # stage user custom modules in adtool_custom COPY libs/adtool_custom /usr/src/libs/adtool_custom WORKDIR /usr/src/libs @@ -55,4 +55,4 @@ RUN poetry lock; poetry install # start daemons WORKDIR /usr/src/services/flask_app -CMD gunicorn -w 4 -b 0.0.0.0:5201 app:app --access-logfile '-' --log-level 'debug' & nginx -g "daemon off;" +CMD gunicorn -w 4 -b 0.0.0.0:5201 app:app --access-logfile '-' --log-level 'debug' --reload & nginx -g "daemon off;" diff --git a/services/base/AutoDiscServer/flask_app/app.py b/services/base/AutoDiscServer/flask_app/app.py index b34abf56..db922b7d 100644 --- a/services/base/AutoDiscServer/flask_app/app.py +++ b/services/base/AutoDiscServer/flask_app/app.py @@ -46,6 +46,7 @@ def list_experiments(): return make_response(jsonify({"ID": experiment_ids}), 200) + @app.route("/experiments", methods=["POST"]) def create_experiment(): try: @@ -70,7 +71,6 @@ def stop_experiment(id): # Explorers - @app.route("/explorers", methods=["GET"]) def list_explorers(): info = get_auto_disc_registered_modules_info(get_modules("explorers")) @@ -144,4 +144,5 @@ def list_hosts(): if __name__ == "__main__": - app.run(host=config.FLASK_HOST, port=config.FLASK_PORT) + app.run(host=config.FLASK_HOST, port=config.FLASK_PORT, + debug= True, use_reloader=True) diff --git a/services/base/AutoDiscServer/flask_app/experiments/experiments_handler.py b/services/base/AutoDiscServer/flask_app/experiments/experiments_handler.py index f88aac9f..42a193f0 100644 --- a/services/base/AutoDiscServer/flask_app/experiments/experiments_handler.py +++ b/services/base/AutoDiscServer/flask_app/experiments/experiments_handler.py @@ -7,7 +7,7 @@ from utils import AutoDiscServerConfig, CheckpointsStatusEnum, reconstruct_parameters from utils.DB import AppDBCaller, AppDBMethods from utils.experiment_status_enum import ExperimentStatusEnum - +import sys class ExperimentsHandler: def __init__(self): @@ -27,6 +27,7 @@ def _get_experiment(self, id): iter(filter(lambda element: element.id == id, self._experiments)), None ) if experiment is None: + print("experiments", self._experiments, file=sys.stderr) raise Exception("Unknown experiment ID !") return experiment @@ -56,6 +57,7 @@ def _create_experiment(self, id, parameters): ) # Add it in the list + self._experiments.append(experiment) return experiment @@ -114,7 +116,6 @@ def add_experiment(self, parameters): try: # Add experiment in DB and obtain the id exp_date = datetime.datetime.now().strftime("%Y-%m-%d %H:%M %Z") - print("Before response") request = { "name": parameters["experiment"]["name"], "created_on": exp_date, diff --git a/services/base/AutoDiscServer/libs/adtool_default/systems/ExponentialMixture.py b/services/base/AutoDiscServer/libs/adtool_default/systems/ExponentialMixture.py index 2815226d..3b018a8d 100644 --- a/services/base/AutoDiscServer/libs/adtool_default/systems/ExponentialMixture.py +++ b/services/base/AutoDiscServer/libs/adtool_default/systems/ExponentialMixture.py @@ -90,9 +90,6 @@ def test(): assert len(ExponentialMixture.CONFIG_DEFINITION) > 0 -print("ExponentialMixture", ExponentialMixture, file=sys.stderr) if __name__ == "__main__": test() - -print("ExponentialMixture.CONFIG_DEFINITION", ExponentialMixture.CONFIG_DEFINITION, file=sys.stderr) \ No newline at end of file diff --git a/services/base/AutoDiscServer/libs/auto_disc/ExperimentPipeline.py b/services/base/AutoDiscServer/libs/auto_disc/ExperimentPipeline.py index d49dd8c4..21a1e370 100644 --- a/services/base/AutoDiscServer/libs/auto_disc/ExperimentPipeline.py +++ b/services/base/AutoDiscServer/libs/auto_disc/ExperimentPipeline.py @@ -199,8 +199,10 @@ def run(self, n_exploration_runs: int): run_idx_start_from_one % self.save_frequency == 0 or run_idx_start_from_one == n_exploration_runs ): + print("############ saving", self.resource_uri) self.save(resource_uri=self.resource_uri) + self.run_idx += 1 except Exception: diff --git a/services/base/AutoDiscServer/libs/auto_disc/auto_disc/utils/expose_config/defaults.py b/services/base/AutoDiscServer/libs/auto_disc/auto_disc/utils/expose_config/defaults.py index f5c1802c..a7924ead 100644 --- a/services/base/AutoDiscServer/libs/auto_disc/auto_disc/utils/expose_config/defaults.py +++ b/services/base/AutoDiscServer/libs/auto_disc/auto_disc/utils/expose_config/defaults.py @@ -84,9 +84,7 @@ def _dataclass_to_config_dict(cls) -> Dict: # inner function to recurse through the dataclass def recurse(dc: type, parent: str): - print("dc", dc, file=sys.stderr) for k, v in dc.__dataclass_fields__.items(): - print("kv", k, v, file=sys.stderr) # unwrap from the Field object unwrap_v = v.default diff --git a/services/base/AutoDiscServer/libs/auto_disc/utils/leafutils/leafintegrations/expedb_locators.py b/services/base/AutoDiscServer/libs/auto_disc/utils/leafutils/leafintegrations/expedb_locators.py index c1c05b1a..03864152 100644 --- a/services/base/AutoDiscServer/libs/auto_disc/utils/leafutils/leafintegrations/expedb_locators.py +++ b/services/base/AutoDiscServer/libs/auto_disc/utils/leafutils/leafintegrations/expedb_locators.py @@ -16,14 +16,14 @@ def _initialize_checkpoint(entrypoint: str, dict: Dict = {}) -> str: """ Inserts a Mongo document and retrieves the unique key generated """ - response = json.loads(requests.post(entrypoint, json=dict).content) + response = requests.post(entrypoint, json=dict).json() return response["ID"] def _query_uid(resource_uri: str, uid: LeafUID) -> List[Dict]: uid_filter = {"uid": uid} uid_filter = _format_filter_from_dict(uid_filter) - response = json.loads(requests.get(resource_uri + "?filter=" + uid_filter).content) + response = requests.get(resource_uri + "?filter=" + uid_filter).json() return response @@ -102,6 +102,7 @@ def retrieve(self, uid: "LeafUID", *args, **kwargs) -> bytes: def _retrieve_mongo_id(self, uid: LeafUID) -> str: response = _query_uid(self.resource_uri, uid) + print('_retrieve_mongo_id response', response) if len(response) == 0: mongo_id = _initialize_checkpoint(self.resource_uri) elif len(response) == 1: diff --git a/services/base/AutoDiscServer/libs/auto_disc/utils/leafutils/leafintegrations/tests/test_expedb_locators.py b/services/base/AutoDiscServer/libs/auto_disc/utils/leafutils/leafintegrations/tests/test_expedb_locators.py index 2eccd60f..cd0b96c0 100644 --- a/services/base/AutoDiscServer/libs/auto_disc/utils/leafutils/leafintegrations/tests/test_expedb_locators.py +++ b/services/base/AutoDiscServer/libs/auto_disc/utils/leafutils/leafintegrations/tests/test_expedb_locators.py @@ -59,14 +59,21 @@ def mock_checkpoint(): def test_ExpeDBLocator_store(): - bin = b"123" + bin = b"123 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA" loc = ExpeDBLocator(resource_uri=RESOURCE_URI) + print('loc', loc) uid = loc.store(bin) + print('uid', uid) # test by making a manual API call mongo_id = loc._retrieve_mongo_id(uid) + print('mongo_id', mongo_id) response_bin = requests.get(RESOURCE_URI + "/" + mongo_id + "/metadata").content + response_bin = codecs.decode(response_bin, encoding="base64") + + print('response_bin', response_bin) + assert response_bin == bin # TODO: test that duplicate inserts result in update @@ -79,6 +86,8 @@ def test_ExpeDBLocator_retrieve(): retrieved_bin = loc.retrieve(uid) + print("retrieved_bin", retrieved_bin) + assert bin == retrieved_bin diff --git a/services/base/AutoDiscServer/libs/debug_libs/debug.ipynb b/services/base/AutoDiscServer/libs/debug_libs/debug.ipynb new file mode 100644 index 00000000..7da2e903 --- /dev/null +++ b/services/base/AutoDiscServer/libs/debug_libs/debug.ipynb @@ -0,0 +1,90 @@ +{ + "cells": [ + { + "cell_type": "code", + "execution_count": 2, + "metadata": {}, + "outputs": [], + "source": [ + "import sys\n", + "\n", + "sys.path.append('..')" + ] + }, + { + "cell_type": "code", + "execution_count": 5, + "metadata": {}, + "outputs": [], + "source": [ + "import adtool_default" + ] + }, + { + "cell_type": "code", + "execution_count": 11, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Traceback (most recent call last):\n", + " File \"\", line 198, in _run_module_as_main\n", + " File \"\", line 88, in _run_code\n", + " File \"/home/flowers-user/anaconda3/envs/adtool/lib/python3.11/unittest/__main__.py\", line 18, in \n", + " main(module=None)\n", + " File \"/home/flowers-user/anaconda3/envs/adtool/lib/python3.11/unittest/main.py\", line 101, in __init__\n", + " self.parseArgs(argv)\n", + " File \"/home/flowers-user/anaconda3/envs/adtool/lib/python3.11/unittest/main.py\", line 150, in parseArgs\n", + " self.createTests()\n", + " File \"/home/flowers-user/anaconda3/envs/adtool/lib/python3.11/unittest/main.py\", line 161, in createTests\n", + " self.test = self.testLoader.loadTestsFromNames(self.testNames,\n", + " ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n", + " File \"/home/flowers-user/anaconda3/envs/adtool/lib/python3.11/unittest/loader.py\", line 232, in loadTestsFromNames\n", + " suites = [self.loadTestsFromName(name, module) for name in names]\n", + " ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n", + " File \"/home/flowers-user/anaconda3/envs/adtool/lib/python3.11/unittest/loader.py\", line 232, in \n", + " suites = [self.loadTestsFromName(name, module) for name in names]\n", + " ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n", + " File \"/home/flowers-user/anaconda3/envs/adtool/lib/python3.11/unittest/loader.py\", line 162, in loadTestsFromName\n", + " module = __import__(module_name)\n", + " ^^^^^^^^^^^^^^^^^^^^^^^\n", + "ValueError: Empty module name\n" + ] + } + ], + "source": [ + "!python3 -m unittest ." + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [] + } + ], + "metadata": { + "kernelspec": { + "display_name": "adtool", + "language": "python", + "name": "python3" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.11.8" + } + }, + "nbformat": 4, + "nbformat_minor": 2 +} diff --git a/services/base/AutoDiscServer/libs/poetry.lock b/services/base/AutoDiscServer/libs/poetry.lock index c997f045..24dfb19b 100644 --- a/services/base/AutoDiscServer/libs/poetry.lock +++ b/services/base/AutoDiscServer/libs/poetry.lock @@ -1,9 +1,10 @@ -# This file is automatically @generated by Poetry 1.5.1 and should not be changed by hand. +# This file is automatically @generated by Poetry 1.4.0 and should not be changed by hand. 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install -y curl procps vim # placed here to allowed efficient caching of src changes # TODO: actually need to put app.py here for efficient caching -COPY ./flask_app/ /usr/src/services/flask_app/ +#COPY ./flask_app/ /usr/src/services/flask_app/ +#COPY ./flask_app/app.py /usr/src/services/flask_app/app.py # start daemons -VOLUME ["/usr/src/services"] +# VOLUME ["/usr/src/services"] WORKDIR /usr/src/services/flask_app -CMD gunicorn -w 4 -b 0.0.0.0:8000 app:app --access-logfile '-' --log-level 'debug' & nginx -g "daemon off;" \ No newline at end of file +CMD gunicorn -w 4 -b 0.0.0.0:8000 app:app --access-logfile '-' --log-level 'debug' \ + --reload & nginx -g "daemon off;" \ No newline at end of file diff --git a/services/base/ExpeDB/API/flask_app/app.py b/services/base/ExpeDB/API/flask_app/app.py index 14a2d7ca..9b4ff087 100644 --- a/services/base/ExpeDB/API/flask_app/app.py +++ b/services/base/ExpeDB/API/flask_app/app.py @@ -7,6 +7,9 @@ from pymongo import MongoClient from utils import ExpeDBConfig + +import sys + config = ExpeDBConfig() app = Flask(__name__) CORS(app) @@ -67,7 +70,8 @@ def _get_file_from_document(document, filename, _filename: str = ""): return make_response(error_msg, 403) else: try: - file = fs.get(ObjectId(document[filename])) + print("filename", filename, file=sys.stderr) + file = fs.get(document[filename]) except: # if can't find file, try to follow pointer one level new_filename = str(document[filename]) @@ -373,9 +377,16 @@ def delete_data_saves(): else: return make_response("You must provide a " "data_id in the request args", 403) - # endregion - + if __name__ == "__main__": - app.run(host=config.FLASK_HOST, port=config.FLASK_PORT) + app.run(host=config.FLASK_HOST, port=config.FLASK_PORT, debug=True, use_reloader=True, extra_files=[ + +"/usr/src/libs/auto_disc/utils/leafutils/leafintegrations/", +"/usr/src/libs/auto_disc/utils/leafutils/", +"/usr/src/libs/auto_disc/utils/", +"/usr/src/libs/auto_disc/", +"/usr/src/libs/", + ]) + diff --git a/services/base/docker-compose-gpu.override.yml b/services/base/docker-compose-gpu.override.yml index 28e96bbe..edd3d169 100644 --- a/services/base/docker-compose-gpu.override.yml +++ b/services/base/docker-compose-gpu.override.yml @@ -1,6 +1,6 @@ # docker-compose.yml # THIS FILE MERGES AN OVERRIDE WHICH ENABLES GPU -version: "3" # TODO +version: "3" services: autodisc-server: deploy: diff --git a/services/base/docker-compose.yml b/services/base/docker-compose.yml index b4b97fa2..e0f458be 100644 --- a/services/base/docker-compose.yml +++ b/services/base/docker-compose.yml @@ -1,5 +1,5 @@ # docker-compose.yml -version: "3.7" # TODO +version: "3.7" services: ##### FRONTEND APP ##### app: @@ -78,7 +78,7 @@ services: MONGODB_HOST: expe-db MONGODB_PORT: 27017 volumes: - - "./ExpeDB/API/flask_app:/usr/src/flask_app" + - "./ExpeDB/API/flask_app:/usr/src/services/flask_app" depends_on: - expe-db ##### AUTODISC SERVER ##### @@ -112,7 +112,7 @@ services: environment: EXPEDB_CALLER_HOST: ${EXPE_DB_API_HOST-expe-db-api} EXPEDB_CALLER_PORT: ${EXPE_DB_API_PORT-80} - PYTHONPATH: "/usr/src/auto_disc_db" + PYTHONPATH: "/usr/src/" volumes: - "./JupyterLab/Notebooks:/usr/src/notebooks" - "../base/AutoDiscServer/libs/auto_disc_db:/usr/src/auto_disc_db" diff --git a/services/dev/sample.env b/services/dev/sample.env index 8fafab70..330fecb9 100644 --- a/services/dev/sample.env +++ b/services/dev/sample.env @@ -26,7 +26,7 @@ PGADMIN_DEFAULT_PASSWORD=autodisc EXPOSED_APP_DB_PORT=5432 EXPOSED_APP_DB_API_PORT=8000 EXPOSED_EXPE_DB_PORT=27017 -EXPOSED_EXPE_DB_API_PORT=8001 +EXPOSED_EXPE_DB_API_PORT=5001 EXPOSED_AUTODISC_SERVER_PORT=8002 DOZZLE_PORT=8080 PGADMIN_PORT=5050