From 8b176108a3c15cabc93dbfbaeb3cc7e5e6d510d4 Mon Sep 17 00:00:00 2001 From: cmdoret Date: Wed, 25 Sep 2024 15:59:54 +0200 Subject: [PATCH 01/39] feat: code matching client --- modos/codes.py | 60 ++++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 60 insertions(+) create mode 100644 modos/codes.py diff --git a/modos/codes.py b/modos/codes.py new file mode 100644 index 00000000..be58d446 --- /dev/null +++ b/modos/codes.py @@ -0,0 +1,60 @@ +"""Utilities to automatically find / recommend terminology codes from text.""" +import requests +from typing import Optional, Protocol + + +SLOT_TERMINOLOGIES = { + "cell_type": "https://purl.obolibrary.org/obo/cl.owl", + "source_material": "https://purl.obolibrary.org/obo/uberon.owl", + "taxid": "https://purl.obolibrary.org/obo/ncbitaxon/subsets/taxslim.owl", +} + + +class CodeMatcher(Protocol): + def find_codes(self, query: str) -> list[str]: + ... + + +class LocalCodeMatcher(CodeMatcher): + """Find ontology codes for a given text by running a local term matcher.""" + + def __init__(self, slot: str): + self.slot = slot + try: + from pyfuzon import TermMatcher + + self.matcher = TermMatcher.from_files([SLOT_TERMINOLOGIES[slot]]) + except ImportError: + raise ValueError( + """No endpoint provided and pyfuzon not installed, + cannot do code matching.""" + ) + + def find_codes(self, query: str) -> list[str]: + return self.matcher.rank(query) + + +class RemoteCodeMatcher(CodeMatcher): + """Find ontology codes for a given text relying on a remote term matcher.""" + + def __init__(self, slot: str, endpoint: str): + self.endpoint = endpoint + self.slot = slot + + def find_codes(self, query: str) -> list[str]: + return requests.get( + f"{self.endpoint}?collection={self.slot}?query={query}" + ).json()["codes"] + + +def get_slot_matchers( + endpoint: Optional[str] = None, +) -> dict[str, CodeMatcher]: + """Instantiates a code matcher for each slot. If the endpoint is provided, remote matchers are used.""" + matchers = {} + for slot in SLOT_TERMINOLOGIES.keys(): + if endpoint: + matchers[slot] = RemoteCodeMatcher(slot, endpoint) + else: + matchers[slot] = LocalCodeMatcher(slot) + return matchers From 42d8635d660881e01ad673a4efe1a90e80298c57 Mon Sep 17 00:00:00 2001 From: cmdoret Date: Wed, 25 Sep 2024 16:00:23 +0200 Subject: [PATCH 02/39] feat(remote): register fuzon endpoint in client --- modos/remote.py | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/modos/remote.py b/modos/remote.py index e6cc6c6e..92c0c92d 100644 --- a/modos/remote.py +++ b/modos/remote.py @@ -54,6 +54,10 @@ def list(self) -> dict[str, HttpUrl]: def s3(self) -> Optional[HttpUrl]: return self.list().get("s3") + @property + def fuzon(self) -> Optional[HttpUrl]: + return self.list().get("fuzon") + @property def htsget(self) -> Optional[HttpUrl]: return self.list().get("htsget") From 48cd565824bf12b1ac60d239c7825971a1c1ce19 Mon Sep 17 00:00:00 2001 From: cmdoret Date: Wed, 25 Sep 2024 16:00:59 +0200 Subject: [PATCH 03/39] refactor(cli): prompt logic to dedicated prompt module --- modos/cli.py | 103 +++++++-------------------------------------------- 1 file changed, 13 insertions(+), 90 deletions(-) diff --git a/modos/cli.py b/modos/cli.py index 0bab9a8f..3bcb9ed1 100644 --- a/modos/cli.py +++ b/modos/cli.py @@ -2,35 +2,28 @@ # Use typer for CLI -from datetime import date from enum import Enum import os from pathlib import Path from typing import Any, List, Mapping, Optional from typing_extensions import Annotated -import click from linkml_runtime.loaders import json_loader import modos_schema.datamodel as model -from pydantic import validate_call, HttpUrl +from pydantic import HttpUrl import sys import typer from types import SimpleNamespace import zarr from .api import MODO -from .helpers.schema import ( - UserElementType, - get_enum_values, - get_slots, - get_slot_range, - load_schema, -) +from .helpers.schema import UserElementType from . import __version__ from .genomics.htsget import HtsgetConnection from .genomics.region import Region from .io import parse_instance +from .prompt import SlotPrompter from .remote import EndpointManager from .storage import connect_s3 @@ -54,75 +47,6 @@ class RdfFormat(str, Enum): ] -def prompt_for_slot(slot_name: str, prefix: str = "", optional: bool = False): - """Prompt for a slot value.""" - slot_range = get_slot_range(slot_name) - choices, default = None, None - if slot_range == "datetime": - default = date.today() - elif load_schema().get_enum(slot_range): - choices = click.Choice(get_enum_values(slot_range)) - elif optional: - default = "" - - output = typer.prompt( - f"{prefix}Enter a value for {slot_name}", default=default, type=choices - ) - if output == "": - output = None - - return output - - -def prompt_for_slots( - target_class: type, - exclude: Optional[Mapping[str, List]] = None, - # add dict with exclude -) -> dict[str, Any]: - """Prompt the user to provide values for the slots of input class. - values of required fields can be excluded to repeat the prompt. - - Parameters - ---------- - target_class - Class to build - exclude - Mapping with the name of a slot as key and list of invalid entries as values. - """ - - entries = {} - required_slots = set(get_slots(target_class, required_only=True)) - optional_slots = ( - set(get_slots(target_class, required_only=False)) - required_slots - ) - - # Always require identifiers if possible - if "id" in optional_slots: - optional_slots.remove("id") - required_slots.add("id") - - for slot_name in required_slots: - entries[slot_name] = prompt_for_slot(slot_name, prefix="(required) ") - if entries[slot_name] is None: - raise ValueError(f"Missing required slot: {slot_name}") - if exclude and entries.get(slot_name) in exclude.get(slot_name, []): - print( - f"Invalid value: {slot_name} must differ from {exclude[slot_name]}." - ) - entries[slot_name] = prompt_for_slot( - slot_name, prefix="(required) " - ) - - if optional_slots: - for slot_name in optional_slots: - entries[slot_name] = prompt_for_slot( - slot_name, - prefix="(optional) ", - optional=True, - ) - return entries - - # Create command @cli.command() def create( @@ -148,11 +72,11 @@ def create( """Create a modo interactively or from a file.""" typer.echo("Creating a digital object.", err=True) - endpoint = ctx.obj.endpoint + endpoint = EndpointManager(ctx.obj.endpoint) + # Initialize object's directory - if endpoint: - s3 = EndpointManager(endpoint).s3 - fs = connect_s3(s3, {"anon": True}) # type: ignore + if endpoint.s3: + fs = connect_s3(endpoint.s3, {"anon": True}) # type: ignore if fs.exists(object_path): raise ValueError(f"Remote directory already exists: {object_path}") elif Path(object_path).exists(): @@ -162,17 +86,17 @@ def create( if from_file and meta: raise ValueError("Only one of --from-file or --data can be used.") elif from_file: - _ = MODO.from_file(from_file, object_path, endpoint=endpoint) + _ = MODO.from_file(from_file, object_path, endpoint=endpoint.modos) return elif meta: obj = json_loader.loads(meta, target_class=model.MODO) else: - filled = prompt_for_slots(model.MODO) + filled = SlotPrompter(endpoint).prompt_for_slots(model.MODO) obj = model.MODO(**filled) attrs = obj.__dict__ # Dump object to zarr metadata - MODO(path=object_path, endpoint=endpoint, **attrs) + MODO(path=object_path, endpoint=endpoint.modos, **attrs) @cli.command() @@ -366,16 +290,15 @@ def stream( # NOTE: bucket is not included in htsget paths source = Path(*Path(file_path.removeprefix("s3://")).parts[1:]) - endpoint = ctx.obj.endpoint + endpoint = EndpointManager(ctx.obj.endpoint) if not endpoint: raise ValueError("Streaming requires a remote endpoint.") - htsget_endpoint = EndpointManager(endpoint).htsget # type: ignore - if not htsget_endpoint: + if not endpoint.htsget: raise ValueError("No htsget service found.") - con = HtsgetConnection(htsget_endpoint, source, _region) + con = HtsgetConnection(endpoint.htsget, source, _region) with con.open() as f: for chunk in f: sys.stdout.buffer.write(chunk) From b90072d1dea00d500ffa5c05bf71340b4e87b223 Mon Sep 17 00:00:00 2001 From: cmdoret Date: Wed, 25 Sep 2024 16:01:24 +0200 Subject: [PATCH 04/39] refactor(cli): prompt logic to dedicated prompt module --- modos/prompt.py | 109 ++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 109 insertions(+) create mode 100644 modos/prompt.py diff --git a/modos/prompt.py b/modos/prompt.py new file mode 100644 index 00000000..c872c257 --- /dev/null +++ b/modos/prompt.py @@ -0,0 +1,109 @@ +from datetime import date +from typing import Any, List, Mapping, Optional + +import click +from prompt_toolkit import prompt +from prompt_toolkit.completion import Completer, Completion +import typer + +from .codes import CodeMatcher, get_slot_matchers +from .helpers.schema import ( + get_enum_values, + get_slots, + get_slot_range, + load_schema, +) +from .remote import EndpointManager + + +class SlotCodeCompleter(Completer): + def __init__(self, matcher: CodeMatcher): + self.matcher = matcher + + def get_completions(self, document, complete_event): + self.matcher.find_codes(document.text) + + for rec in self.matcher.find_codes(document.text): + yield Completion(rec, start_position=-document.cursor_position) + + +def fuzzy_complete(matcher: CodeMatcher): + result = prompt( + "> ", completer=SlotCodeCompleter(matcher), complete_while_typing=True + ) + return result + + +class SlotPrompter: + def __init__(self, endpoint: Optional[EndpointManager] = None): + self.slot_matchers = get_slot_matchers(endpoint.fuzon) + + def prompt_for_slot(self, slot_name: str, optional: bool = False): + slot_range = get_slot_range(slot_name) + choices, default = None, None + if slot_range == "datetime": + default = date.today() + elif load_schema().get_enum(slot_range): + choices = click.Choice(get_enum_values(slot_range)) + elif optional: + default = "" + + prefix = "(optional) " if optional else "(required) " + + if slot_name in self.slot_matchers: + output = fuzzy_complete(self.slot_matchers[slot_name]) + else: + output = typer.prompt( + f"{prefix}Enter a value for {slot_name}", + default=default, + type=choices, + ) + + if output == "": + output = None + + return output + + def prompt_for_slots( + self, target_class: type, exclude: Optional[Mapping[str, List]] = None + ) -> dict[str, Any]: + """Prompt the user to provide values for the slots of input class. + values of required fields can be excluded to repeat the prompt. + + Parameters + ---------- + target_class + Class to build + exclude + Mapping with the name of a slot as key and list of invalid entries as values. + """ + + entries = {} + required_slots = set(get_slots(target_class, required_only=True)) + optional_slots = ( + set(get_slots(target_class, required_only=False)) - required_slots + ) + + # Always require identifiers if possible + if "id" in optional_slots: + optional_slots.remove("id") + required_slots.add("id") + + for slot_name in required_slots: + entries[slot_name] = self.prompt_for_slot(slot_name) + if entries[slot_name] is None: + raise ValueError(f"Missing required slot: {slot_name}") + if exclude and entries.get(slot_name) in exclude.get( + slot_name, [] + ): + print( + f"Invalid value: {slot_name} must differ from {exclude[slot_name]}." + ) + entries[slot_name] = self.prompt_for_slot(slot_name) + + if optional_slots: + for slot_name in optional_slots: + entries[slot_name] = self.prompt_for_slot( + slot_name, optional=True + ) + return entries From 5c93ea485b78f2e4908127c09ffb8fa8a15c02a0 Mon Sep 17 00:00:00 2001 From: cmdoret Date: Wed, 25 Sep 2024 16:01:42 +0200 Subject: [PATCH 05/39] chore(deps): pyfuzon as extra dep --- poetry.lock | 2112 +++++++++++++++++++++++++----------------------- pyproject.toml | 5 + 2 files changed, 1117 insertions(+), 1000 deletions(-) diff --git a/poetry.lock b/poetry.lock index feb9a102..d55bc2f2 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json_loader.loads(element, target_class=target_class) else: exclude = {"id": [Path(id).name for id in modo.metadata.keys()]} - filled = prompt_for_slots(target_class, exclude) + filled = SlotPrompter(endpoint).prompt_for_slots(target_class, exclude) obj = target_class(**filled) modo.add_element(obj, source_file=source_file, part_of=parent) From 8d59c3e279ee8e8b2260826ac017fa79b7128922 Mon Sep 17 00:00:00 2001 From: cmdoret Date: Wed, 25 Sep 2024 18:30:19 +0200 Subject: [PATCH 08/39] perf(codes): limit suggestions to 50 codes --- modos/codes.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/modos/codes.py b/modos/codes.py index be58d446..9da3b84d 100644 --- a/modos/codes.py +++ b/modos/codes.py @@ -6,7 +6,7 @@ SLOT_TERMINOLOGIES = { "cell_type": "https://purl.obolibrary.org/obo/cl.owl", "source_material": "https://purl.obolibrary.org/obo/uberon.owl", - "taxid": "https://purl.obolibrary.org/obo/ncbitaxon/subsets/taxslim.owl", + "taxon_id": 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CodeMatcher): From 37f5150dc084e4b0c3ffccde746085defa176709 Mon Sep 17 00:00:00 2001 From: cmdoret Date: Wed, 25 Sep 2024 18:34:44 +0200 Subject: [PATCH 10/39] refactor(codes): custom Code struct --- modos/codes.py | 16 ++++++++++++---- 1 file changed, 12 insertions(+), 4 deletions(-) diff --git a/modos/codes.py b/modos/codes.py index 9da3b84d..78003d21 100644 --- a/modos/codes.py +++ b/modos/codes.py @@ -1,4 +1,5 @@ """Utilities to automatically find / recommend terminology codes from text.""" +from dataclasses import dataclass import requests from typing import Optional, Protocol @@ -10,8 +11,14 @@ } +@dataclass +class Code: + label: str + uri: str + + class CodeMatcher(Protocol): - def find_codes(self, query: str) -> list[str]: + def find_codes(self, query: str) -> list[Code]: ... @@ -30,7 +37,7 @@ def __init__(self, slot: str): cannot do code matching.""" ) - def find_codes(self, query: str) -> list[str]: + def find_codes(self, query: str) -> list[Code]: return 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prompt autocompletes text, persists uris --- modos/prompt.py | 35 +++++++++++++++++++++++++++-------- 1 file changed, 27 insertions(+), 8 deletions(-) diff --git a/modos/prompt.py b/modos/prompt.py index c3fce455..5097224c 100644 --- a/modos/prompt.py +++ b/modos/prompt.py @@ -1,4 +1,5 @@ from datetime import date +import re from typing import Any, List, Mapping, Optional import click @@ -17,6 +18,8 @@ class SlotCodeCompleter(Completer): + """Auto-suggestions for terminology codes.""" + def __init__(self, matcher: CodeMatcher): self.matcher = matcher @@ -25,20 +28,36 @@ def get_completions(self, document, complete_event): for rec in self.matcher.find_codes(document.text): yield Completion( - rec.label, start_position=-document.cursor_position + f"{rec.label} {rec.uri}", + start_position=-document.cursor_position, ) -def fuzzy_complete(matcher: CodeMatcher): +def fuzzy_complete(prompt_txt: str, matcher: CodeMatcher): + """Given a pre-configured matcher, prompt the user with live auto-suggestions.""" result = prompt( - "> ", completer=SlotCodeCompleter(matcher), complete_while_typing=True + f"{prompt_txt}: ", + completer=SlotCodeCompleter(matcher), + complete_while_typing=True, ) + + # If the user selected a suggestion with a URI, return that URI. + if match := re.match(r".* <(http[^>]*)>$", result): + uri = match.groups()[0] + return uri return result class SlotPrompter: - def __init__(self, endpoint: Optional[EndpointManager] = None): - self.slot_matchers = get_slot_matchers(endpoint.fuzon) + """Introspects the schema to prompt the user for values based on input class/slot.""" + + def __init__( + self, endpoint: Optional[EndpointManager] = None, suggest=True + ): + if suggest: + self.slot_matchers = get_slot_matchers(endpoint.fuzon) + else: + self.slot_matchers = {} def prompt_for_slot(self, slot_name: str, optional: bool = False): slot_range = get_slot_range(slot_name) @@ -51,12 +70,12 @@ def prompt_for_slot(self, slot_name: str, optional: bool = False): default = "" prefix = "(optional) " if optional else "(required) " - + prompt = f"{prefix}Enter a value for {slot_name}" if slot_name in self.slot_matchers: - output = fuzzy_complete(self.slot_matchers[slot_name]) + output = fuzzy_complete(prompt, self.slot_matchers[slot_name]) else: output = typer.prompt( - f"{prefix}Enter a value for {slot_name}", + prompt, default=default, type=choices, ) From 49a2ad6f61c28aa01d83f0f138b30e3047acc0dc Mon Sep 17 00:00:00 2001 From: cmdoret Date: Tue, 1 Oct 2024 15:13:06 +0200 Subject: [PATCH 13/39] fix(cli): disable unnecessary autocomplete on modos create --- modos/cli.py | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/modos/cli.py b/modos/cli.py index ac7822a7..ba42e06d 100644 --- a/modos/cli.py +++ b/modos/cli.py @@ -91,7 +91,9 @@ def create( elif meta: obj = json_loader.loads(meta, target_class=model.MODO) else: - filled = SlotPrompter(endpoint).prompt_for_slots(model.MODO) + filled = SlotPrompter(endpoint, suggest=False).prompt_for_slots( + model.MODO + ) obj = model.MODO(**filled) attrs = obj.__dict__ From 216916502cc255d0f9ad7f6b69275c53b10477c6 Mon Sep 17 00:00:00 2001 From: cmdoret Date: Tue, 1 Oct 2024 15:25:59 +0200 Subject: [PATCH 14/39] test(data): use uris when required --- data/ex/data.zarr/.zmetadata | 8 ++++---- data/ex/data.zarr/sample/sample1/.zattrs | 4 ++-- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/data/ex/data.zarr/.zmetadata b/data/ex/data.zarr/.zmetadata index d16e74d8..6c697b57 100644 --- a/data/ex/data.zarr/.zmetadata +++ b/data/ex/data.zarr/.zmetadata @@ -61,10 +61,10 @@ "data_path": "demo1.cram", "description": "Dummy data for tests", "has_reference": [ - "reference1" + "reference/reference1" ], "has_sample": [ - "sample1" + "sample/sample1" ], "name": "Demo 1" }, @@ -88,11 +88,11 @@ }, "sample/sample1/.zattrs": { "@type": "Sample", - "cell_type": "astrocyte", + "cell_type": "http://purl.obolibrary.org/obo/CL_0002627", "description": "Dummy sample for tests", "name": "Sample 1", "sex": "Male", - "source_material": "brain tissue" + "source_material": "http://purl.obolibrary.org/obo/UBERON_0002316" }, "sample/sample1/.zgroup": { "zarr_format": 2 diff --git a/data/ex/data.zarr/sample/sample1/.zattrs b/data/ex/data.zarr/sample/sample1/.zattrs index 3f93a630..933542a7 100644 --- a/data/ex/data.zarr/sample/sample1/.zattrs +++ b/data/ex/data.zarr/sample/sample1/.zattrs @@ -1,8 +1,8 @@ { "@type": "Sample", - "cell_type": "astrocyte", + "cell_type": "http://purl.obolibrary.org/obo/CL_0002627", "description": "Dummy sample for tests", "name": "Sample 1", "sex": "Male", - "source_material": "brain tissue" + "source_material": "http://purl.obolibrary.org/obo/UBERON_0002316" } From 53dbc849f631d40bfdd2f4563d12356dc9c8bf50 Mon Sep 17 00:00:00 2001 From: cmdoret Date: Tue, 1 Oct 2024 16:39:23 +0200 Subject: [PATCH 15/39] fix(codes): fuzon-http api parameters --- modos/codes.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modos/codes.py b/modos/codes.py index 78003d21..91e6699c 100644 --- a/modos/codes.py +++ b/modos/codes.py @@ -50,7 +50,7 @@ def __init__(self, slot: str, endpoint: str): def find_codes(self, query: str) -> list[Code]: codes = requests.get( - f"{self.endpoint}?collection={self.slot}?query={query}" + f"{self.endpoint}/top?collection={self.slot}&query={query}&top=50" ).json()["codes"] return [Code(label=code["label"], uri=code["uri"]) for code in codes] From ab0a807532f1de374fe7cdc8df78c5953626056f Mon Sep 17 00:00:00 2001 From: cmdoret Date: Wed, 2 Oct 2024 13:52:12 +0200 Subject: [PATCH 16/39] chore(make): document deploy recipe --- Makefile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Makefile b/Makefile index 5f6a0601..686ecf8c 100644 --- a/Makefile +++ b/Makefile @@ -36,7 +36,7 @@ test: ## Test the code with pytest @poetry run pytest .PHONY: deploy -deploy: +deploy: ## Deploy services using docker compose @echo "$(LOCAL_IP)";exit 0 @echo "🐋 Deploying server with docker compose" cd deploy; S3_PUBLC_URL="http://$(LOCAL_IP):9000" docker compose up --build --force-recreate From 2ab52c7589e15ab85fe708f35885a0c94649048b Mon Sep 17 00:00:00 2001 From: cmdoret Date: Wed, 2 Oct 2024 13:52:45 +0200 Subject: [PATCH 17/39] feat(compose): add fuzon service --- deploy/docker-compose.yml | 10 ++++++++++ 1 file changed, 10 insertions(+) diff --git a/deploy/docker-compose.yml b/deploy/docker-compose.yml index 771a3531..29cbbe8c 100644 --- a/deploy/docker-compose.yml +++ b/deploy/docker-compose.yml @@ -64,6 +64,16 @@ services: - RUST_LOG=debug + fuzon: + build: ./fuzon + volumes: + - ./fuzon/config.json.template:/fuzon/config.json.template:ro + expose: + - "8080" # ticket server + networks: + - modos-network + + modos-server: build: ./modos-server expose: From 85e3ea5b8d9ca9855b9ca00a2681b7fa666d3440 Mon Sep 17 00:00:00 2001 From: cmdoret Date: Wed, 2 Oct 2024 13:53:11 +0200 Subject: [PATCH 18/39] feat(nginx): register fuzon in reverse proxy --- deploy/nginx/default.conf.template | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/deploy/nginx/default.conf.template b/deploy/nginx/default.conf.template index 67609a67..e1bd4cbf 100644 --- a/deploy/nginx/default.conf.template +++ b/deploy/nginx/default.conf.template @@ -15,6 +15,7 @@ server { "status": "success", "s3": "${S3_PUBLIC_URL}", "htsget": "${HTSGET_PUBLIC_URL}" + "fuzon": "${FUZON_PUBLIC_URL}" }' ; } # S3 bucket service @@ -41,4 +42,9 @@ server { location / { proxy_pass ${MODOS_LOCAL_URL} ; } + # terminology code matching server + location /fuzon { + rewrite ^/fuzon/(.*) /$1 break ; + proxy_pass ${FUZON_LOCAL_URL} ; + } } From 653c73a01014f3b580dceb9cb170ab6a14bc089b Mon Sep 17 00:00:00 2001 From: cmdoret Date: Wed, 2 Oct 2024 13:53:41 +0200 Subject: [PATCH 19/39] feat(fuzon): dockerized fuzon-http setup --- deploy/fuzon/Dockerfile | 26 ++++++++++++++++++++++++++ deploy/fuzon/config.json.template | 9 +++++++++ deploy/fuzon/docker-entrypoint.sh | 24 ++++++++++++++++++++++++ 3 files changed, 59 insertions(+) create mode 100644 deploy/fuzon/Dockerfile create mode 100644 deploy/fuzon/config.json.template create mode 100755 deploy/fuzon/docker-entrypoint.sh diff --git a/deploy/fuzon/Dockerfile b/deploy/fuzon/Dockerfile new file mode 100644 index 00000000..45e74a95 --- /dev/null +++ b/deploy/fuzon/Dockerfile @@ -0,0 +1,26 @@ +FROM rust:1.75.0 AS builder + +WORKDIR /build + +RUN cargo install cargo-strip + +RUN apt-get update && apt-get install -y git + +RUN git clone https://github.com/sdsc-ordes/fuzon.git --branch feat/fuzon-http . + +RUN cd fuzon-http && cargo build --release && cargo strip + +FROM debian:stable-slim + +# gettext-base is required for envsubst (config templating) +RUN apt update && apt install -y gettext-base libc6-dev && rm -rf /var/lib/apt/lists/* + +COPY --from=builder /etc/ssl/certs/ /etc/ssl/certs/ +COPY --from=builder /build/target/release/fuzon-http /usr/local/bin/fuzon-http +COPY docker-entrypoint.sh / + +EXPOSE 8080 + +ENTRYPOINT ["/docker-entrypoint.sh"] + +CMD ["fuzon-http", "--config", "/fuzon/config.json"] diff --git a/deploy/fuzon/config.json.template b/deploy/fuzon/config.json.template new file mode 100644 index 00000000..c63b105f --- /dev/null +++ b/deploy/fuzon/config.json.template @@ -0,0 +1,9 @@ +{ + "host": "::", + "port": 8080, + "collections": { + "cell_type": ["https://purl.obolibrary.org/obo/cl.owl"], + "source_material": ["https://purl.obolibrary.org/obo/uberon.owl"], + "taxon_id": ["https://purl.obolibrary.org/obo/ncbitaxon/subsets/taxslim.owl"] + } +} diff --git a/deploy/fuzon/docker-entrypoint.sh b/deploy/fuzon/docker-entrypoint.sh new file mode 100755 index 00000000..744906c8 --- /dev/null +++ b/deploy/fuzon/docker-entrypoint.sh @@ -0,0 +1,24 @@ +#!/bin/sh +set -e + +# only use entrypoint if running fuzon-http +if [ "$1" = "fuzon-http" ] ; then + + # Templating + if [ -e "/fuzon/config.json" ]; then + echo "Using existing config.json" + + elif [ -e "/fuzon/config.json.template" ]; then + echo "Generating config.json from config.json.template" + envsubst < /fuzon/config.json.template > /fuzon/config.json + cat /fuzon/config.json + echo "$@" + + else + echo "No config.json or config.json.template found. Exiting." + exit 1 + + fi +fi + +exec "$@" From a85dc514daa366be2579497de231df9222d0b498 Mon Sep 17 00:00:00 2001 From: cmdoret Date: Wed, 2 Oct 2024 13:56:19 +0200 Subject: [PATCH 20/39] fix(compose): add envvar for fuzon service --- deploy/.example.env | 1 + deploy/docker-compose.yml | 3 ++- 2 files changed, 3 insertions(+), 1 deletion(-) diff --git a/deploy/.example.env b/deploy/.example.env index ccce2277..287a3e3c 100644 --- a/deploy/.example.env +++ b/deploy/.example.env @@ -14,4 +14,5 @@ HTSGET_DATA_DIR="/data" # PUBLIC # URL_PREFIX="https://modos.example.org" # S3_PUBLIC_URL="${URL_PREFIX}/s3" +# FUZON_PUBLIC_URL="${URL_PREFIX}/fuzon" # HTSGET_PUBLIC_URL="${URL_PREFIX}/htsget" diff --git a/deploy/docker-compose.yml b/deploy/docker-compose.yml index 29cbbe8c..77357e26 100644 --- a/deploy/docker-compose.yml +++ b/deploy/docker-compose.yml @@ -17,6 +17,7 @@ services: environment: - S3_PUBLIC_URL=${S3_PUBLIC_URL:-http://localhost/s3/} - S3_LOCAL_URL=${S3_lOCAL_URL:-http://minio:9000} + - FUZON_PUBLIC_URL=${FUZON_PUBLIC_URL:-http://localhost/fuzon} - HTSGET_PUBLIC_URL=${HTSGET_PUBLIC_URL:-http://localhost/htsget} - HTSGET_LOCAL_URL=${HTSGET_LOCAL_URL:-http://htsget:8080} - MODOS_LOCAL_URL=${MODOS_LOCAL_URL:-http://modos-server:8000} @@ -69,7 +70,7 @@ services: volumes: - ./fuzon/config.json.template:/fuzon/config.json.template:ro expose: - - "8080" # ticket server + - "8080" networks: - modos-network From 5afc4efcb3714d65c60f174a5260639f72c342a8 Mon Sep 17 00:00:00 2001 From: cmdoret Date: Wed, 2 Oct 2024 13:59:13 +0200 Subject: [PATCH 21/39] fix(compose): fuzon envvars --- deploy/docker-compose.yml | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/deploy/docker-compose.yml b/deploy/docker-compose.yml index 77357e26..cd319f88 100644 --- a/deploy/docker-compose.yml +++ b/deploy/docker-compose.yml @@ -15,12 +15,13 @@ services: volumes: - ./nginx/default.conf.template:/etc/nginx/templates/default.conf.template:ro environment: - - S3_PUBLIC_URL=${S3_PUBLIC_URL:-http://localhost/s3/} - - S3_LOCAL_URL=${S3_lOCAL_URL:-http://minio:9000} - FUZON_PUBLIC_URL=${FUZON_PUBLIC_URL:-http://localhost/fuzon} - HTSGET_PUBLIC_URL=${HTSGET_PUBLIC_URL:-http://localhost/htsget} + - S3_PUBLIC_URL=${S3_PUBLIC_URL:-http://localhost/s3/} + - FUZON_LOCAL_URL=${FUZON_LOCAL_URL:-http://fuzon:8080} - HTSGET_LOCAL_URL=${HTSGET_LOCAL_URL:-http://htsget:8080} - MODOS_LOCAL_URL=${MODOS_LOCAL_URL:-http://modos-server:8000} + - S3_LOCAL_URL=${S3_lOCAL_URL:-http://minio:9000} ports: - "80:80" networks: From 8df4cf307fc483447070ab066aad2bec2494c4db Mon Sep 17 00:00:00 2001 From: cmdoret Date: Wed, 2 Oct 2024 14:27:21 +0200 Subject: [PATCH 22/39] fix(nginx): typo --- deploy/nginx/default.conf.template | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/deploy/nginx/default.conf.template b/deploy/nginx/default.conf.template index e1bd4cbf..29b9ae81 100644 --- a/deploy/nginx/default.conf.template +++ b/deploy/nginx/default.conf.template @@ -14,7 +14,7 @@ server { { "status": "success", "s3": "${S3_PUBLIC_URL}", - "htsget": "${HTSGET_PUBLIC_URL}" + "htsget": "${HTSGET_PUBLIC_URL}", "fuzon": "${FUZON_PUBLIC_URL}" }' ; } From b4eeb47c088e8be0ce6c52b53d2d6591d5bb98d9 Mon Sep 17 00:00:00 2001 From: cmdoret Date: Wed, 2 Oct 2024 14:49:34 +0200 Subject: [PATCH 23/39] chore(deps): add prompt-toolkit --- poetry.lock | 27 ++++++++++++++++++++++++++- pyproject.toml | 1 + 2 files changed, 27 insertions(+), 1 deletion(-) diff --git a/poetry.lock b/poetry.lock index 791c1ccd..b14cd9aa 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1977,6 +1977,20 @@ files = [ curies = ">=0.5.3" pyyaml = ">=5.3.1" +[[package]] +name = "prompt-toolkit" +version = "3.0.48" +description = "Library for building powerful interactive command lines in Python" +optional = false +python-versions = ">=3.7.0" +files = [ + {file = "prompt_toolkit-3.0.48-py3-none-any.whl", hash = "sha256:f49a827f90062e411f1ce1f854f2aedb3c23353244f8108b89283587397ac10e"}, + {file = "prompt_toolkit-3.0.48.tar.gz", hash = "sha256:d6623ab0477a80df74e646bdbc93621143f5caf104206aa29294d53de1a03d90"}, +] + +[package.dependencies] +wcwidth = "*" + [[package]] name = "pycparser" version = "2.22" @@ -3012,6 +3026,17 @@ platformdirs = ">=3.9.1,<5" docs = ["furo (>=2023.7.26)", "proselint (>=0.13)", "sphinx (>=7.1.2,!=7.3)", "sphinx-argparse (>=0.4)", "sphinxcontrib-towncrier (>=0.2.1a0)", "towncrier (>=23.6)"] test = ["covdefaults (>=2.3)", "coverage (>=7.2.7)", "coverage-enable-subprocess (>=1)", "flaky (>=3.7)", "packaging (>=23.1)", "pytest (>=7.4)", "pytest-env (>=0.8.2)", "pytest-freezer (>=0.4.8)", "pytest-mock (>=3.11.1)", "pytest-randomly (>=3.12)", "pytest-timeout (>=2.1)", "setuptools (>=68)", "time-machine (>=2.10)"] +[[package]] +name = "wcwidth" +version = "0.2.13" +description = "Measures the displayed width of unicode strings in a terminal" +optional = false +python-versions = "*" +files = [ + {file = "wcwidth-0.2.13-py2.py3-none-any.whl", hash = "sha256:3da69048e4540d84af32131829ff948f1e022c1c6bdb8d6102117aac784f6859"}, + {file = "wcwidth-0.2.13.tar.gz", hash = "sha256:72ea0c06399eb286d978fdedb6923a9eb47e1c486ce63e9b4e64fc18303972b5"}, +] + [[package]] name = "wrapt" version = "1.16.0" @@ -3223,4 +3248,4 @@ pyfuzon = ["pyfuzon"] [metadata] lock-version = "2.0" python-versions = "^3.10" -content-hash = "c7e8d4f5c190869b9facc9e4ecdfd9f61ebbc912856d5511b4487f4efc40e9c8" +content-hash = "30d0ac8505b9a534c8dcbb66830b477b7428be845abc5e6ec4c5e267fa9bb5c0" diff --git a/pyproject.toml b/pyproject.toml index 610f1db2..81ab0b62 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -20,6 +20,7 @@ zarr = "^2.16.1" pydantic = "^2.8.2" pyfuzon = { version = "^0.2", optional = true} +prompt-toolkit = "^3.0.48" [tool.poetry.extras] pyfuzon = ["pyfuzon"] From 8d9deb2dbe7dbc5cc9a191b18fc6e30dc94779bd Mon Sep 17 00:00:00 2001 From: cmdoret Date: Thu, 3 Oct 2024 14:44:15 +0200 Subject: [PATCH 24/39] fix(deploy): pin fuzon to tag 0.2.3 --- deploy/fuzon/Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/deploy/fuzon/Dockerfile b/deploy/fuzon/Dockerfile index 45e74a95..f51ffa40 100644 --- a/deploy/fuzon/Dockerfile +++ b/deploy/fuzon/Dockerfile @@ -6,7 +6,7 @@ RUN cargo install cargo-strip RUN apt-get update && apt-get install -y git -RUN git clone https://github.com/sdsc-ordes/fuzon.git --branch feat/fuzon-http . +RUN git clone https://github.com/sdsc-ordes/fuzon.git --branch v0.2.3 . RUN cd fuzon-http && cargo build --release && cargo strip From 772b47c817256775942ee8d32a45c800b6074737 Mon Sep 17 00:00:00 2001 From: Cyril Matthey-Doret Date: Wed, 16 Oct 2024 10:51:38 +0000 Subject: [PATCH 25/39] fix(compose): env var typo Co-authored-by: supermaxiste --- deploy/docker-compose.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/deploy/docker-compose.yml b/deploy/docker-compose.yml index cd319f88..973540c3 100644 --- a/deploy/docker-compose.yml +++ b/deploy/docker-compose.yml @@ -21,7 +21,7 @@ services: - FUZON_LOCAL_URL=${FUZON_LOCAL_URL:-http://fuzon:8080} - HTSGET_LOCAL_URL=${HTSGET_LOCAL_URL:-http://htsget:8080} - MODOS_LOCAL_URL=${MODOS_LOCAL_URL:-http://modos-server:8000} - - S3_LOCAL_URL=${S3_lOCAL_URL:-http://minio:9000} + - S3_LOCAL_URL=${S3_LOCAL_URL:-http://minio:9000} ports: - "80:80" networks: From 06ca00bade6c6e0a11f79f786ea93293c48651f0 Mon Sep 17 00:00:00 2001 From: cmdoret Date: Thu, 17 Oct 2024 09:49:27 +0200 Subject: [PATCH 26/39] docs(deploy): describe config variables --- deploy/README.md | 12 +++++++----- 1 file changed, 7 insertions(+), 5 deletions(-) diff --git a/deploy/README.md b/deploy/README.md index 2cf63135..3c388581 100644 --- a/deploy/README.md +++ b/deploy/README.md @@ -45,15 +45,14 @@ end ## Setup > [!IMPORTANT] -> The instructions below are meant for local testing. +> The instructions below are meant for development. > Production use would require changing the default > credentials and use authentication. 1. Start the server ```sh -cd deploy -docker compose up --build +make deploy ``` 2. Upload MODO(s) to the default bucket from the minio console (default is http://localhost:9001) @@ -80,14 +79,17 @@ docker compose up --build # docker compose automatically reads the .env file ``` +In the `.env` file, each service has a `_PUBLIC_URL` and a `_LOCAL_URL` variable. The public URL is the address used by external clients, whereas LOCAL_URL is the address used by other services. For services deployed as part of the compose setup, the local address is `http://:` and the public address is the endpoint exposed by the nginx reverse proxy, typically `http:///`. If a service is deployed outside the compose, e.g. an external s3 bucket, the public and local address will both be pointing to the external address. + ### Streaming with minio There are two options to use htsget streaming with the minio embedded in the compose setup: -1. Either manually create a host mapping from the minio service to localhost: +1. Set `S3_PUBLIC_URL=http://:9000` where `` is your local IP address (find it using hostname -I). **This is done automatically when starting the server with `make deploy`**. + +2. Manually create a host mapping from the minio service to localhost on the machine: > `echo "127.0.0.1 minio" >> /etc/hosts` -2. Or set `S3_PUBLIC_URL=http://:9000` where `` is your local IP address (find it using hostname -I). These steps are not needed when using an external S3 server, in which case `S3_PUBLIC_URL` can just be set to the external S3 endpoint. From ac78fa1854073a8ad04c21937eea880a5ed1b587 Mon Sep 17 00:00:00 2001 From: cmdoret Date: Fri, 18 Oct 2024 15:31:05 +0200 Subject: [PATCH 27/39] feat(codes): parametrize n top code matches --- modos/codes.py | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/modos/codes.py b/modos/codes.py index 91e6699c..7f100e97 100644 --- a/modos/codes.py +++ b/modos/codes.py @@ -37,8 +37,8 @@ def __init__(self, slot: str): cannot do code matching.""" ) - def find_codes(self, query: str) -> list[Code]: - return self.matcher.top(query, 50) + def find_codes(self, query: str, top: int = 50) -> list[Code]: + return self.matcher.top(query, top) class RemoteCodeMatcher(CodeMatcher): @@ -48,9 +48,9 @@ def __init__(self, slot: str, endpoint: str): self.endpoint = endpoint self.slot = slot - def find_codes(self, query: str) -> list[Code]: + def find_codes(self, query: str, top: int = 50) -> list[Code]: codes = requests.get( - f"{self.endpoint}/top?collection={self.slot}&query={query}&top=50" + f"{self.endpoint}/top?collection={self.slot}&query={query}&top={top}" ).json()["codes"] return [Code(label=code["label"], uri=code["uri"]) for code in codes] From 4b9c8af0494bff21edcfc61d8181a52ae3fa3e77 Mon Sep 17 00:00:00 2001 From: cmdoret Date: Fri, 18 Oct 2024 15:32:22 +0200 Subject: [PATCH 28/39] fix(codes): update protocol signatures --- modos/codes.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modos/codes.py b/modos/codes.py index 7f100e97..a2f56be3 100644 --- a/modos/codes.py +++ b/modos/codes.py @@ -18,7 +18,7 @@ class Code: class CodeMatcher(Protocol): - def find_codes(self, query: str) -> list[Code]: + def find_codes(self, query: str, top: int) -> list[Code]: ... From 2e5590f3b7711b75445670612a5ee845f4a20d51 Mon Sep 17 00:00:00 2001 From: cmdoret Date: Fri, 18 Oct 2024 16:05:40 +0200 Subject: [PATCH 29/39] fix(codes): default top value in code matcher protocol --- modos/codes.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modos/codes.py b/modos/codes.py index a2f56be3..ad56cc43 100644 --- a/modos/codes.py +++ b/modos/codes.py @@ -18,7 +18,7 @@ class Code: class CodeMatcher(Protocol): - def find_codes(self, query: str, top: int) -> list[Code]: + def find_codes(self, query: str, top: int = 50) -> list[Code]: ... From 270aec05c1011bc9ac8763513ec5b92aeed45d08 Mon Sep 17 00:00:00 2001 From: cmdoret Date: Fri, 18 Oct 2024 16:08:23 +0200 Subject: [PATCH 30/39] docs(prompt): clearer comments --- modos/prompt.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modos/prompt.py b/modos/prompt.py index 5097224c..dc0bec57 100644 --- a/modos/prompt.py +++ b/modos/prompt.py @@ -105,7 +105,7 @@ def prompt_for_slots( set(get_slots(target_class, required_only=False)) - required_slots ) - # Always require identifiers if possible + # Always require identifiers if "id" in optional_slots: optional_slots.remove("id") required_slots.add("id") From 7dd1c6e74fe3c8a707abefce209a87e2500245cf Mon Sep 17 00:00:00 2001 From: cmdoret Date: Fri, 18 Oct 2024 16:12:21 +0200 Subject: [PATCH 31/39] fix(deploy): typo in env var --- Makefile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Makefile b/Makefile index 686ecf8c..3febcf73 100644 --- a/Makefile +++ b/Makefile @@ -39,7 +39,7 @@ test: ## Test the code with pytest deploy: ## Deploy services using docker compose @echo "$(LOCAL_IP)";exit 0 @echo "🐋 Deploying server with docker compose" - cd deploy; S3_PUBLC_URL="http://$(LOCAL_IP):9000" docker compose up --build --force-recreate + cd deploy; S3_PUBLIC_URL="http://$(LOCAL_IP):9000" docker compose up --build --force-recreate .PHONY: help From f827c30e57ba14d473a1f18e029f3f85ff7b0aaf Mon Sep 17 00:00:00 2001 From: cmdoret Date: Wed, 23 Oct 2024 03:23:42 +0200 Subject: [PATCH 32/39] feat(cli): list remote modos --- deploy/modos-server/server.py | 2 +- modos/cli.py | 14 +++++++++++++- 2 files changed, 14 insertions(+), 2 deletions(-) diff --git a/deploy/modos-server/server.py b/deploy/modos-server/server.py index d2aa3499..f960d324 100644 --- a/deploy/modos-server/server.py +++ b/deploy/modos-server/server.py @@ -29,7 +29,7 @@ def list_modos() -> list[str]: """List MODO entries in bucket.""" modos = minio.ls(BUCKET, refresh=True) # NOTE: modo contains bucket name - return [modo for modo in modos] + return [f"s3://{modo}" for modo in modos] @app.get("/meta") diff --git a/modos/cli.py b/modos/cli.py index ba42e06d..670925fc 100644 --- a/modos/cli.py +++ b/modos/cli.py @@ -24,7 +24,7 @@ from .genomics.region import Region from .io import parse_instance from .prompt import SlotPrompter -from .remote import EndpointManager +from .remote import EndpointManager, list_remote_items from .storage import connect_s3 @@ -269,6 +269,18 @@ def publish( ) +@cli.command() +def list( + ctx: typer.Context, +): + """List remote modos on the endpoint.""" + if ctx.obj.endpoint is None: + raise ValueError("Must provide an endpoint using modos --endpoint") + + for item in list_remote_items(ctx.obj.endpoint): + print(item) + + @cli.command() def stream( ctx: typer.Context, From 234524d342997bca49f43ae757ebb3190c3a085f Mon Sep 17 00:00:00 2001 From: cmdoret Date: Wed, 23 Oct 2024 10:40:02 +0200 Subject: [PATCH 33/39] fix(server): nest /list values in response --- deploy/modos-server/server.py | 4 ++-- modos/remote.py | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/deploy/modos-server/server.py b/deploy/modos-server/server.py index f960d324..e25bdb60 100644 --- a/deploy/modos-server/server.py +++ b/deploy/modos-server/server.py @@ -25,11 +25,11 @@ @app.get("/list") -def list_modos() -> list[str]: +def list_modos() -> dict[str, list[str]]: """List MODO entries in bucket.""" modos = minio.ls(BUCKET, refresh=True) # NOTE: modo contains bucket name - return [f"s3://{modo}" for modo in modos] + return {"modos": [f"s3://{modo}" for modo in modos]} @app.get("/meta") diff --git a/modos/remote.py b/modos/remote.py index 92c0c92d..a0f218e7 100644 --- a/modos/remote.py +++ b/modos/remote.py @@ -65,7 +65,7 @@ def htsget(self) -> Optional[HttpUrl]: @validate_call def list_remote_items(url: HttpUrl) -> list[HttpUrl]: - return requests.get(url=f"{url}/list").json() + return requests.get(url=f"{url}/list").json()["modos"] @validate_call From e672524e7d98db6bc5473be87929413d0785809d Mon Sep 17 00:00:00 2001 From: cmdoret Date: Wed, 23 Oct 2024 10:59:19 +0200 Subject: [PATCH 34/39] chore: bump pyfuzon to 0.2.5 for blank node fix and caching support --- poetry.lock | 1396 ++++++++++++++++++++++++++++----------------------- 1 file changed, 757 insertions(+), 639 deletions(-) diff --git a/poetry.lock b/poetry.lock index b14cd9aa..db9a8259 100644 --- a/poetry.lock +++ b/poetry.lock @@ -20,24 +20,24 @@ tests = ["hypothesis", "pytest"] [[package]] name = "aiobotocore" -version = "2.15.1" +version = "2.15.2" description = "Async client for aws services using botocore and aiohttp" optional = false python-versions = ">=3.8" files = [ - {file = "aiobotocore-2.15.1-py3-none-any.whl", hash = "sha256:0f738cde74108553b753b24655094289a3c7ea0f0f179ed1c0f8cea488999a35"}, - {file = "aiobotocore-2.15.1.tar.gz", hash = "sha256:1f9f16eec2a3da32df162b5db12da779ec6d6c6311715c936cad511f436efa74"}, + {file = 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9cec3451e5e1bd67b9398198f5899f08ec3c7ad3 Mon Sep 17 00:00:00 2001 From: cmdoret Date: Wed, 23 Oct 2024 13:40:57 +0200 Subject: [PATCH 35/39] feat(cli): add search-codes command --- modos/cli.py | 49 ++++++++++++++++++++++++++++++++++++++++++------- 1 file changed, 42 insertions(+), 7 deletions(-) diff --git a/modos/cli.py b/modos/cli.py index 670925fc..b09f9c57 100644 --- a/modos/cli.py +++ b/modos/cli.py @@ -19,13 +19,14 @@ from .api import MODO from .helpers.schema import UserElementType -from . import __version__ -from .genomics.htsget import HtsgetConnection -from .genomics.region import Region -from .io import parse_instance -from .prompt import SlotPrompter -from .remote import EndpointManager, list_remote_items -from .storage import connect_s3 +from modos import __version__ +from modos.codes import get_slot_matcher, SLOT_TERMINOLOGIES +from modos.genomics.htsget import HtsgetConnection +from modos.genomics.region import Region +from modos.io import parse_instance +from modos.prompt import SlotPrompter +from modos.remote import EndpointManager, list_remote_items +from modos.storage import connect_s3 class RdfFormat(str, Enum): @@ -281,6 +282,40 @@ def list( print(item) +@cli.command() +def search_codes( + ctx: typer.Context, + slot: Annotated[ + str, + typer.Argument( + ..., + help=f"The slot to search for codes. Possible values are {', '.join(SLOT_TERMINOLOGIES.keys())}", + ), + ], + query: Annotated[ + Optional[str], + typer.Option( + "--query", "-q", help="Predefined text to use when search codes." + ), + ] = None, + top: Annotated[ + int, + typer.Option( + "--top", + "-t", + help="Show at most N codes when using a prefedined query.", + ), + ] = 10, +): + """Search for terminology codes using free text.""" + prompter = SlotPrompter( + EndpointManager(ctx.obj.endpoint), + prompt=f'Browsing terms for slot "{slot}". Use tab to cycle suggestions.\n> ', + ) + out = prompter.prompt_for_slot(slot) + print(out) + + @cli.command() def stream( ctx: typer.Context, From 091c7bda9ae77e2de6ce68d571c075f268c5fe86 Mon Sep 17 00:00:00 2001 From: cmdoret Date: Wed, 23 Oct 2024 13:41:06 +0200 Subject: [PATCH 36/39] chore(deploy): bump fuzon server to 0.2.5 --- deploy/fuzon/Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/deploy/fuzon/Dockerfile b/deploy/fuzon/Dockerfile index f51ffa40..12de4e0f 100644 --- a/deploy/fuzon/Dockerfile +++ b/deploy/fuzon/Dockerfile @@ -6,7 +6,7 @@ RUN cargo install cargo-strip RUN apt-get update && apt-get install -y git -RUN git clone https://github.com/sdsc-ordes/fuzon.git --branch v0.2.3 . +RUN git clone https://github.com/sdsc-ordes/fuzon.git --branch v0.2.5 . RUN cd fuzon-http && cargo build --release && cargo strip From 8685064b77c5e6a8496e98e740ba89af22974a51 Mon Sep 17 00:00:00 2001 From: cmdoret Date: Wed, 23 Oct 2024 13:41:51 +0200 Subject: [PATCH 37/39] refactor(prompt): allow prompt override in SlotPrompter --- modos/prompt.py | 27 +++++++++++++++++++++++---- 1 file changed, 23 insertions(+), 4 deletions(-) diff --git a/modos/prompt.py b/modos/prompt.py index dc0bec57..5620a8e5 100644 --- a/modos/prompt.py +++ b/modos/prompt.py @@ -49,11 +49,25 @@ def fuzzy_complete(prompt_txt: str, matcher: CodeMatcher): class SlotPrompter: - """Introspects the schema to prompt the user for values based on input class/slot.""" + """Introspects the schema to prompt the user for values based on input class/slot. + + Parameters + --------- + endpoint: + Endpoint running a fuzon server for code matching. + suggest: + Whether to generate auto-suggestion dynamically. + prompt: + Override the default prompt messages. + """ def __init__( - self, endpoint: Optional[EndpointManager] = None, suggest=True + self, + endpoint: Optional[EndpointManager] = None, + suggest=True, + prompt: Optional[str] = None, ): + self.prompt = prompt if suggest: self.slot_matchers = get_slot_matchers(endpoint.fuzon) else: @@ -69,8 +83,13 @@ def prompt_for_slot(self, slot_name: str, optional: bool = False): elif optional: default = "" - prefix = "(optional) " if optional else "(required) " - prompt = f"{prefix}Enter a value for {slot_name}" + # generate slot-specific prompt unless overridden + if self.prompt is None: + prefix = "(optional) " if optional else "(required) " + prompt = f"{prefix}Enter a value for {slot_name}" + else: + prompt = self.prompt + if slot_name in self.slot_matchers: output = fuzzy_complete(prompt, self.slot_matchers[slot_name]) else: From 74524e47f08ef34dd8d6dda2e00c52b0418523bf Mon Sep 17 00:00:00 2001 From: cmdoret Date: Wed, 23 Oct 2024 13:42:25 +0200 Subject: [PATCH 38/39] refactor(codes): define protocol attributes in CodeMatcher --- modos/codes.py | 39 ++++++++++++++++++++++++++++----------- 1 file changed, 28 insertions(+), 11 deletions(-) diff --git a/modos/codes.py b/modos/codes.py index ad56cc43..83e3d932 100644 --- a/modos/codes.py +++ b/modos/codes.py @@ -18,15 +18,22 @@ class Code: class CodeMatcher(Protocol): - def find_codes(self, query: str, top: int = 50) -> list[Code]: + endpoint: Optional[str] + slot: str + top: int + + def find_codes(self, query: str) -> list[Code]: ... class LocalCodeMatcher(CodeMatcher): """Find ontology codes for a given text by running a local term matcher.""" - def __init__(self, slot: str): + def __init__(self, slot: str, top: int = 50): + self.endpoint = None self.slot = slot + self.top = top + try: from pyfuzon import TermMatcher @@ -37,32 +44,42 @@ def __init__(self, slot: str): cannot do code matching.""" ) - def find_codes(self, query: str, top: int = 50) -> list[Code]: - return self.matcher.top(query, top) + def find_codes(self, query: str) -> list[Code]: + return self.matcher.top(query, self.top) class RemoteCodeMatcher(CodeMatcher): """Find ontology codes for a given text relying on a remote term matcher.""" - def __init__(self, slot: str, endpoint: str): + def __init__(self, slot: str, endpoint: str, top: int = 50): self.endpoint = endpoint self.slot = slot + self.top = top - def find_codes(self, query: str, top: int = 50) -> list[Code]: + def find_codes(self, query: str) -> list[Code]: codes = requests.get( - f"{self.endpoint}/top?collection={self.slot}&query={query}&top={top}" + f"{self.endpoint}/top?collection={self.slot}&query={query}&top={self.top}" ).json()["codes"] return [Code(label=code["label"], uri=code["uri"]) for code in codes] +def get_slot_matcher( + slot: str, + endpoint: Optional[str] = None, +) -> CodeMatcher: + """Instantiates a code matcher based on input slot name.""" + if endpoint: + matcher = RemoteCodeMatcher(slot, endpoint) + else: + matcher = LocalCodeMatcher(slot) + return matcher + + def get_slot_matchers( endpoint: Optional[str] = None, ) -> dict[str, CodeMatcher]: """Instantiates a code matcher for each slot. If the endpoint is provided, remote matchers are used.""" matchers = {} for slot in SLOT_TERMINOLOGIES.keys(): - if endpoint: - matchers[slot] = RemoteCodeMatcher(slot, endpoint) - else: - matchers[slot] = LocalCodeMatcher(slot) + matchers[slot] = get_slot_matcher(slot, endpoint) return matchers From 17c0309d97ea7dd38d2dfdaead922459fd588898 Mon Sep 17 00:00:00 2001 From: cmdoret Date: Wed, 23 Oct 2024 13:49:45 +0200 Subject: [PATCH 39/39] feat(cli): non-interactive code search --- modos/cli.py | 10 ++++++++-- 1 file changed, 8 insertions(+), 2 deletions(-) diff --git a/modos/cli.py b/modos/cli.py index b09f9c57..fbd75129 100644 --- a/modos/cli.py +++ b/modos/cli.py @@ -305,14 +305,20 @@ def search_codes( "-t", help="Show at most N codes when using a prefedined query.", ), - ] = 10, + ] = 50, ): """Search for terminology codes using free text.""" prompter = SlotPrompter( EndpointManager(ctx.obj.endpoint), prompt=f'Browsing terms for slot "{slot}". Use tab to cycle suggestions.\n> ', ) - out = prompter.prompt_for_slot(slot) + for matcher in prompter.slot_matchers.values(): + matcher.top = top + if query: + matches = prompter.slot_matchers[slot].find_codes(query) + out = "\n".join([f"{m.uri} | {m.label}" for m in matches]) + else: + out = prompter.prompt_for_slot(slot) print(out)