diff --git a/.gitignore b/.gitignore index 8412098..716569f 100644 --- a/.gitignore +++ b/.gitignore @@ -130,3 +130,5 @@ dmypy.json # intellij .idea + +Cargo.lock \ No newline at end of file diff --git a/Dockerfile b/Dockerfile index ec51b53..7d018ee 100644 --- a/Dockerfile +++ b/Dockerfile @@ -7,9 +7,7 @@ WORKDIR /code COPY ./requirements.txt requirements.txt COPY ./setup.py setup.py COPY ./node_normalizer node_normalizer -COPY ./config.json config.json COPY ./redis_config.yaml redis_config.yaml -COPY ./load.py load.py # install requirements RUN pip install -r requirements.txt diff --git a/Dockerfile-test b/Dockerfile-test index 94cff00..311af51 100644 --- a/Dockerfile-test +++ b/Dockerfile-test @@ -7,9 +7,7 @@ WORKDIR /code COPY ./requirements.txt requirements.txt COPY ./setup.py setup.py COPY ./node_normalizer node_normalizer -COPY ./tests/config.json config.json -COPY ./tests/redis_config.yaml redis_config.yaml -COPY ./load.py load.py +COPY ./redis_config.yaml redis_config.yaml COPY ./tests tests # install requirements diff --git a/KGX_converter.py b/KGX_converter.py deleted file mode 100644 index bbcb9b1..0000000 --- a/KGX_converter.py +++ /dev/null @@ -1,20 +0,0 @@ -import os -from node_normalizer.loader import NodeLoader - - -def convert_to_kgx(): - # instantiate the class that does all the work - loader = NodeLoader() - - # call to load redis instances with normalized node data - success: bool = loader.convert_to_kgx('KGX_NN_data') - - # check the return - if not success: - loader.print_debug_msg(f'Failed to convert compendia data.', True) - else: - loader.print_debug_msg(f'Success', True) - - -if __name__ == '__main__': - convert_to_kgx() diff --git a/README.md b/README.md index fe15225..47e0118 100644 --- a/README.md +++ b/README.md @@ -1,133 +1,5 @@ [![Build Status](https://travis-ci.com/TranslatorIIPrototypes/NodeNormalization.svg?branch=master)](https://travis-ci.com/TranslatorIIPrototypes/NodeNormalization) -# NodeNormalization +# Welcome to the NodeNormalization project -## Introduction - -Node normalization takes a CURIE, and returns: - -* The preferred CURIE for this entity -* All other known equivalent identifiers for the entity -* Semantic types for the entity as defined by the [Biolink Model](https://biolink.github.io/biolink-model/) - -The data currently served by Node Normalization is created by the prototype project -[Babel](https://github.com/TranslatorSRI/Babel), which attempts to find identifier equivalences, -and makes sure that CURIE prefixes are BioLink Model compliant. The NodeNormalization service, however, -is independent of Babel and as improved identifier equivalence tools are developed, their results -can be easily incorporated. - -To determine whether Node Normalization is likely to be useful, check /get_semantic_types, which lists the BioLink -semantic types for which normalization has been attempted, and /get_curie_prefixes, -which lists the number of times each prefix is used for a semantic type. - -For examples of service usage, see the example [notebook](documentation/NodeNormalization.ipynb). - -The Node normalization website leverages the [R3 (Redis-REST with referencing)](https://github.com/TranslatorSRI/r3) Redis data design and configuration. - -Users can find the publicly available website at [service](https://nodenormalization-sri.renci.org/docs). - -## Installation - -Create a virtual environment -``` - python -m venv nodeNormalization-env -``` -Activate the virtual environment -``` - source nodeNormalization-env/bin/activate -``` -Install requirements -``` - > pip install -r requirements.txt -``` -## Generating equivalence data - -The equivalence data can be generated by running [Babel](https://github.com/TranslatorSRI/Babel). An example of the contents of a compendia file is shown below: -``` - {"id": {"identifier": "PUBCHEM:50986940"}, "equivalent_identifiers": [{"identifier": "PUBCHEM:50986940"}, {"identifier": "INCHIKEY:CYMOSKLLKPIPCD-UHFFFAOYSA-N"}], "type": ["chemical_substance", "named_thing", "biological_entity", "molecular_entity"]} - {"id": {"identifier": "CHEMBL.COMPOUND:CHEMBL1546789", "label": "CHEMBL1546789"}, "equivalent_identifiers": [{"identifier": "CHEMBL.COMPOUND:CHEMBL1546789", "label": "CHEMBL1546789"}, {"identifier": "PUBCHEM:4879549"}, {"identifier": "INCHIKEY:FUIYIXDZTPMQEH-UHFFFAOYSA-N"}], "type": ["chemical_substance", "named_thing", "biological_entity", "molecular_entity"]} -``` -## Creating and loading a Redis container with data - -A running instance of Redis is needed to house the node normalization data. a Redis Docker container image can be downloaded from [Docker hub](https://hub.docker.com/_/redis). The Redis caonteriner can be started with thie following docker command: -``` - docker run --name node-norm-redis -p 6379:6379 -d redis redis-server --appendonly yes -``` -Note that the dataset for Node normalization is quite large and 256Gb of memory and disk space should be made available to the Redis instance to insure proper loading of the complete compendia. -### Configuration -Insure that the `./config.json` file is created and contains the parameters for the node normalization load specific to your environment. - -The configuration parameters `compendium_directory` and `data_files` specify the location of the compendia files. An example of the files' contents -are listed below: -``` - { - "compendium_directory": "", - "data_files": "anatomy.txt,BiologicalProcess.txt,cell.txt,cellular_component.txt,disease.txt,gene_compendium.txt,gene_family_compendium.txt,MolecularActivity.txt,pathways.txt,phenotypes.txt,taxon_compendium.txt", - "redis_host": "", - "redis_port": , - "redis_password": " - - pip install -r requirements.txt - - uvicorn --host 0.0.0.0 --port 8000 --workers 1 node_normalizer.server:app -``` - -Then navigate to http://localhost:8000/docs to run the application - -### Webserver Docker container creation and execution -Much like the Redis Docker container noted above, a Docker container can also be created and executed to run the webserver. - -#### Build the webserver Docker image -``` - cd - - docker build --tag . -``` - -#### Start the container: - -_Note the Dockerfile specifies port 6380 for the webservice container._ -``` - docker run --name Node-normalization -p 8000:6380 node-norm -``` - -Then navigate to: http://localhost:8000/docs to run the application - -### Kubernetes configurations -Kubernetes configurations and helm charts for this project can be found at: -``` - https://github.com/helxplatform/translator-devops/helm/r3 -``` +Please visit the [WIKI](https://github.com/TranslatorSRI/NodeNormalization/wiki) page for this project for more documentation diff --git a/config.json b/config.json deleted file mode 100644 index a650184..0000000 --- a/config.json +++ /dev/null @@ -1,17 +0,0 @@ -{ - "compendium_directory": "comps", - "conflation_directory": "confs", - "redis_host": "127.0.0.1", - "redis_port": 6379, - "redis_password": "", - "data_files": ["Gene.txt", "Protein.txt"], - "test_mode": 0, - "debug_messages": 0, - "conflations": [ - { - "types": ["biolink:Gene", "biolink:Protein"], - "file": "GeneProtein.txt", - "redis_db": "gene_protein_db" - } - ] -} diff --git a/docker-compose-test.yml b/docker-compose-test.yml index a7397bc..6b77b8f 100644 --- a/docker-compose-test.yml +++ b/docker-compose-test.yml @@ -1,34 +1,41 @@ version: "3" services: - r3: - container_name: r3 - image: r3 - build: - context: . - dockerfile: Dockerfile-test - env_file: .env + redis_eq_id_to_id_db: + container_name: redis_eq_id_to_id_db + image: redis:alpine expose: - - 8080 - ports: - - "8080:8080" -# links: -# - callback-app -# networks: -# - nn_network - depends_on: - - redis - - callback-app + - 6379 - redis: - container_name: redis + redis_id_to_eqids_db: + container_name: redis_id_to_eqids_db + image: redis:alpine + expose: + - 6379 + + redis_id_to_type_db: + container_name: redis_id_to_type_db + image: redis:alpine + expose: + - 6379 + + redis_curie_to_bl_type_db: + container_name: redis_curie_to_bl_type_db + image: redis:alpine + expose: + - 6379 + + redis_info_content_db: + container_name: redis_info_content_db + image: redis:alpine + expose: + - 6379 + + redis_conflation_db: + container_name: redis_conflation_db image: redis:alpine - ports: - - "6379:6379" expose: - 6379 -# networks: -# - nn_network callback-app: container_name: callback-app @@ -39,10 +46,23 @@ services: - 8008 ports: - "8008:8008" -# networks: -# - nn_network -#networks: -# nn_network: -# name: nn -# external: false \ No newline at end of file + node-norm: + container_name: node-norm + image: node-norm + build: + context: . + dockerfile: Dockerfile-test + env_file: .env + expose: + - 8080 + ports: + - "8080:8080" + depends_on: + - redis_eq_id_to_id_db + - redis_id_to_eqids_db + - redis_id_to_type_db + - redis_curie_to_bl_type_db + - redis_info_content_db + - redis_conflation_db + - callback-app diff --git a/docker-compose.yml b/docker-compose.yml index ef66e5a..661edf4 100644 --- a/docker-compose.yml +++ b/docker-compose.yml @@ -1,18 +1,57 @@ version: "3" services: - redis: - container_name: redis + redis_eq_id_to_id_db: + container_name: redis_eq_id_to_id_db image: redis:alpine expose: - 6379 - - r3: - container_name: r3 - image: r3 - build: . - env_file: - - .env + + redis_id_to_eqids_db: + container_name: redis_id_to_eqids_db + image: redis:alpine + expose: + - 6379 + + redis_id_to_type_db: + container_name: redis_id_to_type_db + image: redis:alpine + expose: + - 6379 + + redis_curie_to_bl_type_db: + container_name: redis_curie_to_bl_type_db + image: redis:alpine + expose: + - 6379 + + redis_info_content_db: + container_name: redis_info_content_db + image: redis:alpine + expose: + - 6379 + + redis_conflation_db: + container_name: redis_conflation_db + image: redis:alpine + expose: + - 6379 + + node-norm: + container_name: node-norm + image: node-norm + build: + context: . + dockerfile: Dockerfile + env_file: .env + expose: + - 8080 ports: - "8080:8080" depends_on: - - redis \ No newline at end of file + - redis_eq_id_to_id_db + - redis_id_to_eqids_db + - redis_id_to_type_db + - redis_curie_to_bl_type_db + - redis_info_content_db + - redis_conflation_db + diff --git a/load.py b/load.py deleted file mode 100644 index d9b24a7..0000000 --- a/load.py +++ /dev/null @@ -1,20 +0,0 @@ -from node_normalizer.loader import NodeLoader -import asyncio - - -async def load_redis(): - # instantiate the class that does all the work - loader = NodeLoader() - - # call to load redis instances with normalized node data - success: bool = await loader.load(1_000) - - # check the return - if not success: - print('Failed to load node normalization data.') - else: - print('Success') - - -if __name__ == '__main__': - asyncio.run(load_redis()) diff --git a/nn_io_rs/Cargo.toml b/nn_io_rs/Cargo.toml new file mode 100644 index 0000000..601be9e --- /dev/null +++ b/nn_io_rs/Cargo.toml @@ -0,0 +1,21 @@ +[package] +name = "nn_io_rs" +version = "0.1.0" +edition = "2021" + +# See more keys and their definitions at https://doc.rust-lang.org/cargo/reference/manifest.html +[lib] +name = "nn_io_rs" +crate-type = ["cdylib"] + +[dependencies] +clap = { version = "^4.0", features = ["derive"] } +csv = "^1.1" +humantime = "^2.1" +itertools = "^0.10" +pyo3 = { version = "^0.17", features = ["extension-module"] } +reqwest = { version = "^0.11", features = ["json"] } +tokio = { version = "^1", features = ["full"] } +serde = "^1.0" +serde_derive = "^1.0" +serde_json = "^1.0" diff --git a/nn_io_rs/rustfmt.toml b/nn_io_rs/rustfmt.toml new file mode 100644 index 0000000..69eb2bb --- /dev/null +++ b/nn_io_rs/rustfmt.toml @@ -0,0 +1,4 @@ +max_width = 180 +newline_style = "Unix" +use_field_init_shorthand = true +use_try_shorthand = true diff --git a/nn_io_rs/src/bin/pull_and_filter_compendia_data.rs b/nn_io_rs/src/bin/pull_and_filter_compendia_data.rs new file mode 100644 index 0000000..93e9e75 --- /dev/null +++ b/nn_io_rs/src/bin/pull_and_filter_compendia_data.rs @@ -0,0 +1,68 @@ +use clap::Parser; +use reqwest::StatusCode; +use serde_json::Value; +use std::error; +use std::fs::File; +use std::io::{BufWriter, Write}; +use std::path; + +#[derive(Parser, PartialEq, Debug)] +#[command(author, version, about, long_about = None)] +struct Options { + #[arg(short, long, default_value_t = 3_000)] + entry_limit: usize, + + #[arg(short, long, long_help = "identifiers greater than", default_value_t = 2)] + identifier_floor: usize, + + #[arg(short, long)] + output_dir: path::PathBuf, + + #[arg(short, long)] + file_name: Vec, +} +#[tokio::main] +async fn main() -> Result<(), Box> { + let options = Options::parse(); + + let output_dir: path::PathBuf = options.output_dir.to_path_buf(); + std::fs::create_dir_all(&output_dir).ok(); + + for file_name in options.file_name.iter() { + let mut output: path::PathBuf = output_dir.clone(); + output.push(file_name); + + let file = File::create(output.as_path()).unwrap(); + let mut writer = BufWriter::new(file); + + let cell_data_response = reqwest::get(format!("https://stars.renci.org/var/babel_outputs/2022oct13/compendia/{}", file_name)).await?; + + match cell_data_response.status() { + StatusCode::OK => { + let content = cell_data_response.text().await?; + let mut cache = vec![]; + for line in content.lines() { + let json: Value = serde_json::from_str(line).expect("could not parse line to json"); + if json["identifiers"].is_array() { + let identifiers = json["identifiers"].as_array().expect("could not convert to array"); + if identifiers.len() >= options.identifier_floor { + cache.push(line); + } + } + if cache.len() == options.entry_limit { + break; + } + } + + cache.iter().for_each(|line| { + writer.write(format!("{}\n", line).as_bytes()).expect("Unable to write data"); + }); + } + _ => { + print!("response status was not OK (200)"); + } + } + } + + Ok(()) +} diff --git a/nn_io_rs/src/bin/pull_and_filter_conflation_data.rs b/nn_io_rs/src/bin/pull_and_filter_conflation_data.rs new file mode 100644 index 0000000..1fda07b --- /dev/null +++ b/nn_io_rs/src/bin/pull_and_filter_conflation_data.rs @@ -0,0 +1,87 @@ +use clap::Parser; +use reqwest::StatusCode; +use serde_json::Value; +use std::error; +use std::fs::File; +use std::io; +use std::io::{BufRead, Write}; +use std::path; + +#[derive(Parser, PartialEq, Debug)] +#[command(author, version, about, long_about = None)] +struct Options { + #[arg(short, long, default_value_t = 3_000)] + entry_limit: usize, + + #[arg(short, long)] + compendia_path: path::PathBuf, + + #[arg(short, long)] + output_dir: path::PathBuf, + + #[arg(short, long)] + file_name: Vec, +} +#[tokio::main] +async fn main() -> Result<(), Box> { + let options = Options::parse(); + + let output_dir = options.output_dir; + std::fs::create_dir_all(&output_dir).ok(); + + let compendia_identifier_data = parse_file(&options.compendia_path)?; + + for file_name in options.file_name.iter() { + let mut output: path::PathBuf = output_dir.clone(); + output.push(file_name); + + let file = File::create(output.as_path()).unwrap(); + let mut writer = io::BufWriter::new(file); + + let conflation_data_response = reqwest::get(format!("https://stars.renci.org/var/babel_outputs/2022oct13/conflation/{}", file_name)).await?; + + match conflation_data_response.status() { + StatusCode::OK => { + let content = conflation_data_response.text().await?; + let mut cache = vec![]; + for line in content.lines() { + let json: Value = serde_json::from_str(line).expect("could not parse line to json"); + if json.is_array() { + let identifier = json[0].as_str().unwrap(); + if compendia_identifier_data.contains(&identifier.to_string()) { + cache.push(line); + } + } + if cache.len() == options.entry_limit { + break; + } + } + + cache.iter().for_each(|line| { + writer.write(format!("{}\n", line).as_bytes()).expect("Unable to write data"); + }); + } + _ => { + print!("response status was not OK (200)"); + } + } + } + + Ok(()) +} + +fn parse_file(file_path: &path::PathBuf) -> Result, Box> { + let mut results = vec![]; + let reader = io::BufReader::new(File::open(file_path.as_path())?); + + for line in reader.lines() { + let line = line.unwrap(); + let json: Value = serde_json::from_str(line.as_str()).expect("could not parse line to json"); + if json["identifiers"].is_array() { + let identifiers = json["identifiers"].as_array().expect("could not convert to array"); + let identifier = identifiers[0]["i"].as_str().unwrap(); + results.push(identifier.to_string()); + } + } + Ok(results) +} diff --git a/nn_io_rs/src/lib.rs b/nn_io_rs/src/lib.rs new file mode 100644 index 0000000..d5c29fb --- /dev/null +++ b/nn_io_rs/src/lib.rs @@ -0,0 +1,110 @@ +#[macro_use] +extern crate serde_derive; + +use pyo3::prelude::*; +use std::path::{Path, PathBuf}; +use itertools::Itertools; +use serde_json::Value; +use std::error::Error; + +// {"type": "biolink:Cell", "ic": "100", "identifiers": [{"i": "CL:0002010", "l": "pre-conventional dendritic cell"}]} + +#[derive(Serialize, Deserialize, Debug)] +pub struct CompendiaIdentifier { + #[serde(rename = "i")] + pub id: String, + #[serde(rename = "l", skip_serializing_if = "String::is_empty")] + pub label: String, +} + +#[derive(Serialize, Deserialize, Debug)] +pub struct CompendiaEntry { + #[serde(rename = "type")] + pub compendia_type: String, + #[serde(rename = "ic", skip_serializing_if = "Option::is_none")] + pub information_content: Option, + pub identifiers: Vec, +} + +#[derive(Serialize, Deserialize, Debug)] +pub struct SSSOMEntry { + pub subject_id: String, + pub subject_label: String, + pub subject_category: String, + pub predicate_id: String, + pub object_id: String, + pub object_label: String, + pub object_category: String, + pub match_type: String, + pub other: String, +} + +#[pyfunction] +pub fn sssom_to_legacy_format(path: &str) -> PyResult> { + let path_instance = PathBuf::from(path); + let data = read_sssom_file(path_instance.as_path()).unwrap(); + let mut ret = vec![]; + + let grouping = data.iter().map(|a| ((a.subject_category.clone(), a.subject_id.clone(), a.subject_label.clone()), a)).into_group_map(); + for (key, values) in grouping.iter() { + + let mut identifiers = vec![ + CompendiaIdentifier { + id: key.1.clone(), + label: key.2.clone(), + } + ]; + + let mut ic_values = values + .iter() + .map(|a| a.other.clone()) + .map(|a| { + let json: Value = serde_json::from_str(a.as_str()).unwrap(); + match json["subject_information_content"].is_null() { + true => None, + false => Some(json["subject_information_content"].to_string()), + } + }) + .flatten() + .collect_vec(); + + ic_values.dedup(); + + values.iter().filter(|a| key.1 != a.object_id).for_each(|a| identifiers.push(CompendiaIdentifier { + id: a.object_id.clone(), + label: a.object_label.clone(), + })); + + let compendia_entry = CompendiaEntry { + compendia_type: key.0.clone(), + information_content: ic_values.into_iter().next(), + identifiers + }; + ret.push(serde_json::to_string(&compendia_entry).unwrap()); + } + + Ok(ret) +} + +// conflations of chemicals and chemicals +// conflations of chemicals and drug + +fn read_sssom_file(path: &Path) -> Result, Box> { + let raw_data = std::fs::read_to_string(path).unwrap(); + let raw_data_str = raw_data.as_str(); + let mut data_reader = csv::ReaderBuilder::new().delimiter(b'\t').has_headers(true).from_reader(raw_data_str.as_bytes()); + let mut data = vec![]; + for record in data_reader.deserialize() { + let record: SSSOMEntry = record.unwrap(); + data.push(record); + } + Ok(data) +} + + +/// A Python module implemented in Rust. +#[pymodule] +fn nn_io_rs(_py: Python, m: &PyModule) -> PyResult<()> { + m.add_function(wrap_pyfunction!(sssom_to_legacy_format, m)?)?; + Ok(()) +} diff --git a/node_normalizer/convert_compendia_to_kgx.py b/node_normalizer/convert_compendia_to_kgx.py new file mode 100644 index 0000000..76ae79e --- /dev/null +++ b/node_normalizer/convert_compendia_to_kgx.py @@ -0,0 +1,156 @@ +import asyncio +import hashlib +import os +from pathlib import Path +from itertools import combinations +import json + +import click +from node_normalizer.util import validate_compendium, LoggingUtil + +logger = LoggingUtil.init_logging() + + +@click.command(no_args_is_help=True) +@click.option("--compendium-file", "-c", help="Compendia File", multiple=True) +@click.option("--output-directory", "-o", help="Output Directory") +@click.option("--output-file-prefix", "-p", help="Output File Prefix") +@click.option("--dry-run", "-d", help="Dry Run", default=False) +@click.option("--redis-config", "-r", help="Redis Config File", type=click.Path(), default=Path(__file__).parent.parent / "redis_config.yaml") +def convert_to_kgx(compendium_file, output_directory, output_file_prefix, dry_run, redis_config) -> bool: + """ + Given a compendia directory, create a KGX node file + """ + + # init the return value + ret_val = True + + line_counter: int = 0 + + try: + + nodes: list = [] + edges: list = [] + pass_nodes: list = [] + + for comp in compendium_file: + if not validate_compendium(comp, logger): + logger.warning(f"Compendia file {comp} is invalid.") + return False + + # open the output file and start loading it + with open(os.path.join(output_directory, output_file_prefix + "_nodes.jsonl"), "w", encoding="utf-8") as node_file, open( + os.path.join(output_directory, output_file_prefix + "_edges.jsonl"), "w", encoding="utf-8" + ) as edge_file: + + # set the flag for suppressing the first ",\n" in the written data + first = True + + # for each file validate and process + for comp in compendium_file: + + with open(comp, "r", encoding="utf-8") as compendium: + logger.info(f"Processing {comp}...") + + # get the name of the source + # source = os.path.split(comp)[-1] + + # for each line in the file + for line in compendium: + # increment the record counter + line_counter += 1 + + # clear storage for this pass + pass_nodes.clear() + + # load the line into memory + instance: dict = json.loads(line) + + # all ids (even the root one) are in the equivalent identifiers + if len(instance["identifiers"]) > 0: + # loop through each identifier and create a node + for equiv_id in instance["identifiers"]: + # check to see if there is a label. if there is use it + if "l" in equiv_id: + name = equiv_id["l"] + else: + name = "" + + # add the node to the ones in this pass + pass_nodes.append( + { + "id": equiv_id["i"], + "name": name, + "category": instance["type"], + "equivalent_identifiers": list(x["i"] for x in instance["identifiers"]), + } + ) + + # get the combinations of the nodes in this pass + combos = combinations(pass_nodes, 2) + + # for all the node combinations create an edge between them + for c in combos: + # create a unique id + record_id: str = c[0]["id"] + c[1]["id"] + f"{comp}" + + # save the edge + edges.append( + { + "id": f'{hashlib.md5(record_id.encode("utf-8")).hexdigest()}', + "subject": c[0]["id"], + "predicate": "biolink:same_as", + "object": c[1]["id"], + } + ) + + # save the nodes in this pass to the big list + nodes.extend(pass_nodes) + + # did we reach the write threshold + if line_counter == 10000: + # first time in doesnt get a leading comma + # if first: + # prefix = "" + # else: + # prefix = "\n" + + # reset the first record flag + first = False + + # reset the line counter for the next group + line_counter = 0 + + # get all the nodes in a string and write them out + nodes_to_write = "\n".join([json.dumps(node) for node in nodes]) + node_file.write(nodes_to_write + "\n") + + # are there any edges to output + if len(edges) > 0: + # get all the edges in a string and write them out + edges_to_write = "\n".join([json.dumps(edge) for edge in edges]) + edge_file.write(edges_to_write + "\n") + + # reset for the next group + nodes.clear() + edges.clear() + + # pick up any remainders in the file + if len(nodes) > 0: + nodes_to_write = "\n".join([json.dumps(node) for node in nodes]) + node_file.write(nodes_to_write + "\n") + + if len(edges) > 0: + edges_to_write = "\n".join([json.dumps(edge) for edge in edges]) + edge_file.write(edges_to_write + "\n") + + except Exception as e: + logger.error(f"Exception thrown in convert_to_KGX(): {e}") + ret_val = False + + # return to the caller + return ret_val + + +if __name__ == "__main__": + convert_to_kgx() diff --git a/node_normalizer/load_compendia.py b/node_normalizer/load_compendia.py deleted file mode 100644 index 49e2178..0000000 --- a/node_normalizer/load_compendia.py +++ /dev/null @@ -1,337 +0,0 @@ -import asyncio -import os -from pathlib import Path -from itertools import islice -import json -from typing import Dict - -import bmt as bmt -import click -import jsonschema -import redis_adapter -import util - - -logger = util.LoggingUtil.init_logging() - -redis_config_path = Path(__file__).parent.parent / "redis_config.yaml" -connection_factory: redis_adapter.RedisConnectionFactory = await redis_adapter.RedisConnectionFactory.create_connection_pool(redis_config_path) - -BIOLINK_VERSION = os.getenv("BIOLINK_VERSION", "2.1.0") -toolkit = bmt.Toolkit(f"https://raw.githubusercontent.com/biolink/biolink-model/{BIOLINK_VERSION}/biolink-model.yaml") - -# class NodeLoader: -# """ -# Class that gets all node definitions from a series of flat files -# and produces Translator compliant nodes which are then loaded into -# a redis database. -# """ -# -# def __init__(self): -# self._config = self.get_config() -# -# self._compendium_directory: Path = Path(self._config["compendium_directory"]) -# self._test_mode: int = self._config["test_mode"] -# self._data_files: list = self._config["data_files"] -# self._conflations: list = self._config["conflations"] -# -# json_schema = Path(__file__).parent / "resources" / "valid_data_format.json" -# -# with open(json_schema) as json_file: -# self._validate_with = json.load(json_file) -# -# # Initialize storage instance vars for the semantic types and source prefixes -# self.semantic_types: set = set() -# self.source_prefixes: Dict = {} -# -# self.toolkit = Toolkit("https://raw.githubusercontent.com/biolink/biolink-model/2.1.0/biolink-model.yaml") -# self.ancestor_map = {} - - - - -@click.command() -@click.option("--compendia_file", "-c", help="Compendia File", multiple=True) -@click.option("--block-size", "-b", help="Block Size", default=1000) -@click.option("--dry-run", "-d", help="Dry Run", default=False) -async def load(compendia_files, block_size, dry_run) -> bool: - """ - Given a compendia directory, load every file there into a running - redis instance so that it can be read by R3 - """ - # The new style compendia files look like: - # {"type": "biolink:Disease", "identifiers": [{"i": "UMLS:C4331330", "l": "Stage III Oropharyngeal (p16-Negative) Carcinoma AJCC v8"}, {"i": "NCIT:C132998", "l": "Stage III Oropharyngeal (p16-Negative) Carcinoma AJCC v8"}]} - # {"type": "biolink:Disease", "identifiers": [{"i": "UMLS:C1274244", "l": "Dermatosis in a child"}, {"i": "SNOMEDCT:402803008"}]} - - # Update 11/4/2021: The files now look like: - # {"type": "biolink:Disease", "ic": "100", "identifiers": [{"i": "UMLS:C4331330", "l": "Stage III Oropharyngeal (p16-Negative) Carcinoma AJCC v8"}, {"i": "NCIT:C132998", "l": "Stage III Oropharyngeal (p16-Negative) Carcinoma AJCC v8"}]} - # {"type": "biolink:Disease", "identifiers": [{"i": "UMLS:C1274244", "l": "Dermatosis in a child"}, {"i": "SNOMEDCT:402803008"}]} - - # Update 11/4/2021: a new key of 'ic' (information content) is now incorporated for enhanced filtering of results. - # Type is now a single biolink type so that we can save space rather than the gigantic array - # identifiers replaces equivalent identifiers, and the keys are "i" and "l" rather than 'identifier" and "label". - - # the identifiers are ordered, such that the first identifier is the best identifier. - # We are going to put these different parts into a few different redis tables, and reassemble and nicify on - # output. This will be a touch slower, but it will save a lot of space, and make conflation easier as well. - - # We will have the following redis databases: - # 0: contains identifier.upper() -> canonical_id - # 1: canonical_id -> equivalent_identifiers - # 2: canonical_id -> biolink type - # 3: types -> prefix counts - # Update 11/4/2021: 4: info_content -> filtering value - # 5-X: conflation databases consisting of canonical_id -> (list of conflated canonical_ids) - # Each of these databases corresponds to a particular conflation e.g. gene/protein or chemical/drug - - try: - # get the list of files in the directory - types_prefixes_redis: redis_adapter.RedisConnection = await get_redis("curie_to_bl_type_db") - # for each file validate and process - - # check the validity of the files - for comp in compendia_files: - if not validate_compendia(comp): - logger.warning(f"Compendia file {comp} is invalid.") - return False - - for comp in compendia_files: - if not validate_compendia(comp): - logger.warning(f"Compendia file {comp} is invalid.") - return False - - - for comp in compendia_files: - # check the validity of the file - - if not validate_compendia(comp): - logger.warning(f"Compendia file {comp} is invalid.") - continue - - # try to load the file - loaded = await load_compendium(comp, block_size, dry_run) - semantic_types_redis_pipeline = types_prefixes_redis.pipeline() - # @TODO add meta data about files eg. checksum to this object - # semantic_types_redis_pipeline.set(f"file-{str(comp)}", json.dumps({"source_prefixes": self.source_prefixes})) - if dry_run: - response = await redis_adapter.RedisConnection.execute_pipeline(semantic_types_redis_pipeline) - if asyncio.coroutines.iscoroutine(response): - await response - # self.source_prefixes = {} - if not loaded: - logger.warning(f"Compendia file {comp} did not load.") - continue - # merge all semantic counts from other files / loaders - await merge_semantic_meta_data() - except Exception as e: - logger.error(f"Exception thrown in load(): {e}") - raise e - - # return to the caller - return True - - -async def merge_semantic_meta_data(dry_run): - # get the connection and pipeline to the database - - types_prefixes_redis: redis_adapter.RedisConnection = await get_redis("curie_to_bl_type_db") - meta_data_keys = await types_prefixes_redis.keys("file-*") - # recreate pipeline - - types_prefixes_pipeline = types_prefixes_redis.pipeline() - # capture all keys except semenatic_types , as that would be the one that will contain the sum of all semantic types - meta_data_keys = list(filter(lambda key: key != "semantic_types", meta_data_keys[0])) - - # get actual data - for meta_data_key in meta_data_keys: - types_prefixes_pipeline.get(meta_data_key) - - meta_data = types_prefixes_pipeline.execute() - - if asyncio.coroutines.iscoroutine(meta_data): - meta_data = await meta_data - - all_meta_data = {} - - for meta_data_key, meta_datum in zip(meta_data_keys, meta_data): - if meta_datum: - all_meta_data[meta_data_key.decode("utf-8")] = json.loads(meta_datum.decode("utf-8")) - - sources_prefix = {} - - for meta_data_key, data in all_meta_data.items(): - prefix_counts = data["source_prefixes"] - for bl_type, curie_counts in prefix_counts.items(): - # if - sources_prefix[bl_type] = sources_prefix.get(bl_type, {}) - for curie_prefix, count in curie_counts.items(): - # get count of this curie prefix - sources_prefix[bl_type][curie_prefix] = sources_prefix[bl_type].get(curie_prefix, 0) - # add up the new count - sources_prefix[bl_type][curie_prefix] += count - - types_prefixes_pipeline = types_prefixes_redis.pipeline() - - if len(sources_prefix.keys()) > 0: - # add all the semantic types - types_prefixes_pipeline.lpush("semantic_types", *list(sources_prefix.keys())) - - # for each semantic type insert the list of source prefixes - for item in sources_prefix: - types_prefixes_pipeline.set(item, json.dumps(sources_prefix[item])) - - if dry_run: - # add the data to redis - response = await redis_adapter.RedisConnection.execute_pipeline(types_prefixes_pipeline) - if asyncio.coroutines.iscoroutine(response): - await response - - -def validate_compendia(in_file): - # open the file to validate - json_schema = Path(__file__).parent / "resources" / "valid_data_format.json" - with open(in_file, "r") as compendium, open(json_schema) as json_file: - logger.info(f"Validating {in_file}...") - # sample the file - for line in islice(compendium, 5): - try: - instance: dict = json.loads(line) - # validate the incoming json against the spec - jsonschema.validate(instance=instance, schema=json.load(json_file)) - # catch any exceptions - except Exception as e: - logger.error(f"Exception thrown in validate_compendia({in_file}): {e}") - return False - - return True - - -# TODO: this strikes me as backwards. Caller has to know and look up by index. So the info about what index does what is scattered. Instead this should -# look up by what kind of redis you want and map to dbid for you. -async def get_redis(db_name): - """ - Return a redis instance - """ - connection = connection_factory.get_connection(db_name) - return connection - - -async def load_compendium(compendium_filename: str, block_size: int, dry_run: bool) -> bool: - """ - Given the full path to a compendium, load it into redis so that it can - be read by R3. We also load extra keys, which are the upper-cased - identifiers, for ease of use - """ - ancestor_map = {} - source_prefixes: Dict = {} - - def get_ancestors(input_type): - if input_type in ancestor_map: - return ancestor_map[input_type] - a = toolkit.get_ancestors(input_type) - ancs = [toolkit.get_element(ai)["class_uri"] for ai in a] - if input_type not in ancs: - ancs = [input_type] + ancs - ancestor_map[input_type] = ancs - return ancs - - # init a line counter - line_counter: int = 0 - try: - term2id_redis: redis_adapter.RedisConnection = await get_redis("eq_id_to_id_db") - id2eqids_redis: redis_adapter.RedisConnection = await get_redis("id_to_eqids_db") - id2type_redis: redis_adapter.RedisConnection = await get_redis("id_to_type_db") - info_content_redis: redis_adapter.RedisConnection = await get_redis("info_content_db") - - term2id_pipeline = term2id_redis.pipeline() - id2eqids_pipeline = id2eqids_redis.pipeline() - id2type_pipeline = id2type_redis.pipeline() - info_content_pipeline = info_content_redis.pipeline() - - with open(compendium_filename, "r", encoding="utf-8") as compendium: - logger.info(f"Processing {compendium_filename}...") - - # for each line in the file - for line in compendium: - line_counter = line_counter + 1 - - # load the line into memory - instance: dict = json.loads(line) - - # save the identifier - # "The" identifier is the first one in the presorted identifiers list - identifier: str = instance["identifiers"][0]["i"] - - # We want to accumulate statistics for each implied type as well, though we are only keeping the - # leaf type in the file (and redis). so now is the time to expand. We'll regenerate the same - # list on output. - semantic_types = get_ancestors(instance["type"]) - - # for each semantic type in the list - for semantic_type in semantic_types: - # save the semantic type in a set to avoid duplicates - semantic_types.add(semantic_type) - - # create a source prefix if it has not been encountered - if source_prefixes.get(semantic_type) is None: - source_prefixes[semantic_type] = {} - - # go through each equivalent identifier in the data row - # each will be assigned the semantic type information - for equivalent_id in instance["identifiers"]: - # split the identifier to just get the data source out of the curie - source_prefix: str = equivalent_id["i"].split(":")[0] - - # save the source prefix if no already there - if source_prefixes[semantic_type].get(source_prefix) is None: - source_prefixes[semantic_type][source_prefix] = 1 - # else just increment the count for the semantic type/source - else: - source_prefixes[semantic_type][source_prefix] += 1 - - # equivalent_id might be an array, where the first element is - # the identifier, or it might just be a string. not worrying about that case yet. - equivalent_id = equivalent_id["i"] - term2id_pipeline.set(equivalent_id.upper(), identifier) - # term2id_pipeline.set(equivalent_id, identifier) - - id2eqids_pipeline.set(identifier, json.dumps(instance["identifiers"])) - id2type_pipeline.set(identifier, instance["type"]) - - # if there is information content add it to the cache - if "ic" in instance: - info_content_pipeline.set(identifier, instance["ic"]) - - if not dry_run and line_counter % block_size == 0: - await redis_adapter.RedisConnection.execute_pipeline(term2id_pipeline) - await redis_adapter.RedisConnection.execute_pipeline(id2eqids_pipeline) - await redis_adapter.RedisConnection.execute_pipeline(id2type_pipeline) - await redis_adapter.RedisConnection.execute_pipeline(info_content_pipeline) - - # Pipeline executed create a new one error - term2id_pipeline = term2id_redis.pipeline() - id2eqids_pipeline = id2eqids_redis.pipeline() - id2type_pipeline = id2type_redis.pipeline() - info_content_pipeline = info_content_redis.pipeline() - - logger.info(f"{line_counter} {compendium_filename} lines processed") - - if not dry_run: - await redis_adapter.RedisConnection.execute_pipeline(term2id_pipeline) - await redis_adapter.RedisConnection.execute_pipeline(id2eqids_pipeline) - await redis_adapter.RedisConnection.execute_pipeline(id2type_pipeline) - await redis_adapter.RedisConnection.execute_pipeline(info_content_pipeline) - - logger.info(f"{line_counter} {compendium_filename} total lines processed") - - print(f"Done loading {compendium_filename}...") - except Exception as e: - logger.error(f"Exception thrown in load_compendium({compendium_filename}), line {line_counter}: {e}") - return False - - # return to the caller - return True - - -if __name__ == '__main__': - load() diff --git a/node_normalizer/load_compendium.py b/node_normalizer/load_compendium.py new file mode 100644 index 0000000..4970de9 --- /dev/null +++ b/node_normalizer/load_compendium.py @@ -0,0 +1,285 @@ +import asyncio +import os +from pathlib import Path +import json +from typing import Dict +import bmt as bmt +import asyncclick as click +import redis_adapter +from util import validate_compendium +import logging +from logging.config import dictConfig + +dictConfig( + { + "version": 1, + "disable_existing_loggers": True, + "formatters": {"default": {"format": "%(asctime)s | %(levelname)s | %(module)s:%(funcName)s | %(message)s"}}, + "handlers": { + "console": {"level": "DEBUG", "class": "logging.StreamHandler", "formatter": "default"}, + }, + "loggers": { + "node-norm": {"handlers": ["console"], "level": os.getenv("LOG_LEVEL", "ERROR")}, + }, + } +) +logger = logging.getLogger("node-norm") +logger.propagate = False + +@click.command(no_args_is_help=True) +@click.option("--compendium-file", "-c", help="Compendia File", multiple=True) +@click.option("--block-size", "-b", help="Block Size", default=1000) +@click.option("--dry-run", "-d", help="Dry Run", default=False) +@click.option("--redis-config", "-r", help="Redis Config File", type=click.Path(), default=Path(__file__).parent.parent / "redis_config.yaml") +async def load(compendium_file, block_size, dry_run, redis_config) -> bool: + """ + Given a compendia directory, load every file there into a running + redis instance so that it can be read by R3 + """ + # The new style compendia files look like: + # {"type": "biolink:Disease", "identifiers": [{"i": "UMLS:C4331330", "l": "Stage III Oropharyngeal (p16-Negative) Carcinoma AJCC v8"}, {"i": "NCIT:C132998", "l": "Stage III Oropharyngeal (p16-Negative) Carcinoma AJCC v8"}]} + # {"type": "biolink:Disease", "identifiers": [{"i": "UMLS:C1274244", "l": "Dermatosis in a child"}, {"i": "SNOMEDCT:402803008"}]} + + # Update 11/4/2021: The files now look like: + # {"type": "biolink:Disease", "ic": "100", "identifiers": [{"i": "UMLS:C4331330", "l": "Stage III Oropharyngeal (p16-Negative) Carcinoma AJCC v8"}, {"i": "NCIT:C132998", "l": "Stage III Oropharyngeal (p16-Negative) Carcinoma AJCC v8"}]} + # {"type": "biolink:Disease", "identifiers": [{"i": "UMLS:C1274244", "l": "Dermatosis in a child"}, {"i": "SNOMEDCT:402803008"}]} + + # Update 11/4/2021: a new key of 'ic' (information content) is now incorporated for enhanced filtering of results. + # Type is now a single biolink type so that we can save space rather than the gigantic array + # identifiers replaces equivalent identifiers, and the keys are "i" and "l" rather than 'identifier" and "label". + + # the identifiers are ordered, such that the first identifier is the best identifier. + # We are going to put these different parts into a few different redis tables, and reassemble and nicify on + # output. This will be a touch slower, but it will save a lot of space, and make conflation easier as well. + + # We will have the following redis databases: + # 0: contains identifier.upper() -> canonical_id + # 1: canonical_id -> equivalent_identifiers + # 2: canonical_id -> biolink type + # 3: types -> prefix counts + # Update 11/4/2021: 4: info_content -> filtering value + # 5-X: conflation databases consisting of canonical_id -> (list of conflated canonical_ids) + # Each of these databases corresponds to a particular conflation e.g. gene/protein or chemical/drug + + # for each file validate and process + + # check the existence of files + for comp in compendium_file: + if not os.path.exists(comp): + logger.warning(f"Compendium file {comp} is does not exist") + return False + + # check the validity of the files + for comp in compendium_file: + if not validate_compendium(comp, logger): + logger.warning(f"Compendium file {comp} is invalid") + return False + + try: + + connection_factory: redis_adapter.RedisConnectionFactory = await redis_adapter.RedisConnectionFactory.create_connection_pool(redis_config) + + biolink_version = os.getenv("BIOLINK_VERSION", "2.1.0") + toolkit = bmt.Toolkit(f"https://raw.githubusercontent.com/biolink/biolink-model/{biolink_version}/biolink-model.yaml") + + # get the list of files in the directory + types_prefixes_redis: redis_adapter.RedisConnection = connection_factory.get_connection("curie_to_bl_type_db") + term2id_redis: redis_adapter.RedisConnection = connection_factory.get_connection("eq_id_to_id_db") + id2eqids_redis: redis_adapter.RedisConnection = connection_factory.get_connection("id_to_eqids_db") + id2type_redis: redis_adapter.RedisConnection = connection_factory.get_connection("id_to_type_db") + info_content_redis: redis_adapter.RedisConnection = connection_factory.get_connection("info_content_db") + + for comp in compendium_file: + + ancestor_map = {} + source_prefixes: Dict = {} + + def get_ancestors(input_type): + if input_type in ancestor_map: + return ancestor_map[input_type] + a = toolkit.get_ancestors(input_type) + ancs = {toolkit.get_element(ai)["class_uri"] for ai in a} + if input_type not in ancs: + ancs = ancs.add(input_type) + ancestor_map[input_type] = ancs + return ancs + + # init a line counter + line_counter: int = 0 + try: + + term2id_pipeline = term2id_redis.pipeline() + id2eqids_pipeline = id2eqids_redis.pipeline() + id2type_pipeline = id2type_redis.pipeline() + info_content_pipeline = info_content_redis.pipeline() + + with open(comp, "r", encoding="utf-8") as compendium: + logger.info(f"Processing {comp}...") + + # for each line in the file + for line in compendium: + line_counter = line_counter + 1 + + # example line: + # {"type": "biolink:Cell", "ic": "100", "identifiers": [{"i": "UMLS:C0229659", "l": "Myelomonocyte"}, {"i": "NCIT:C37041", + # "l": "Neoplastic Monocyte"}, {"i": "SNOMEDCT:41621006"}]} + + # load the line into memory + instance: dict = json.loads(line) + + # save the identifier + # "The" identifier is the first one in the presorted identifiers list + identifier: str = instance["identifiers"][0]["i"] + + # We want to accumulate statistics for each implied type as well, though we are only keeping the + # leaf type in the file (and redis). so now is the time to expand. We'll regenerate the same + # list on output. + semantic_types = get_ancestors(instance["type"]) + + # for each semantic type in the list + for semantic_type in semantic_types: + # save the semantic type in a set to avoid duplicates + semantic_types.add(semantic_type) + + # create a source prefix if it has not been encountered + if source_prefixes.get(semantic_type) is None: + source_prefixes[semantic_type] = {} + + # go through each equivalent identifier in the data row + # each will be assigned the semantic type information + for equivalent_id in instance["identifiers"]: + # split the identifier to just get the data source out of the curie + source_prefix: str = equivalent_id["i"].split(":")[0] + + # save the source prefix if no already there + if source_prefixes[semantic_type].get(source_prefix) is None: + source_prefixes[semantic_type][source_prefix] = 1 + # else just increment the count for the semantic type/source + else: + source_prefixes[semantic_type][source_prefix] += 1 + + # equivalent_id might be an array, where the first element is + # the identifier, or it might just be a string. not worrying about that case yet. + equivalent_id = equivalent_id["i"] + term2id_pipeline.set(equivalent_id.upper(), identifier) + # term2id_pipeline.set(equivalent_id, identifier) + + id2eqids_pipeline.set(identifier, json.dumps(instance["identifiers"])) + id2type_pipeline.set(identifier, instance["type"]) + + # if there is information content add it to the cache + if "ic" in instance: + info_content_pipeline.set(identifier, instance["ic"]) + + if not dry_run and line_counter % block_size == 0: + await redis_adapter.RedisConnection.execute_pipeline(term2id_pipeline) + await redis_adapter.RedisConnection.execute_pipeline(id2eqids_pipeline) + await redis_adapter.RedisConnection.execute_pipeline(id2type_pipeline) + await redis_adapter.RedisConnection.execute_pipeline(info_content_pipeline) + + # Pipeline executed create a new one error + term2id_pipeline = term2id_redis.pipeline() + id2eqids_pipeline = id2eqids_redis.pipeline() + id2type_pipeline = id2type_redis.pipeline() + info_content_pipeline = info_content_redis.pipeline() + + logger.info(f"{line_counter} {comp} lines processed") + + if not dry_run: + await redis_adapter.RedisConnection.execute_pipeline(term2id_pipeline) + await redis_adapter.RedisConnection.execute_pipeline(id2eqids_pipeline) + await redis_adapter.RedisConnection.execute_pipeline(id2type_pipeline) + await redis_adapter.RedisConnection.execute_pipeline(info_content_pipeline) + + logger.info(f"{line_counter} {comp} total lines processed") + + print(f"Done loading {comp}...") + except Exception as e: + logger.error(f"Exception thrown in load_compendium({comp}), line {line_counter}: {e}") + return False + + semantic_types_redis_pipeline = types_prefixes_redis.pipeline() + # @TODO add meta data about files eg. checksum to this object + semantic_types_key = f"file-{os.path.basename(comp)}" + logger.debug(f"semantic_types_key: {semantic_types_key}") + semantic_types_values = json.dumps({"source_prefixes": source_prefixes}) + logger.debug(f"semantic_types_values: {semantic_types_values}") + semantic_types_redis_pipeline.set(semantic_types_key, semantic_types_values) + if not dry_run: + response = await redis_adapter.RedisConnection.execute_pipeline(semantic_types_redis_pipeline) + if asyncio.coroutines.iscoroutine(response): + await response + # merge all semantic counts from other files / loaders + await merge_semantic_meta_data(connection_factory, dry_run) + except Exception as e: + logger.exception(f"Exception thrown in load(): {e}") + + # return to the caller + return True + + +async def merge_semantic_meta_data(connection_factory: redis_adapter.RedisConnectionFactory, dry_run: bool): + # get the connection and pipeline to the database + + types_prefixes_redis: redis_adapter.RedisConnection = connection_factory.get_connection("curie_to_bl_type_db") + meta_data_keys = await types_prefixes_redis.keys("file-*") + # recreate pipeline + + types_prefixes_pipeline = types_prefixes_redis.pipeline() + # capture all keys except semenatic_types , as that would be the one that will contain the sum of all semantic types + meta_data_keys = list(filter(lambda key: key != "semantic_types", meta_data_keys)) + + logger.debug(f"meta_data_keys: {meta_data_keys}") + + # get actual data + # for meta_data_key in meta_data_keys: + meta_data = await types_prefixes_redis.mget(*meta_data_keys) + + # meta_data = types_prefixes_pipeline.execute() + logger.debug(f"meta_data: {meta_data}") + + # if asyncio.coroutines.iscoroutine(meta_data): + # meta_data = await meta_data + + all_meta_data = {} + + for meta_data_key, meta_datum in zip(meta_data_keys, meta_data): + if meta_datum: + all_meta_data[meta_data_key] = json.loads(meta_datum) + + logger.debug(f"all_meta_data: {all_meta_data}") + sources_prefix = {} + + for meta_data_key, data in all_meta_data.items(): + prefix_counts = data["source_prefixes"] + for bl_type, curie_counts in prefix_counts.items(): + # if + sources_prefix[bl_type] = sources_prefix.get(bl_type, {}) + for curie_prefix, count in curie_counts.items(): + # get count of this curie prefix + sources_prefix[bl_type][curie_prefix] = sources_prefix[bl_type].get(curie_prefix, 0) + # add up the new count + sources_prefix[bl_type][curie_prefix] += count + + types_prefixes_pipeline = types_prefixes_redis.pipeline() + + if len(sources_prefix.keys()) > 0: + logger.debug(f"sources_prefix.keys(): {sources_prefix.keys()}") + # add all the semantic types + types_prefixes_pipeline.lpush("semantic_types", *list(sources_prefix.keys())) + + # for each semantic type insert the list of source prefixes + for item in sources_prefix: + source_prefix_item_json = json.dumps(sources_prefix[item]) + logger.debug(f"item: {item}, source_prefix_item_json: {source_prefix_item_json}") + types_prefixes_pipeline.set(item, source_prefix_item_json) + + if not dry_run: + # add the data to redis + response = await redis_adapter.RedisConnection.execute_pipeline(types_prefixes_pipeline) + if asyncio.coroutines.iscoroutine(response): + await response + + +if __name__ == "__main__": + load() diff --git a/node_normalizer/load_conflation.py b/node_normalizer/load_conflation.py index e1771a6..66b1edb 100644 --- a/node_normalizer/load_conflation.py +++ b/node_normalizer/load_conflation.py @@ -1,183 +1,110 @@ -import asyncio -import logging from pathlib import Path -from itertools import islice -from datetime import datetime -from typing import Dict, Any -import json -import hashlib -from itertools import combinations -import jsonschema import os -from .redis_adapter import RedisConnectionFactory, RedisConnection -from bmt import Toolkit -from .util import LoggingUtil +import json +import model.response as nn_model +import redis_adapter +from redis_adapter import RedisConnection +import asyncclick as click +import logging +from logging.config import dictConfig + +dictConfig( + { + "version": 1, + "disable_existing_loggers": True, + "formatters": {"default": {"format": "%(asctime)s | %(levelname)s | %(module)s:%(funcName)s | %(message)s"}}, + "handlers": { + "console": {"level": "DEBUG", "class": "logging.StreamHandler", "formatter": "default"}, + }, + "loggers": { + "node-norm": {"handlers": ["console"], "level": os.getenv("LOG_LEVEL", "ERROR")}, + }, + } +) +logger = logging.getLogger("node-norm") +logger.propagate = False + + +@click.command(no_args_is_help=True) +@click.option("--conflation-file", "-c", help="Conflation File", type=click.Path()) +@click.option("--conflation-type", "-s", type=click.Choice(nn_model.ConflationType), help="Conflation Type") +@click.option("--block-size", "-b", help="Block Size", default=1000) +@click.option("--dry-run", "-d", help="Dry Run", default=False, is_flag=True) +@click.option("--redis-config", "-r", help="Redis Config File", type=click.Path(), default=Path(__file__).parent.parent / "redis_config.yaml") +async def main(conflation_file, conflation_type, block_size, dry_run, redis_config): + """ + Given a conflation, load it into a redis so that it can + be read by R3. + """ -logger = LoggingUtil.init_logging() + # check the validity + if not os.path.exists(conflation_file): + logger.warning(f"Conflation file {conflation_file} is invalid.") + return False + try: + connection_factory: redis_adapter.RedisConnectionFactory = await redis_adapter.RedisConnectionFactory.create_connection_pool(redis_config) -class NodeLoader: - """ - Class that gets all node definitions from a series of flat files - and produces Translator compliant nodes which are then loaded into - a redis database. - """ + conflation_db_conn: redis_adapter.RedisConnection = connection_factory.get_connection("conflation_db") + + conflation_pipeline = conflation_db_conn.pipeline() - def __init__(self): - self._config = self.get_config() - - self._compendium_directory: Path = Path(self._config["compendium_directory"]) - self._conflation_directory: Path = Path(self._config["conflation_directory"]) - self._test_mode: int = self._config["test_mode"] - self._data_files: list = self._config["data_files"] - self._conflations: list = self._config["conflations"] - - json_schema = Path(__file__).parent / "resources" / "valid_data_format.json" - - with open(json_schema) as json_file: - self._validate_with = json.load(json_file) - - # Initialize storage instance vars for the semantic types and source prefixes - self.semantic_types: set = set() - self.source_prefixes: Dict = {} - - self.toolkit = Toolkit("https://raw.githubusercontent.com/biolink/biolink-model/2.1.0/biolink-model.yaml") - self.ancestor_map = {} - - def get_ancestors(self, input_type): - if input_type in self.ancestor_map: - return self.ancestor_map[input_type] - a = self.toolkit.get_ancestors(input_type) - ancs = [self.toolkit.get_element(ai)["class_uri"] for ai in a] - if input_type not in ancs: - ancs = [input_type] + ancs - self.ancestor_map[input_type] = ancs - return ancs - - async def merge_semantic_meta_data(self): - - # get the connection and pipeline to the database - - types_prefixes_redis: RedisConnection = await self.get_redis("curie_to_bl_type_db") - meta_data_keys = await types_prefixes_redis.keys("file-*") - # recreate pipeline - - types_prefixes_pipeline = types_prefixes_redis.pipeline() - # capture all keys except semenatic_types , as that would be the one that will contain the sum of all semantic types - meta_data_keys = list(filter(lambda key: key != "semantic_types", meta_data_keys[0])) - - # get actual data - for meta_data_key in meta_data_keys: - types_prefixes_pipeline.get(meta_data_key) - meta_data = types_prefixes_pipeline.execute() - if asyncio.coroutines.iscoroutine(meta_data): - meta_data = await meta_data - all_meta_data = {} - for meta_data_key, meta_datum in zip(meta_data_keys, meta_data): - if meta_datum: - all_meta_data[meta_data_key.decode("utf-8")] = json.loads(meta_datum.decode("utf-8")) - sources_prefix = {} - for meta_data_key, data in all_meta_data.items(): - prefix_counts = data["source_prefixes"] - for bl_type, curie_counts in prefix_counts.items(): - # if - sources_prefix[bl_type] = sources_prefix.get(bl_type, {}) - for curie_prefix, count in curie_counts.items(): - # get count of this curie prefix - sources_prefix[bl_type][curie_prefix] = sources_prefix[bl_type].get(curie_prefix, 0) - # add up the new count - sources_prefix[bl_type][curie_prefix] += count - - types_prefixes_pipeline = types_prefixes_redis.pipeline() - - if len(sources_prefix.keys()) > 0: - # add all the semantic types - types_prefixes_pipeline.lpush("semantic_types", *list(sources_prefix.keys())) - - # for each semantic type insert the list of source prefixes - for item in sources_prefix: - types_prefixes_pipeline.set(item, json.dumps(sources_prefix[item])) - - if self._test_mode != 1: - # add the data to redis - response = await RedisConnection.execute_pipeline(types_prefixes_pipeline) - if asyncio.coroutines.iscoroutine(response): - await response - - def validate_compendia(self, in_file): - # open the file to validate - with open(in_file, "r") as compendium: - logger.info(f"Validating {in_file}...") - - # sample the file - for line in islice(compendium, 5): - try: - instance: dict = json.loads(line) - - # validate the incoming json against the spec - jsonschema.validate(instance=instance, schema=self._validate_with) - # catch any exceptions - except Exception as e: - logger.error(f"Exception thrown in validate_compendia({in_file}): {e}") - return False - - return True - - # TODO: this strikes me as backwards. Caller has to know and look up by index. So the info about what index - # does what is scattered. Instead this should look up by what kind of redis you want and map to dbid for you. - @staticmethod - async def get_redis(db_name): - """ - Return a redis instance - """ - redis_config_path = Path(__file__).parent.parent / "redis_config.yaml" - connection_factory: RedisConnectionFactory = await RedisConnectionFactory.create_connection_pool(redis_config_path) - connection = connection_factory.get_connection(db_name) - return connection - - async def load_conflation(self, conflation: dict, block_size: int) -> bool: - """ - Given a conflation, load it into a redis so that it can - be read by R3. - """ - - conflation_file = conflation["file"] - conflation_redis_connection_name = conflation["redis_db"] - # init a line counter line_counter: int = 0 - try: - conflation_redis: RedisConnection = await self.get_redis(conflation_redis_connection_name) - conflation_pipeline = conflation_redis.pipeline() + with open(conflation_file, "r", encoding="utf-8") as cfile: + logger.info(f"Processing {conflation_file}...") - with open(f"{self._conflation_directory}/{conflation_file}", "r", encoding="utf-8") as cfile: - logger.info(f"Processing {conflation_file}...") + # for each line in the file + for line in cfile: - # for each line in the file - for line in cfile: - line_counter = line_counter + 1 + # example line: + # {"id": {"identifier": "NCBIGene:105021066", "label": "tet2"}, "equivalent_identifiers": [{"identifier": "NCBIGene:105021066", + # "label": "tet2"}, {"identifier": "ENSEMBL:ENSELUG00000017237"}], "type": ["biolink:Gene", "biolink:GeneOrGeneProduct", + # "biolink:BiologicalEntity", "biolink:NamedThing", "biolink:Entity", "biolink:MacromolecularMachineMixin"]} + + # new format: + # ["NCBIGene:246497", "UniProtKB:Q8MLQ0"] + # ["NCBIGene:303135", "UniProtKB:G3V9Z6"] + # ["NCBIGene:191570", "UniProtKB:G3V782"] + # ["NCBIGene:101886961", "UniProtKB:A0A0R4IQ08"] + + # load the line into memory + instance = json.loads(line) - # load the line into memory - instance: dict = json.loads(line) + # We need to include the identifier in the list of identifiers so that we know its position + key = {"conflation_type": conflation_type.value, "canonical_id": instance[0]} + equivalent_identifiers = list(instance[1:]) + + if equivalent_identifiers: + line_counter = line_counter + 1 - for identifier in instance: - # We need to include the identifier in the list of identifiers so that we know its position - conflation_pipeline.set(identifier, line) + logger.debug(f"key: {key}") - if self._test_mode != 1 and line_counter % block_size == 0: - await RedisConnection.execute_pipeline(conflation_pipeline) - # Pipeline executed create a new one error - conflation_pipeline = conflation_redis.pipeline() - logger.info(f"{line_counter} {conflation_file} lines processed") + value = {"equivalent_identifiers": equivalent_identifiers} + # conflation_pipeline.set(identifier, line) + logger.debug(f"conflations: {value}") + conflation_pipeline.set(str(key), str(value)) - if self._test_mode != 1: + if not dry_run and line_counter % block_size == 0: await RedisConnection.execute_pipeline(conflation_pipeline) - logger.info(f"{line_counter} {conflation_file} total lines processed") - print(f"Done loading {conflation_file}...") - except Exception as e: - logger.error(f"Exception thrown in load_conflation({conflation_file}), line {line_counter}: {e}") - return False + # pipelines executed...create a new one + conflation_pipeline = conflation_db_conn.pipeline() + + logger.info(f"{line_counter} {conflation_file} lines processed") + + # break + if not dry_run: + await RedisConnection.execute_pipeline(conflation_pipeline) + logger.info(f"{line_counter} {conflation_file} total lines processed") + + logger.info(f"Done loading {conflation_file}...") + except Exception as e: + logger.error(f"Exception thrown in load_conflation({conflation_file}), line {line_counter}: {e}") + return False + + # return to the caller + return True - # return to the caller - return True +if __name__ == "__main__": + main() diff --git a/node_normalizer/loader.py b/node_normalizer/loader.py deleted file mode 100644 index b38790b..0000000 --- a/node_normalizer/loader.py +++ /dev/null @@ -1,529 +0,0 @@ -import asyncio -import logging -from pathlib import Path -from itertools import islice -from datetime import datetime -from typing import Dict, Any -import json -import hashlib -from itertools import combinations -import jsonschema -import os -from .redis_adapter import RedisConnectionFactory, RedisConnection -from bmt import Toolkit - -from .util import LoggingUtil - -logger = LoggingUtil.init_logging() - - -class NodeLoader: - """ - Class that gets all node definitions from a series of flat files - and produces Translator compliant nodes which are then loaded into - a redis database. - """ - - def __init__(self): - self._config = self.get_config() - - self._compendium_directory: Path = Path(self._config["compendium_directory"]) - self._conflation_directory: Path = Path(self._config["conflation_directory"]) - self._test_mode: int = self._config["test_mode"] - self._data_files: list = self._config["data_files"] - self._conflations: list = self._config["conflations"] - - json_schema = Path(__file__).parent / "resources" / "valid_data_format.json" - - with open(json_schema) as json_file: - self._validate_with = json.load(json_file) - - # Initialize storage instance vars for the semantic types and source prefixes - self.semantic_types: set = set() - self.source_prefixes: Dict = {} - - self.toolkit = Toolkit("https://raw.githubusercontent.com/biolink/biolink-model/2.1.0/biolink-model.yaml") - self.ancestor_map = {} - - def get_ancestors(self, input_type): - if input_type in self.ancestor_map: - return self.ancestor_map[input_type] - a = self.toolkit.get_ancestors(input_type) - ancs = [self.toolkit.get_element(ai)["class_uri"] for ai in a] - if input_type not in ancs: - ancs = [input_type] + ancs - self.ancestor_map[input_type] = ancs - return ancs - - @staticmethod - def get_config() -> Dict[str, Any]: - """get configuration file""" - cname = Path(__file__).parents[1] / "config.json" - - with open(cname, "r") as json_file: - data = json.load(json_file) - - return data - - def convert_to_kgx(self, outfile_name) -> bool: - """ - Given a compendia directory, create a KGX node file - """ - - # init the return value - ret_val = True - - line_counter: int = 0 - - try: - # get the list of files in the directory - compendia: list = self.get_compendia() - - nodes: list = [] - edges: list = [] - pass_nodes: list = [] - - # did we get all the files - if len(compendia) == len(self._data_files): - # open the output file and start loading it - with open(os.path.join(self._compendium_directory, outfile_name + "_nodes.jsonl"), "w", encoding="utf-8") as node_file, open( - os.path.join(self._compendium_directory, outfile_name + "_edges.jsonl"), "w", encoding="utf-8" - ) as edge_file: - - # set the flag for suppressing the first ",\n" in the written data - first = True - - # for each file validate and process - for comp in compendia: - # get the true path to the file - comp = os.path.join(self._compendium_directory, comp) - - # check the validity of the file - if self.validate_compendia(comp): - with open(comp, "r", encoding="utf-8") as compendium: - logger.info(f"Processing {comp}...") - - # get the name of the source - # source = os.path.split(comp)[-1] - - # for each line in the file - for line in compendium: - # increment the record counter - line_counter += 1 - - # clear storage for this pass - pass_nodes.clear() - - # load the line into memory - instance: dict = json.loads(line) - - # all ids (even the root one) are in the equivalent identifiers - if len(instance["identifiers"]) > 0: - # loop through each identifier and create a node - for equiv_id in instance["identifiers"]: - # check to see if there is a label. if there is use it - if "l" in equiv_id: - name = equiv_id["l"] - else: - name = "" - - # add the node to the ones in this pass - pass_nodes.append( - { - "id": equiv_id["i"], - "name": name, - "category": instance["type"], - "equivalent_identifiers": list(x["i"] for x in instance["identifiers"]), - } - ) - - # get the combinations of the nodes in this pass - combos = combinations(pass_nodes, 2) - - # for all the node combinations create an edge between them - for c in combos: - # create a unique id - record_id: str = c[0]["id"] + c[1]["id"] + f"{comp}" - - # save the edge - edges.append( - { - "id": f'{hashlib.md5(record_id.encode("utf-8")).hexdigest()}', - "subject": c[0]["id"], - "predicate": "biolink:same_as", - "object": c[1]["id"], - } - ) - - # save the nodes in this pass to the big list - nodes.extend(pass_nodes) - - # did we reach the write threshold - if line_counter == 10000: - # first time in doesnt get a leading comma - if first: - prefix = "" - else: - prefix = "\n" - - # reset the first record flag - first = False - - # reset the line counter for the next group - line_counter = 0 - - # get all the nodes in a string and write them out - nodes_to_write = prefix + "\n".join([json.dumps(node) for node in nodes]) - node_file.write(nodes_to_write) - - # are there any edges to output - if len(edges) > 0: - # get all the edges in a string and write them out - edges_to_write = prefix + "\n".join([json.dumps(edge) for edge in edges]) - edge_file.write(edges_to_write) - - # reset for the next group - nodes.clear() - edges.clear() - - # pick up any remainders in the file - if len(nodes) > 0: - nodes_to_write = "\n" + "\n".join([json.dumps(node) for node in nodes]) - node_file.write(nodes_to_write) - - if len(edges) > 0: - edges_to_write = "\n" + "\n".join([json.dumps(edge) for edge in edges]) - edge_file.write(edges_to_write) - else: - logger.warning(f"Compendia file {comp} is invalid.") - continue - - except Exception as e: - logger.error(f"Exception thrown in convert_to_KGX(): {e}") - ret_val = False - - # return to the caller - return ret_val - - async def load(self, block_size) -> bool: - """ - Given a compendia directory, load every file there into a running - redis instance so that it can be read by R3 - """ - # The new style compendia files look like: - # {"type": "biolink:Disease", "identifiers": [{"i": "UMLS:C4331330", "l": "Stage III Oropharyngeal (p16-Negative) Carcinoma AJCC v8"}, {"i": "NCIT:C132998", "l": "Stage III Oropharyngeal (p16-Negative) Carcinoma AJCC v8"}]} - # {"type": "biolink:Disease", "identifiers": [{"i": "UMLS:C1274244", "l": "Dermatosis in a child"}, {"i": "SNOMEDCT:402803008"}]} - - # Update 11/4/2021: The files now look like: - # {"type": "biolink:Disease", "ic": "100", "identifiers": [{"i": "UMLS:C4331330", "l": "Stage III Oropharyngeal (p16-Negative) Carcinoma AJCC v8"}, {"i": "NCIT:C132998", "l": "Stage III Oropharyngeal (p16-Negative) Carcinoma AJCC v8"}]} - # {"type": "biolink:Disease", "identifiers": [{"i": "UMLS:C1274244", "l": "Dermatosis in a child"}, {"i": "SNOMEDCT:402803008"}]} - - # Update 11/4/2021: a new key of 'ic' (information content) is now incorporated for enhanced filtering of results. - # Type is now a single biolink type so that we can save space rather than the gigantic array - # identifiers replaces equivalent identifiers, and the keys are "i" and "l" rather than 'identifier" and "label". - - # the identifiers are ordered, such that the first identifier is the best identifier. - # We are going to put these different parts into a few different redis tables, and reassemble and nicify on - # output. This will be a touch slower, but it will save a lot of space, and make conflation easier as well. - - # We will have the following redis databases: - # 0: contains identifier.upper() -> canonical_id - # 1: canonical_id -> equivalent_identifiers - # 2: canonical_id -> biolink type - # 3: types -> prefix counts - # Update 11/4/2021: 4: info_content -> filtering value - # 5-X: conflation databases consisting of canonical_id -> (list of conflated canonical_ids) - # Each of these databases corresponds to a particular conflation e.g. gene/protein or chemical/drug - - # init the return value - ret_val = True - - if self._test_mode == 1: - logger.debug(f"Test mode enabled. No data will be produced.") - - try: - # get the list of files in the directory - compendia: list = self.get_compendia() - types_prefixes_redis: RedisConnection = await self.get_redis("curie_to_bl_type_db") - # did we get all the files - if len(compendia) == len(self._data_files): - # for each file validate and process - for comp in compendia: - # check the validity of the file - if self.validate_compendia(comp): - # try to load the file - loaded = await self.load_compendium(comp, block_size) - semantic_types_redis_pipeline = types_prefixes_redis.pipeline() - # @TODO add meta data about files eg. checksum to this object - semantic_types_redis_pipeline.set(f"file-{str(comp)}", json.dumps({"source_prefixes": self.source_prefixes})) - if self._test_mode != 1: - response = await RedisConnection.execute_pipeline(semantic_types_redis_pipeline) - if asyncio.coroutines.iscoroutine(response): - await response - self.source_prefixes = {} - if not loaded: - logger.warning(f"Compendia file {comp} did not load.") - continue - else: - logger.warning(f"Compendia file {comp} is invalid.") - continue - for conf in self._conflations: - loaded = await self.load_conflation(conf, block_size) - if not loaded: - logger.warning(f"Conflation file {conf} did not load.") - continue - # merge all semantic counts from other files / loaders - await self.merge_semantic_meta_data() - else: - logger.error(f"Error: 1 or more data files were incorrect") - ret_val = False - except Exception as e: - logger.error(f"Exception thrown in load(): {e}") - raise e - - # return to the caller - return ret_val - - async def merge_semantic_meta_data(self): - - # get the connection and pipeline to the database - - types_prefixes_redis: RedisConnection = await self.get_redis("curie_to_bl_type_db") - meta_data_keys = await types_prefixes_redis.keys("file-*") - # recreate pipeline - - types_prefixes_pipeline = types_prefixes_redis.pipeline() - # capture all keys except semenatic_types , as that would be the one that will contain the sum of all semantic types - meta_data_keys = list(filter(lambda key: key != "semantic_types", meta_data_keys[0])) - - # get actual data - for meta_data_key in meta_data_keys: - types_prefixes_pipeline.get(meta_data_key) - meta_data = types_prefixes_pipeline.execute() - if asyncio.coroutines.iscoroutine(meta_data): - meta_data = await meta_data - all_meta_data = {} - for meta_data_key, meta_datum in zip(meta_data_keys, meta_data): - if meta_datum: - all_meta_data[meta_data_key.decode("utf-8")] = json.loads(meta_datum.decode("utf-8")) - sources_prefix = {} - for meta_data_key, data in all_meta_data.items(): - prefix_counts = data["source_prefixes"] - for bl_type, curie_counts in prefix_counts.items(): - # if - sources_prefix[bl_type] = sources_prefix.get(bl_type, {}) - for curie_prefix, count in curie_counts.items(): - # get count of this curie prefix - sources_prefix[bl_type][curie_prefix] = sources_prefix[bl_type].get(curie_prefix, 0) - # add up the new count - sources_prefix[bl_type][curie_prefix] += count - - types_prefixes_pipeline = types_prefixes_redis.pipeline() - - if len(sources_prefix.keys()) > 0: - # add all the semantic types - types_prefixes_pipeline.lpush("semantic_types", *list(sources_prefix.keys())) - - # for each semantic type insert the list of source prefixes - for item in sources_prefix: - types_prefixes_pipeline.set(item, json.dumps(sources_prefix[item])) - - if self._test_mode != 1: - # add the data to redis - response = await RedisConnection.execute_pipeline(types_prefixes_pipeline) - if asyncio.coroutines.iscoroutine(response): - await response - - def validate_compendia(self, in_file): - # open the file to validate - with open(in_file, "r") as compendium: - logger.info(f"Validating {in_file}...") - - # sample the file - for line in islice(compendium, 5): - try: - instance: dict = json.loads(line) - - # validate the incoming json against the spec - jsonschema.validate(instance=instance, schema=self._validate_with) - # catch any exceptions - except Exception as e: - logger.error(f"Exception thrown in validate_compendia({in_file}): {e}") - return False - - return True - - def get_compendia(self): - """ - Return the list of compendium files to load - """ - file_list = [self._compendium_directory / file_name for file_name in self._data_files] - - for file in file_list: - if not file.exists(): - # This should probably raise an exception - logger.warning(f"file not found: {file.name}") - - return file_list - - # TODO: this strikes me as backwards. Caller has to know and look up by index. So the info about what index - # does what is scattered. Instead this should look up by what kind of redis you want and map to dbid for you. - @staticmethod - async def get_redis(db_name): - """ - Return a redis instance - """ - redis_config_path = Path(__file__).parent.parent / "redis_config.yaml" - connection_factory: RedisConnectionFactory = await RedisConnectionFactory.create_connection_pool(redis_config_path) - connection = connection_factory.get_connection(db_name) - return connection - - async def load_conflation(self, conflation: dict, block_size: int) -> bool: - """ - Given a conflation, load it into a redis so that it can - be read by R3. - """ - - conflation_file = conflation["file"] - conflation_redis_connection_name = conflation["redis_db"] - # init a line counter - line_counter: int = 0 - try: - conflation_redis: RedisConnection = await self.get_redis(conflation_redis_connection_name) - conflation_pipeline = conflation_redis.pipeline() - - with open(f"{self._conflation_directory}/{conflation_file}", "r", encoding="utf-8") as cfile: - logger.info(f"Processing {conflation_file}...") - - # for each line in the file - for line in cfile: - line_counter = line_counter + 1 - - # load the line into memory - instance: dict = json.loads(line) - - for identifier in instance: - # We need to include the identifier in the list of identifiers so that we know its position - conflation_pipeline.set(identifier, line) - - if self._test_mode != 1 and line_counter % block_size == 0: - await RedisConnection.execute_pipeline(conflation_pipeline) - # Pipeline executed create a new one error - conflation_pipeline = conflation_redis.pipeline() - logger.info(f"{line_counter} {conflation_file} lines processed") - - if self._test_mode != 1: - await RedisConnection.execute_pipeline(conflation_pipeline) - logger.info(f"{line_counter} {conflation_file} total lines processed") - - print(f"Done loading {conflation_file}...") - except Exception as e: - logger.error(f"Exception thrown in load_conflation({conflation_file}), line {line_counter}: {e}") - return False - - # return to the caller - return True - - async def load_compendium(self, compendium_filename: str, block_size: int) -> bool: - """ - Given the full path to a compendium, load it into redis so that it can - be read by R3. We also load extra keys, which are the upper-cased - identifiers, for ease of use - """ - - # init a line counter - line_counter: int = 0 - try: - term2id_redis: RedisConnection = await self.get_redis("eq_id_to_id_db") - id2eqids_redis: RedisConnection = await self.get_redis("id_to_eqids_db") - id2type_redis: RedisConnection = await self.get_redis("id_to_type_db") - info_content_redis: RedisConnection = await self.get_redis("info_content_db") - - term2id_pipeline = term2id_redis.pipeline() - id2eqids_pipeline = id2eqids_redis.pipeline() - id2type_pipeline = id2type_redis.pipeline() - info_content_pipeline = info_content_redis.pipeline() - - with open(compendium_filename, "r", encoding="utf-8") as compendium: - logger.info(f"Processing {compendium_filename}...") - - # for each line in the file - for line in compendium: - line_counter = line_counter + 1 - - # load the line into memory - instance: dict = json.loads(line) - - # save the identifier - # "The" identifier is the first one in the presorted identifiers list - identifier: str = instance["identifiers"][0]["i"] - - # We want to accumulate statistics for each implied type as well, though we are only keeping the - # leaf type in the file (and redis). so now is the time to expand. We'll regenerate the same - # list on output. - semantic_types = self.get_ancestors(instance["type"]) - - # for each semantic type in the list - for semantic_type in semantic_types: - # save the semantic type in a set to avoid duplicates - self.semantic_types.add(semantic_type) - - # create a source prefix if it has not been encountered - if self.source_prefixes.get(semantic_type) is None: - self.source_prefixes[semantic_type] = {} - - # go through each equivalent identifier in the data row - # each will be assigned the semantic type information - for equivalent_id in instance["identifiers"]: - # split the identifier to just get the data source out of the curie - source_prefix: str = equivalent_id["i"].split(":")[0] - - # save the source prefix if no already there - if self.source_prefixes[semantic_type].get(source_prefix) is None: - self.source_prefixes[semantic_type][source_prefix] = 1 - # else just increment the count for the semantic type/source - else: - self.source_prefixes[semantic_type][source_prefix] += 1 - - # equivalent_id might be an array, where the first element is - # the identifier, or it might just be a string. not worrying about that case yet. - equivalent_id = equivalent_id["i"] - term2id_pipeline.set(equivalent_id.upper(), identifier) - # term2id_pipeline.set(equivalent_id, identifier) - - id2eqids_pipeline.set(identifier, json.dumps(instance["identifiers"])) - id2type_pipeline.set(identifier, instance["type"]) - - # if there is information content add it to the cache - if "ic" in instance: - info_content_pipeline.set(identifier, instance["ic"]) - - if self._test_mode != 1 and line_counter % block_size == 0: - await RedisConnection.execute_pipeline(term2id_pipeline) - await RedisConnection.execute_pipeline(id2eqids_pipeline) - await RedisConnection.execute_pipeline(id2type_pipeline) - await RedisConnection.execute_pipeline(info_content_pipeline) - - # Pipeline executed create a new one error - term2id_pipeline = term2id_redis.pipeline() - id2eqids_pipeline = id2eqids_redis.pipeline() - id2type_pipeline = id2type_redis.pipeline() - info_content_pipeline = info_content_redis.pipeline() - - logger.info(f"{line_counter} {compendium_filename} lines processed") - - if self._test_mode != 1: - await RedisConnection.execute_pipeline(term2id_pipeline) - await RedisConnection.execute_pipeline(id2eqids_pipeline) - await RedisConnection.execute_pipeline(id2type_pipeline) - await RedisConnection.execute_pipeline(info_content_pipeline) - - logger.info(f"{line_counter} {compendium_filename} total lines processed") - - print(f"Done loading {compendium_filename}...") - except Exception as e: - logger.error(f"Exception thrown in load_compendium({compendium_filename}), line {line_counter}: {e}") - return False - - # return to the caller - return True diff --git a/node_normalizer/model/input.py b/node_normalizer/model/input.py index cf46791..249ead0 100644 --- a/node_normalizer/model/input.py +++ b/node_normalizer/model/input.py @@ -6,6 +6,10 @@ from typing import List +from typing import Optional + +from .response import ConflationType + class CurieList(BaseModel): """Curie list input model""" @@ -16,10 +20,11 @@ class CurieList(BaseModel): min_items=1 ) - conflate:bool = Field( - True, - title="Whether to apply conflation" - ) + conflation_type: Optional[ConflationType] + # conflate:bool = Field( + # True, + # title="Whether to apply conflation" + # ) class Config: schema_extra = { diff --git a/node_normalizer/model/response.py b/node_normalizer/model/response.py index ecf9d0c..bf3bdf7 100644 --- a/node_normalizer/model/response.py +++ b/node_normalizer/model/response.py @@ -1,6 +1,7 @@ """ API Response Models not described in reasoner-pydantic """ +from enum import Enum from pydantic import BaseModel @@ -11,21 +12,18 @@ class SemanticTypes(BaseModel): semantic_types: Dict[str, List] class Config: - schema_extra = { - "example": { - "semantic_types": { - "types": [ - "cellular_component", - "named_thing", - "etc." - ] - } - } - } + schema_extra = {"example": {"semantic_types": {"types": ["biolink:Cell", "biolink:AnatomicalEntity", "etc."]}}} class CuriePivot(BaseModel): curie_prefix: Dict[str, str] + class ConflationList(BaseModel): - conflations: List \ No newline at end of file + conflations: List + + +class ConflationType(str, Enum): + GENE_PROTEIN = "gene_protein" + CHEMICAL_DRUG = "chemical_drug" + diff --git a/node_normalizer/normalizer.py b/node_normalizer/normalizer.py index 27f8e47..8703c02 100644 --- a/node_normalizer/normalizer.py +++ b/node_normalizer/normalizer.py @@ -1,6 +1,4 @@ import json -import logging -import os import uuid from typing import List, Dict, Optional, Any, Set, Tuple, Union from uuid import UUID @@ -8,23 +6,25 @@ from fastapi import FastAPI from reasoner_pydantic import KnowledgeGraph, Message, QueryGraph, Result, CURIE, Attribute +from .model.response import ConflationType from .util import LoggingUtil, uniquify_list # logger = LoggingUtil.init_logging(__name__, level=logging.INFO, format='medium', logFilePath=os.path.dirname(__file__), logFileLevel=logging.INFO) logger = LoggingUtil.init_logging() + def get_ancestors(app, input_type): if input_type in app.state.ancestor_map: return app.state.ancestor_map[input_type] a = app.state.toolkit.get_ancestors(input_type) - ancs = [app.state.toolkit.get_element(ai)['class_uri'] for ai in a] + ancs = [app.state.toolkit.get_element(ai)["class_uri"] for ai in a] if input_type not in ancs: ancs = [input_type] + ancs app.state.ancestor_map[input_type] = ancs return ancs -async def normalize_message(app: FastAPI, message: Message) -> Message: +async def normalize_message(app: FastAPI, message: Message, conflation_type: ConflationType = None) -> Message: """ Given a TRAPI message, updates the message to include a normalized qgraph, kgraph, and results @@ -39,7 +39,7 @@ async def normalize_message(app: FastAPI, message: Message) -> Message: logger.debug(f"message.knowledge_graph is None: {message.knowledge_graph is None}") if message.knowledge_graph is not None: - merged_kgraph, node_id_map, edge_id_map = await normalize_kgraph(app, message.knowledge_graph) + merged_kgraph, node_id_map, edge_id_map = await normalize_kgraph(app, message.knowledge_graph, conflation_type) ret.knowledge_graph = merged_kgraph logger.debug(f"message.results is None: {message.results is None}") @@ -49,14 +49,10 @@ async def normalize_message(app: FastAPI, message: Message) -> Message: return ret except Exception as e: - logger.error(f'normalize_message Exception: {e}') + logger.error(f"normalize_message Exception: {e}") -async def normalize_results(app, - results: List[Result], - node_id_map: Dict[str, str], - edge_id_map: Dict[str, str] - ) -> List[Result]: +async def normalize_results(app, results: List[Result], node_id_map: Dict[str, str], edge_id_map: Dict[str, str]) -> List[Result]: """ Given a TRAPI result creates a normalized result object """ @@ -65,10 +61,7 @@ async def normalize_results(app, result_seen = set() for result in results: - merged_result = { - 'node_bindings': {}, - 'edge_bindings': {} - } + merged_result = {"node_bindings": {}, "edge_bindings": {}} node_binding_seen = set() @@ -78,34 +71,31 @@ async def normalize_results(app, for n_bind in node_bindings: merged_binding = n_bind.dict() # merged_binding['id'] = node_id_map[n_bind.id.__root__] - merged_binding['id'] = node_id_map[n_bind.id] + merged_binding["id"] = node_id_map[n_bind.id] # get the information content value - ic_attrib = await get_info_content_attribute(app, merged_binding['id']) + ic_attrib = await get_info_content_attribute(app, merged_binding["id"]) # did we get a good attribute dict if ic_attrib: - if 'attributes' in merged_binding: - merged_binding['attributes'].append(ic_attrib) + if "attributes" in merged_binding: + merged_binding["attributes"].append(ic_attrib) else: - merged_binding['attributes'] = [ic_attrib] + merged_binding["attributes"] = [ic_attrib] node_binding_information = [ - "atts" if k == 'attributes' - else (k, tuple(v)) if isinstance(v, list) - else (k, v) - for k, v in merged_binding.items() + "atts" if k == "attributes" else (k, tuple(v)) if isinstance(v, list) else (k, v) for k, v in merged_binding.items() ] # if there are attributes in the node binding - if 'attributes' in merged_binding: + if "attributes" in merged_binding: # storage for the pydantic Attributes attribs = [] # the items in list of attributes must be of type Attribute # in order to reuse hash method - if merged_binding['attributes'] is not None: - for attrib in merged_binding['attributes']: + if merged_binding["attributes"] is not None: + for attrib in merged_binding["attributes"]: new_attrib = Attribute.parse_obj(attrib) # add the new Attribute to the list @@ -122,7 +112,7 @@ async def normalize_results(app, node_binding_seen.add(node_binding_hash) merged_node_bindings.append(merged_binding) - merged_result['node_bindings'][node_code] = merged_node_bindings + merged_result["node_bindings"][node_code] = merged_node_bindings except Exception as e: logger.exception(e) @@ -134,12 +124,9 @@ async def normalize_results(app, merged_edge_bindings = [] for e_bind in edge_bindings: merged_binding = e_bind.dict() - merged_binding['id'] = edge_id_map[e_bind.id] + merged_binding["id"] = edge_id_map[e_bind.id] - edge_binding_hash = frozenset([ - (k, freeze(v)) - for k, v in merged_binding.items() - ]) + edge_binding_hash = frozenset([(k, freeze(v)) for k, v in merged_binding.items()]) if edge_binding_hash in edge_binding_seen: continue @@ -147,7 +134,7 @@ async def normalize_results(app, edge_binding_seen.add(edge_binding_hash) merged_edge_bindings.append(merged_binding) - merged_result['edge_bindings'][edge_code] = merged_edge_bindings + merged_result["edge_bindings"][edge_code] = merged_edge_bindings except Exception as e: logger.exception(e) @@ -157,7 +144,7 @@ async def normalize_results(app, hashed_result = json.dumps(merged_result, sort_keys=True) except Exception as e: # TODO determine exception(s) to catch - logger.error(f'normalize_results Exception: {e}') + logger.error(f"normalize_results Exception: {e}") hashed_result = False if hashed_result is not False: @@ -202,26 +189,20 @@ async def normalize_qgraph(app: FastAPI, qgraph: QueryGraph) -> QueryGraph: raise Exception("node.ids must be a list") primary_ids = set() for nr in node.ids.__root__: - equivalent_curies = await get_equivalent_curies(app, nr) + equivalent_curies = await get_equivalent_curies(app, nr, None) if equivalent_curies[nr]: - primary_ids.add(equivalent_curies[nr]['id']['identifier']) + primary_ids.add(equivalent_curies[nr]["id"]["identifier"]) else: primary_ids.add(nr) - merged_nodes[node_code]['ids'] = list(primary_ids) + merged_nodes[node_code]["ids"] = list(primary_ids) node_code_map[node_code] = list(primary_ids) except Exception as e: - logger.error(f'normalize_qgraph Exception: {e}') + logger.error(f"normalize_qgraph Exception: {e}") - return QueryGraph.parse_obj({ - 'nodes': merged_nodes, - 'edges': qgraph.edges - }) + return QueryGraph.parse_obj({"nodes": merged_nodes, "edges": qgraph.edges}) -async def normalize_kgraph( - app: FastAPI, - kgraph: KnowledgeGraph -) -> Tuple[KnowledgeGraph, Dict[str, str], Dict[str, str]]: +async def normalize_kgraph(app: FastAPI, kgraph: KnowledgeGraph, conflation_type: ConflationType = None) -> Tuple[KnowledgeGraph, Dict[str, str], Dict[str, str]]: """ Given a TRAPI knowledge graph creates a merged graph by iterating over each node, getting the primary id, @@ -233,10 +214,7 @@ async def normalize_kgraph( being an edge id map """ - merged_kgraph: Dict = { - 'nodes': {}, - 'edges': {} - } + merged_kgraph: Dict = {"nodes": {}, "edges": {}} node_id_map: Dict[str, str] = {} edge_id_map: Dict[str, str] = {} @@ -272,19 +250,17 @@ async def normalize_kgraph( merged_node = node.dict() - equivalent_curies = await get_equivalent_curies(app, node_id) + equivalent_curies = await get_equivalent_curies(app, node_id, conflation_type) if equivalent_curies[node_id]: - primary_id = equivalent_curies[node_id]['id']['identifier'] + primary_id = equivalent_curies[node_id]["id"]["identifier"] node_id_map[node_id] = primary_id if primary_id in primary_nodes_seen: merged_node = _merge_node_attributes( - node_a=merged_kgraph['nodes'][primary_id], - node_b=node.dict(), - merged_count=node_merge_count[primary_id] + node_a=merged_kgraph["nodes"][primary_id], node_b=node.dict(), merged_count=node_merge_count[primary_id] ) - merged_kgraph['nodes'][primary_id] = merged_node + merged_kgraph["nodes"][primary_id] = merged_node node_merge_count[primary_id] += 1 continue else: @@ -292,44 +268,39 @@ async def normalize_kgraph( primary_nodes_seen.add(primary_id) - if 'label' in equivalent_curies[node_id]['id']: - primary_label = equivalent_curies[node_id]['id']['label'] - elif 'name' in merged_node: - primary_label = merged_node['name'] + if "label" in equivalent_curies[node_id]["id"]: + primary_label = equivalent_curies[node_id]["id"]["label"] + elif "name" in merged_node: + primary_label = merged_node["name"] else: - primary_label = '' + primary_label = "" - merged_node['name'] = primary_label + merged_node["name"] = primary_label # Even if there's already a same_as attribute we add another # since it is coming from a new source - if 'equivalent_identifiers' in equivalent_curies[node_id]: + if "equivalent_identifiers" in equivalent_curies[node_id]: same_as_attribute = { - 'attribute_type_id': 'biolink:same_as', - 'value': [ - node['identifier'] - for node in equivalent_curies[node_id]['equivalent_identifiers'] - ], - 'original_attribute_name': 'equivalent_identifiers', + "attribute_type_id": "biolink:same_as", + "value": [node["identifier"] for node in equivalent_curies[node_id]["equivalent_identifiers"]], + "original_attribute_name": "equivalent_identifiers", "value_type_id": "EDAM:data_0006", - # TODO, should we add the app version as the source # or perhaps the babel/redis cache version # This will make unit testing a little more tricky # see https://stackoverflow.com/q/57624731 - # 'source': f'{app.title} {app.version}', } - if 'attributes' in merged_node and merged_node['attributes']: - merged_node['attributes'].append(same_as_attribute) + if "attributes" in merged_node and merged_node["attributes"]: + merged_node["attributes"].append(same_as_attribute) else: - merged_node['attributes'] = [same_as_attribute] + merged_node["attributes"] = [same_as_attribute] - if 'type' in equivalent_curies[node_id]: - if type(equivalent_curies[node_id]['type']) is list: - merged_node['categories'] = equivalent_curies[node_id]['type'] + if "type" in equivalent_curies[node_id]: + if type(equivalent_curies[node_id]["type"]) is list: + merged_node["categories"] = equivalent_curies[node_id]["type"] else: - merged_node['categories'] = [equivalent_curies[node_id]['type']] + merged_node["categories"] = [equivalent_curies[node_id]["type"]] # get the information content value ic_attrib = await get_info_content_attribute(app, node_id) @@ -337,11 +308,11 @@ async def normalize_kgraph( # did we get a good attribute dict if ic_attrib: # add the attribute to the node - merged_node['attributes'].append(ic_attrib) + merged_node["attributes"].append(ic_attrib) - merged_kgraph['nodes'][primary_id] = merged_node + merged_kgraph["nodes"][primary_id] = merged_node else: - merged_kgraph['nodes'][node_id] = merged_node + merged_kgraph["nodes"][node_id] = merged_node for edge_id, edge in kgraph.edges.items(): # Accessing __root__ directly seems wrong, @@ -364,12 +335,7 @@ async def normalize_kgraph( # we couldn't hash the attribute so assume unique hashed_attributes = uuid.uuid4() - triple = ( - primary_subject, - edge.predicate, - primary_object, - hashed_attributes - ) + triple = (primary_subject, edge.predicate, primary_object, hashed_attributes) if triple in edges_seen: edge_id_map[edge_id] = primary_edges[triple] @@ -381,19 +347,16 @@ async def normalize_kgraph( edges_seen.add(triple) merged_edge = edge.dict() - merged_edge['subject'] = primary_subject - merged_edge['object'] = primary_object - merged_kgraph['edges'][edge_id] = merged_edge + merged_edge["subject"] = primary_subject + merged_edge["object"] = primary_object + merged_kgraph["edges"][edge_id] = merged_edge except Exception as e: - logger.error(f'normalize_kgraph Exception: {e}') + logger.error(f"normalize_kgraph Exception: {e}") return KnowledgeGraph.parse_obj(merged_kgraph), node_id_map, edge_id_map -async def get_equivalent_curies( - app: FastAPI, - curie: Union[str, CURIE] -) -> Dict: +async def get_equivalent_curies(app: FastAPI, curie: Union[str, CURIE], conflation_type: ConflationType = None) -> Dict: """ Get primary id and equivalent curies using redis GET @@ -412,7 +375,7 @@ async def get_equivalent_curies( try: # Get the equivalent list primary key identifier - value = await get_normalized_nodes(app, [curie], True) + value = await get_normalized_nodes(app, [curie], conflation_type) # did we get a valid response if value is None: @@ -420,16 +383,14 @@ async def get_equivalent_curies( return default_return except Exception as e: - logger.error(f'get_equivalent_curies Exception: {e}') + logger.error(f"get_equivalent_curies Exception: {e}") return default_return # return the curie normalization data return value -async def get_info_content( - app: FastAPI, - canonical_nonan: List) -> dict: +async def get_info_content(app: FastAPI, canonical_nonan: List) -> dict: """ Gets the information content value for the node id @@ -442,7 +403,7 @@ async def get_info_content( return {} # call redis and get the value - info_contents = await app.state.redis_connection4.mget(*canonical_nonan, encoding='utf8') + info_contents = await app.state.redis_connection4.mget(*canonical_nonan, encoding="utf8") # get this into a list info_contents = [round(float(ic_ids), 1) if ic_ids is not None else None for ic_ids in info_contents] @@ -454,55 +415,48 @@ async def get_info_content( return info_contents -async def get_eqids_and_types( - app: FastAPI, - canonical_nonan: List) -> (List, List): +async def get_eqids_and_types(app: FastAPI, canonical_nonan: List) -> (List, List): if len(canonical_nonan) == 0: return [], [] - eqids = await app.state.redis_connection1.mget(*canonical_nonan, encoding='utf-8') + eqids = await app.state.redis_connection1.mget(*canonical_nonan, encoding="utf-8") eqids = [json.loads(value) if value is not None else None for value in eqids] - types = await app.state.redis_connection2.mget(*canonical_nonan, encoding='utf-8') + types = await app.state.redis_connection2.mget(*canonical_nonan, encoding="utf-8") types = [get_ancestors(app, t) for t in types] return eqids, types -async def get_normalized_nodes( - app: FastAPI, - curies: List[Union[CURIE, str]], - conflate: bool -) -> Dict[str, Optional[str]]: +async def get_normalized_nodes(app: FastAPI, curies: List[Union[CURIE, str]], conflation_type: ConflationType = None) -> Dict[str, Optional[str]]: """ Get value(s) for key(s) using redis MGET """ # malkovich malkovich - curies = [ - curie.__root__ if isinstance(curie, CURIE) else curie - for curie in curies - ] + curies = [curie.__root__ if isinstance(curie, CURIE) else curie for curie in curies] normal_nodes = {} - # TODO: Add an option that lets one choose which conflations to do, and get the details of those conflations from the configs. - # conflation_types = {"biolink:Gene", "biolink:Protein"} - # conflation_redis = 5 + logger.info(f"conflation_type: {conflation_type}") upper_curies = [c.upper() for c in curies] + logger.info(f"upper_curies: {upper_curies}") try: - canonical_ids = await app.state.redis_connection0.mget(*upper_curies, encoding='utf-8') + canonical_ids = await app.state.redis_connection0.mget(*upper_curies, encoding="utf-8") canonical_nonan = [canonical_id for canonical_id in canonical_ids if canonical_id is not None] + logger.info(f"canonical_nonan: {canonical_nonan}") info_contents = {} # did we get some canonical ids if canonical_nonan: + # get the information content values info_contents = await get_info_content(app, canonical_nonan) + logger.info(f"info_contents: {info_contents}") # Get the equivalent_ids and types eqids, types = await get_eqids_and_types(app, canonical_nonan) + logger.info(f"eqids: {eqids}, types: {types}") # are we looking for conflated values - if conflate: - # TODO: filter to just types that have Gene or Protein? I'm not sure it's worth it when we have pipelining - other_ids = await app.state.redis_connection5.mget(*canonical_nonan, encoding='utf8') + if conflation_type: + other_ids = await app.state.redis_connection5.mget(*canonical_nonan, encoding="utf8") # if there are other ids, then we want to rebuild eqids and types. That's because even though we have them, # they're not necessarily first. For instance if what came in and got canonicalized was a protein id @@ -537,6 +491,8 @@ async def get_normalized_nodes( dereference_ids = dict(zip(canonical_nonan, final_eqids)) dereference_types = dict(zip(canonical_nonan, final_types)) else: + logger.info("conflation type is None") + dereference_ids = dict(zip(canonical_nonan, eqids)) dereference_types = dict(zip(canonical_nonan, types)) else: @@ -550,7 +506,7 @@ async def get_normalized_nodes( } except Exception as e: - logger.error(f'Exception: {e}') + logger.exception(e) return normal_nodes @@ -564,13 +520,17 @@ async def get_info_content_attribute(app, canonical_nonan) -> dict: :return: """ # get the information content value - ic_val = await app.state.redis_connection4.get(canonical_nonan, encoding='utf8') + ic_val = await app.state.redis_connection4.get(canonical_nonan, encoding="utf8") # did we get a good value if ic_val is not None: # load up a dict with the attribute data and create a trapi attribute object - new_attrib = dict(attribute_type_id="biolink:has_numeric_value", original_attribute_name="information_content", value_type_id="EDAM:data_0006", - value=round(float(ic_val), 1)) + new_attrib = dict( + attribute_type_id="biolink:has_numeric_value", + original_attribute_name="information_content", + value_type_id="EDAM:data_0006", + value=round(float(ic_val), 1), + ) else: # else return nothing new_attrib = None @@ -589,32 +549,28 @@ async def create_node(canonical_id, equivalent_ids, types, info_contents): eids = equivalent_ids[canonical_id] # First, we need to create the "id" node. The identifier is our input canonical id, but we have to get a label - labels = list(filter(lambda x: len(x) > 0, [eid['l'] for eid in eids if 'l' in eid])) + labels = list(filter(lambda x: len(x) > 0, [eid["l"] for eid in eids if "l" in eid])) # Note that the id will be from the equivalent ids, not the canonical_id. This is to handle conflation if len(labels) > 0: - node = {"id": {"identifier": eids[0]['i'], "label": labels[0]}} + node = {"id": {"identifier": eids[0]["i"], "label": labels[0]}} else: # Sometimes, nothing has a label :( - node = {"id": {"identifier": eids[0]['i']}} + node = {"id": {"identifier": eids[0]["i"]}} # now need to reformat the identifier keys. It could be cleaner but we have to worry about if there is a label - node['equivalent_identifiers'] = [{"identifier": eqid["i"], "label": eqid["l"]} if "l" in eqid - else {"identifier": eqid["i"]} for eqid in eids] + node["equivalent_identifiers"] = [{"identifier": eqid["i"], "label": eqid["l"]} if "l" in eqid else {"identifier": eqid["i"]} for eqid in eids] - node['type'] = types[canonical_id] + node["type"] = types[canonical_id] # add the info content to the node if we got one if info_contents[canonical_id] is not None: - node['information_content'] = info_contents[canonical_id] + node["information_content"] = info_contents[canonical_id] return node -async def get_curie_prefixes( - app: FastAPI, - semantic_types: Optional[List[str]] = None -) -> Dict[str, Any]: +async def get_curie_prefixes(app: FastAPI, semantic_types: Optional[List[str]] = None) -> Dict[str, Any]: """ Get pivot table of semantic type x curie prefix """ @@ -625,33 +581,33 @@ async def get_curie_prefixes( if semantic_types: for item in semantic_types: # get the curies for this type - curies = await app.state.redis_connection3.get(item, encoding='utf-8') + curies = await app.state.redis_connection3.get(item, encoding="utf-8") # did we get any data if not curies: - curies = '{' + f'"{item}"' + ': "Not found"}' + curies = "{" + f'"{item}"' + ': "Not found"}' curies = json.loads(curies) # set the return data - ret_val[item] = {'curie_prefix': curies} + ret_val[item] = {"curie_prefix": curies} else: - types = await app.state.redis_connection3.lrange('semantic_types', 0, -1, encoding='utf-8') + types = await app.state.redis_connection3.lrange("semantic_types", 0, -1, encoding="utf-8") for item in types: # get the curies for this type - curies = await app.state.redis_connection3.get(item, encoding='utf-8') + curies = await app.state.redis_connection3.get(item, encoding="utf-8") # did we get any data if not curies: - curies = '{' + f'"{item}"' + ': "Not found"}' + curies = "{" + f'"{item}"' + ': "Not found"}' curies = json.loads(curies) # set the return data - ret_val[item] = {'curie_prefix': curies} + ret_val[item] = {"curie_prefix": curies} except Exception as e: - logger.error(f'get_curie_prefixes Exception: {e}') + logger.error(f"get_curie_prefixes Exception: {e}") return ret_val @@ -664,33 +620,33 @@ def _merge_node_attributes(node_a: Dict, node_b, merged_count: int) -> Dict: """ try: - if not ('attributes' in node_b and node_b['attributes']): + if not ("attributes" in node_b and node_b["attributes"]): return node_a if merged_count == 0: - if 'attributes' in node_a and node_a['attributes']: + if "attributes" in node_a and node_a["attributes"]: new_attribute_list = [] - for attribute in node_a['attributes']: + for attribute in node_a["attributes"]: new_dict = {} for k, v in attribute.items(): new_dict[f"{k}.1"] = v new_attribute_list.append(new_dict) - node_a['attributes'] = new_attribute_list + node_a["attributes"] = new_attribute_list # Need to DRY this off b_attr_id = merged_count + 2 - if 'attributes' in node_b and node_b['attributes']: + if "attributes" in node_b and node_b["attributes"]: new_attribute_list = [] - for attribute in node_b['attributes']: + for attribute in node_b["attributes"]: new_dict = {} for k, v in attribute.items(): new_dict[f"{k}.{b_attr_id}"] = v new_attribute_list.append(new_dict) - node_a['attributes'] = node_a['attributes'] + new_attribute_list + node_a["attributes"] = node_a["attributes"] + new_attribute_list except Exception as e: - logger.error(f'_merge_node_attributes Exception {e}') + logger.error(f"_merge_node_attributes Exception {e}") return node_a @@ -720,11 +676,7 @@ def _hash_attributes(attributes: List[Attribute] = None) -> Union[int, bool]: # TODO list of lists? hashed_value = tuple(attribute.value) elif isinstance(attribute.value, dict): - hashed_value = tuple( - (k, tuple(v)) - if isinstance(v, list) - else (k, v) - for k, v in attribute.value.items()) + hashed_value = tuple((k, tuple(v)) if isinstance(v, list) else (k, v) for k, v in attribute.value.items()) new_attribute = ( attribute.attribute_type_id, @@ -732,12 +684,12 @@ def _hash_attributes(attributes: List[Attribute] = None) -> Union[int, bool]: attribute.original_attribute_name, attribute.value_url, attribute.attribute_source, - attribute.value_type_id if attribute.value_type_id is not None else '', - attribute.attribute_source + attribute.value_type_id if attribute.value_type_id is not None else "", + attribute.attribute_source, ) new_attributes.append(new_attribute) return hash(frozenset(new_attributes)) except Exception as e: - logger.error(f'_hash_attributes Exception: {e}') + logger.error(f"_hash_attributes Exception: {e}") return False diff --git a/node_normalizer/redis_adapter.py b/node_normalizer/redis_adapter.py index 51d1da1..79a5f49 100644 --- a/node_normalizer/redis_adapter.py +++ b/node_normalizer/redis_adapter.py @@ -1,4 +1,3 @@ - from dataclasses import dataclass, field import rediscluster from rediscluster import RedisCluster @@ -15,7 +14,7 @@ class Resource: @dataclass class RedisInstance: ssl_enabled: bool = False - password: str = '' + password: str = "" is_cluster: bool = True hosts: List[Resource] = field(default_factory=list) host: Resource = None # Use if is_cluster == False @@ -46,6 +45,7 @@ class RedisConnection: Abstraction layer for redis interaction. Supporting both Clustered, standalone redis backends. """ + def __init__(self): self.connector = None @@ -57,30 +57,26 @@ async def create(cls, redis_instance: RedisInstance): self = RedisConnection() other_params = {} if redis_instance.password: - other_params['password'] = redis_instance.password + other_params["password"] = redis_instance.password if redis_instance.ssl_enabled: - other_params['ssl'] = redis_instance.ssl_enabled + other_params["ssl"] = redis_instance.ssl_enabled if redis_instance.is_cluster: host: Resource hosts = [{"host": host.host_name, "port": host.port} for host in redis_instance.hosts] if redis_instance.ssl_enabled: - other_params['ssl_cert_reqs'] = False + other_params["ssl_cert_reqs"] = False - redis_connector = RedisCluster(startup_nodes=hosts, - decode_responses=True, - skip_full_coverage_check=True, - **other_params) + redis_connector = RedisCluster(startup_nodes=hosts, decode_responses=True, skip_full_coverage_check=True, **other_params) else: host: Resource = redis_instance.hosts[0] - redis_connector = await aioredis.create_redis_pool(f'redis://{host.host_name}:{host.port}', - db=redis_instance.db, - **other_params) + print(f"{host.host_name}:{host.port}") + redis_connector = await aioredis.create_redis_pool(f"redis://{host.host_name}:{host.port}", db=redis_instance.db, **other_params) self.connector = redis_connector return self - async def mget(self, *keys, encoding='utf-8'): + async def mget(self, *keys, encoding="utf-8"): """ Execute mget command. """ @@ -91,7 +87,18 @@ async def mget(self, *keys, encoding='utf-8'): self.connector: aioredis.commands.Redis return await self.connector.mget(*keys, encoding=encoding) - async def get(self, key, encoding='utf-8'): + async def set(self, key, value): + """ + Execute set command. + """ + if isinstance(self.connector, RedisCluster): + self.connector: RedisCluster + return self.connector.set(name=key, value=value) + elif isinstance(self.connector, aioredis.commands.Redis): + self.connector: aioredis.commands.Redis + return await self.connector.set(key=key, value=value) + + async def get(self, key, encoding="utf-8"): """ Execute redis get command. """ @@ -120,7 +127,7 @@ async def wait_closed(self): self.connector: aioredis.commands.Redis await self.connector.wait_closed() - async def lrange(self, key, start, stop, encoding='utf-8'): + async def lrange(self, key, start, stop, encoding="utf-8"): """ Execute Lrange command. """ @@ -128,7 +135,7 @@ async def lrange(self, key, start, stop, encoding='utf-8'): self.connector: RedisCluster return self.connector.lrange(name=key, start=start, end=stop) elif isinstance(self.connector, aioredis.commands.Redis): - self.connector: aioredis.commands.Redis + self.connector: aioredis.commands.Redis return await self.connector.lrange(key=key, start=start, stop=stop, encoding=encoding) def pipeline(self): @@ -146,6 +153,7 @@ async def keys(self, pattern, encoding="utf-8"): elif isinstance(self.connector, aioredis.commands.Redis): self.connector: aioredis.commands.Redis return await self.connector.keys(pattern=pattern, encoding=encoding) + @staticmethod def reset_pipeline(pipeline): if isinstance(pipeline, aioredis.commands.transaction.Pipeline): @@ -169,6 +177,7 @@ class RedisConnectionFactory: """ Class to create three redis connections based on config """ + connections: Dict[str, RedisConnection] = {} def __init__(self): @@ -177,6 +186,7 @@ def __init__(self): @staticmethod def get_config(file_name) -> ConnectionConfig: import yaml + with open(file_name) as f: config = ConnectionConfig(yaml.load(f, yaml.FullLoader)) return config @@ -187,8 +197,7 @@ async def create_connection_pool(cls, config_file_path): self = RedisConnectionFactory() if not RedisConnectionFactory.connections: RedisConnectionFactory.connections = { - connection_name: await RedisConnection.create(config.__getattr__(connection_name)) - for connection_name in config.get_connection_names() + connection_name: await RedisConnection.create(config.__getattr__(connection_name)) for connection_name in config.get_connection_names() } return self diff --git a/node_normalizer/resources/valid_data_format.json b/node_normalizer/resources/valid_compendium_data_format.json similarity index 100% rename from node_normalizer/resources/valid_data_format.json rename to node_normalizer/resources/valid_compendium_data_format.json diff --git a/node_normalizer/resources/valid_conflation_data_format.json b/node_normalizer/resources/valid_conflation_data_format.json new file mode 100644 index 0000000..ac26906 --- /dev/null +++ b/node_normalizer/resources/valid_conflation_data_format.json @@ -0,0 +1,97 @@ +{ + "definitions": {}, + "$schema": "http://json-schema.org/draft-07/schema#", + "$id": "https://example.com/object1666265991.json", + "title": "Root", + "type": "object", + "required": [ + "id", + "equivalent_identifiers", + "type" + ], + "properties": { + "id": { + "$id": "#root/id", + "title": "Id", + "type": "object", + "required": [ + "identifier" + ], + "properties": { + "identifier": { + "$id": "#root/id/identifier", + "title": "Identifier", + "type": "string", + "default": "", + "examples": [ + "NCBIGene:117611852" + ], + "pattern": "^.*$" + }, + "label": { + "$id": "#root/id/label", + "title": "Label", + "type": "string", + "default": "", + "examples": [ + "LOC117611852" + ], + "pattern": "^.*$" + } + } + }, + "equivalent_identifiers": { + "$id": "#root/equivalent_identifiers", + "title": "Equivalent_identifiers", + "type": "array", + "default": [], + "items":{ + "$id": "#root/equivalent_identifiers/items", + "title": "Items", + "type": "object", + "required": [ + "identifier" + ], + "properties": { + "identifier": { + "$id": "#root/equivalent_identifiers/items/identifier", + "title": "Identifier", + "type": "string", + "default": "", + "examples": [ + "NCBIGene:117611852" + ], + "pattern": "^.*$" + }, + "label": { + "$id": "#root/equivalent_identifiers/items/label", + "title": "Label", + "type": "string", + "default": "", + "examples": [ + "LOC117611852" + ], + "pattern": "^.*$" + } + } + } + + }, + "type": { + "$id": "#root/type", + "title": "Type", + "type": "array", + "default": [], + "items":{ + "$id": "#root/type/items", + "title": "Items", + "type": "string", + "default": "", + "examples": [ + "biolink:Gene" + ], + "pattern": "^.*$" + } + } + } +} diff --git a/node_normalizer/server.py b/node_normalizer/server.py index ffcec48..f11f990 100644 --- a/node_normalizer/server.py +++ b/node_normalizer/server.py @@ -14,7 +14,6 @@ from bmt import Toolkit from starlette.responses import JSONResponse -from .loader import NodeLoader from .apidocs import get_app_info, construct_open_api_schema from .model import ( SemanticTypes, @@ -23,6 +22,7 @@ SemanticTypesInput, ConflationList, ) +from .model.response import ConflationType from .normalizer import get_normalized_nodes, get_curie_prefixes, normalize_message from .redis_adapter import RedisConnectionFactory from .util import LoggingUtil @@ -31,20 +31,18 @@ # Some metadata not implemented see # https://github.com/tiangolo/fastapi/pull/1812 -app = FastAPI(**get_app_info()) +# app = FastAPI(**get_app_info()) + +app = FastAPI(title="NodeNormalizer") app.add_middleware( CORSMiddleware, - allow_origins=['*'], + allow_origins=["*"], allow_credentials=True, allow_methods=["*"], allow_headers=["*"], ) -loader = NodeLoader() - -redis_host = os.environ.get("REDIS_HOST", loader.get_config()["redis_host"]) -redis_port = os.environ.get("REDIS_PORT", loader.get_config()["redis_port"]) TRAPI_VERSION = os.environ.get("TRAPI_VERSION", "1.3") async_query_tasks = set() @@ -62,7 +60,7 @@ async def startup_event(): app.state.redis_connection2 = connection_factory.get_connection(connection_id="id_to_type_db") app.state.redis_connection3 = connection_factory.get_connection(connection_id="curie_to_bl_type_db") app.state.redis_connection4 = connection_factory.get_connection(connection_id="info_content_db") - app.state.redis_connection5 = connection_factory.get_connection(connection_id="gene_protein_db") + app.state.redis_connection5 = connection_factory.get_connection(connection_id="conflation_db") app.state.toolkit = Toolkit("https://raw.githubusercontent.com/biolink/biolink-model/2.1.0/biolink-model.yaml") app.state.ancestor_map = {} @@ -91,11 +89,11 @@ async def shutdown_event(): summary="Normalizes a TRAPI response object", description="Returns the response object with a merged knowledge graph and query graph bindings", ) -async def query(query: reasoner_pydantic.Query) -> reasoner_pydantic.Query: +async def query(query: reasoner_pydantic.Query, conflation_type: Optional[ConflationType] = None) -> reasoner_pydantic.Query: """ Normalizes a TRAPI compliant knowledge graph """ - query.message = await normalize_message(app, query.message) + query.message = await normalize_message(app, query.message, conflation_type) return query @@ -104,21 +102,21 @@ async def query(query: reasoner_pydantic.Query) -> reasoner_pydantic.Query: summary="Normalizes a TRAPI response object", description="Returns the response object with a merged knowledge graph and query graph bindings", ) -async def async_query(async_query: reasoner_pydantic.AsyncQuery): +async def async_query(async_query: reasoner_pydantic.AsyncQuery, conflation_type: Optional[ConflationType] = None): """ Normalizes a TRAPI compliant knowledge graph """ # need a strong reference to task such that GC doesn't remove it mid execution...https://docs.python.org/3/library/asyncio-task.html#creating-tasks - task = asyncio.create_task(async_query_task(async_query)) + task = asyncio.create_task(async_query_task(async_query, conflation_type)) async_query_tasks.add(task) task.add_done_callback(async_query_tasks.discard) return JSONResponse(content={"description": f"Query commenced. Will send result to {async_query.callback}"}, status_code=200) -async def async_query_task(async_query: reasoner_pydantic.AsyncQuery): +async def async_query_task(async_query: reasoner_pydantic.AsyncQuery, conflation_type: Optional[ConflationType]): try: - async_query.message = await normalize_message(app, async_query.message) + async_query.message = await normalize_message(app, async_query.message, conflation_type) session = requests.Session() retries = Retry( total=3, @@ -157,9 +155,7 @@ async def get_conflations() -> ConflationList: """ Get implemented conflations """ - # TODO: build from config instead of hard-coding. - conflations = ConflationList(conflations=["GeneProtein"]) - + conflations = ConflationList(conflations=list(ConflationType)) return conflations @@ -175,13 +171,13 @@ async def get_normalized_node_handler( example=["MESH:D014867", "NCIT:C34373"], min_items=1, ), - conflate: bool = fastapi.Query(True, description="Whether to apply conflation"), + conflation_type: Optional[ConflationType] = None, ): """ Get value(s) for key(s) using redis MGET """ # no_conflate = request.args.get('dontconflate',['GeneProtein']) - normalized_nodes = await get_normalized_nodes(app, curie, conflate) + normalized_nodes = await get_normalized_nodes(app, curie, conflation_type) # If curie contains at least one entry, then the only way normalized_nodes could be blank # would be if an error occurred during processing. @@ -200,7 +196,7 @@ async def get_normalized_node_handler(curies: CurieList): """ Get value(s) for key(s) using redis MGET """ - normalized_nodes = await get_normalized_nodes(app, curies.curies, curies.conflate) + normalized_nodes = await get_normalized_nodes(app, curies.curies, curies.conflation_type) # If curies.curies contains at least one entry, then the only way normalized_nodes could be blank # would be if an error occurred during processing. @@ -257,4 +253,4 @@ async def get_curie_prefixes_handler( # Override open api schema with custom schema -app.openapi_schema = construct_open_api_schema(app) +# app.openapi_schema = construct_open_api_schema(app) diff --git a/node_normalizer/util.py b/node_normalizer/util.py index 70a3011..e99f0b3 100644 --- a/node_normalizer/util.py +++ b/node_normalizer/util.py @@ -1,6 +1,9 @@ import logging import json import os +from itertools import islice +from pathlib import Path +import jsonschema import yaml from collections import namedtuple import copy @@ -18,7 +21,7 @@ def init_logging(log_file_path=None, log_file_level="ERROR"): "disable_existing_loggers": False, "formatters": {"default": {"format": "%(asctime)s | %(levelname)s | %(module)s:%(funcName)s | %(message)s"}}, "handlers": { - "console": {"level": "ERROR", "class": "logging.StreamHandler", "formatter": "default"}, + "console": {"level": "DEBUG", "class": "logging.StreamHandler", "formatter": "default"}, }, "loggers": { "node-norm": {"handlers": ["console"], "level": os.getenv("LOG_LEVEL", "ERROR")}, @@ -203,4 +206,26 @@ def to_named_tuple(type_name, d): def uniquify_list(seq): seen = set() seen_add = seen.add - return [x for x in seq if not (x in seen or seen_add(x))] \ No newline at end of file + return [x for x in seq if not (x in seen or seen_add(x))] + + +def validate_compendium(in_file, logger): + # open the file to validate + json_schema = Path(__file__).parent / "resources" / "valid_compendium_data_format.json" + with open(in_file, "r") as compendium, open(json_schema) as json_file: + logger.info(f"Validating {in_file}...") + validation_schema = json.load(json_file) + + # sample the file + for line in islice(compendium, 5): + try: + instance: dict = json.loads(line) + # validate the incoming json against the spec + jsonschema.validate(instance=instance, schema=validation_schema) + # catch any exceptions + except Exception as e: + logger.error(f"Exception thrown in validate_compendia({in_file}): {e}") + return False + + return True + diff --git a/redis_config.yaml b/redis_config.yaml index a0f860a..f01f079 100644 --- a/redis_config.yaml +++ b/redis_config.yaml @@ -4,7 +4,7 @@ "db": 0 "hosts": # list of cluster member ips and ports - - "host_name": "127.0.0.1" + - "host_name": "redis_eq_id_to_id_db" "port": "6379" "password": "" @@ -13,7 +13,7 @@ "is_cluster": false "db": 0 "hosts": - - "host_name": "127.0.0.1" + - "host_name": "redis_id_to_eqids_db" "port": "6379" "password": "" @@ -22,7 +22,7 @@ "is_cluster": false "db": 0 "hosts": - - "host_name": "127.0.0.1" + - "host_name": "redis_id_to_type_db" "port": "6379" "password": "" @@ -31,24 +31,24 @@ "is_cluster": false "db": 0 "hosts": - - "host_name": "127.0.0.1" + - "host_name": "redis_curie_to_bl_type_db" "port": "6379" "password": "" -"gene_protein_db": +"info_content_db": "ssl_enabled": false "is_cluster": false "db": 0 "hosts": - - "host_name": "127.0.0.1" + - "host_name": "redis_info_content_db" "port": "6379" "password": "" -"info_content_db": +"conflation_db": "ssl_enabled": false "is_cluster": false "db": 0 "hosts": - - "host_name": "127.0.0.1" + - "host_name": "redis_conflation_db" "port": "6379" - "password": "" + "password": "" \ No newline at end of file diff --git a/requirements.txt b/requirements.txt index 189c3f8..aa22c7b 100644 --- a/requirements.txt +++ b/requirements.txt @@ -1,5 +1,5 @@ aioredis~=1.3.1 -click==8.0.4 +asyncclick==8.1.3.4 bmt==0.8.4 deepdiff==5.8.1 fastapi==0.83.0 diff --git a/sample.env b/sample.env index fef7e48..904758d 100644 --- a/sample.env +++ b/sample.env @@ -1,7 +1,4 @@ LOG_LEVEL=DEBUG -REDIS_HOST=redis -REDIS_PORT=6379 -SERVER_HOST_URL=http://127.0.0.1 MATURITY_VALUE=maturity LOCATION_VALUE=location TRAPI_VERSION=1.3 diff --git a/tests/config.json b/tests/config.json deleted file mode 100644 index 148c042..0000000 --- a/tests/config.json +++ /dev/null @@ -1,11 +0,0 @@ -{ - "compendium_directory": "tests/resources", - "conflation_directory": "", - "redis_host": "redis", - "redis_port": 6379, - "redis_password": "", - "data_files": ["Cell.txt"], - "test_mode": 0, - "debug_messages": 0, - "conflations": [] -} diff --git a/tests/conftest.py b/tests/conftest.py index 7d2bb28..8051554 100644 --- a/tests/conftest.py +++ b/tests/conftest.py @@ -1,49 +1,70 @@ -import sys -import os -import time - import pytest -import logging from testcontainers.compose import DockerCompose -from testcontainers.core.docker_client import DockerClient - -from node_normalizer.util import LoggingUtil - -sys.path.append(os.path.join(os.path.dirname(__file__), "helpers")) - -logger = LoggingUtil.init_logging() @pytest.fixture(scope="session") def session(request): - logger.info("starting docker container") + print("starting docker container") compose = DockerCompose(filepath=".", compose_file_name="docker-compose-test.yml", env_file=".env", build=True, pull=True) compose.start() - nn_service_name = compose.get_service_host(service_name="r3", port=8080) - nn_service_port = compose.get_service_port(service_name="r3", port=8080) + nn_service_name = compose.get_service_host(service_name="node-norm", port=8080) + nn_service_port = compose.get_service_port(service_name="node-norm", port=8080) nn_url = f"http://{nn_service_name}:{nn_service_port}" - logger.info(f"nn_url: {nn_url}") + print(f"nn_url: {nn_url}") compose.wait_for(f"{nn_url}") callback_service_name = compose.get_service_host(service_name="callback-app", port=8008) callback_service_port = compose.get_service_port(service_name="callback-app", port=8008) callback_url = f"http://{callback_service_name}:{callback_service_port}" - logger.info(f"callback_url: {callback_url}") + print(f"callback_url: {callback_url}") compose.wait_for(f"{callback_url}") - (stdout, stderr, exit_code) = compose.exec_in_container(service_name="r3", command=["python", "load.py"]) - logger.info(f"stdout: {stdout}, stderr: {stderr}") + print("loading compendia files") + (stdout, stderr, exit_code) = compose.exec_in_container( + service_name="node-norm", + command=[ + "python", + "node_normalizer/load_compendium.py", + "-c", + "tests/resources/Cell.txt", + "-c", + "tests/resources/Gene.txt", + "-c", + "tests/resources/Disease.txt", + "-c", + "tests/resources/Protein.txt", + "-r", + "redis_config.yaml", + ], + ) + print(f"stdout: {stdout}, stderr: {stderr}") + + print("loading conflation files") + (stdout, stderr, exit_code) = compose.exec_in_container( + service_name="node-norm", + command=[ + "python", + "node_normalizer/load_conflation.py", + "-c", + "tests/resources/GeneProtein.txt", + "-s", + "gene_protein", + "-r", + "redis_config.yaml", + ], + ) + print(f"stdout: {stdout}, stderr: {stderr}") - logger.info(f"done building docker containers...ready to proceed") + print(f"done building docker containers...ready to proceed") def stop(): - logger.info("stopping docker container") - stdout, stderr = compose.get_logs() - if stderr: - logger.error(f"{stderr}") - if stdout: - logger.info(f"{stdout}") + print("stopping docker container") + # stdout, stderr = compose.get_logs() + # if stderr: + # print(f"{stderr}") + # if stdout: + # print(f"{stdout}") compose.stop() request.addfinalizer(stop) diff --git a/tests/helpers/redis_mocks.py b/tests/helpers/redis_mocks.py index e4e6969..bc3536b 100644 --- a/tests/helpers/redis_mocks.py +++ b/tests/helpers/redis_mocks.py @@ -5,7 +5,7 @@ from pathlib import Path -async def mock_get_equivalent_curies(app, curie): +async def mock_get_equivalent_curies(app, curie, conflation_type = None): """ Mock the data returned by redis """ diff --git a/tests/redis_config.yaml b/tests/redis_config.yaml deleted file mode 100644 index a2b823c..0000000 --- a/tests/redis_config.yaml +++ /dev/null @@ -1,54 +0,0 @@ -"eq_id_to_id_db" : - "ssl_enabled": false - "is_cluster": false - "db": 0 - "hosts": - # list of cluster member ips and ports - - "host_name": "redis" - "port": "6379" - "password": "" - -"id_to_eqids_db": - "ssl_enabled": false - "is_cluster": false - "db": 0 - "hosts": - - "host_name": "redis" - "port": "6379" - "password": "" - -"id_to_type_db": - "ssl_enabled": false - "is_cluster": false - "db": 0 - "hosts": - - "host_name": "redis" - "port": "6379" - "password": "" - -"curie_to_bl_type_db": - "ssl_enabled": false - "is_cluster": false - "db": 0 - "hosts": - - "host_name": "redis" - "port": "6379" - "password": "" - -"gene_protein_db": - "ssl_enabled": false - "is_cluster": false - "db": 0 - "hosts": - - "host_name": "redis" - "port": "6379" - "password": "" - -"info_content_db": - "ssl_enabled": false - "is_cluster": false - "db": 0 - "hosts": - - "host_name": "redis" - "port": "6379" - "password": "" diff --git a/tests/resources/Cell.txt b/tests/resources/Cell.txt index 25b432f..ab2bb2f 100644 --- a/tests/resources/Cell.txt +++ b/tests/resources/Cell.txt @@ -1,2547 +1,320 @@ -{"type": "biolink:Cell", "ic": "100", "identifiers": [{"i": "UMLS:C0229659", "l": "Myelomonocyte"}, {"i": "NCIT:C37041", "l": "Neoplastic Monocyte"}, {"i": "SNOMEDCT:41621006"}]} -{"type": "biolink:Cell", "identifiers": [{"i": "UMLS:C0017527", "l": "Giant Cells, Foreign-Body"}, {"i": "MESH:D015743", "l": "Giant Cells, Foreign-Body"}]} -{"type": "biolink:Cell", "ic": "100", "identifiers": [{"i": "UMLS:C0003273", "l": "Antibody-Producing Cells"}, {"i": "NCIT:C12611", "l": "Antibody-Producing Cell"}, {"i": "MESH:D000921", "l": "Antibody-Producing Cells"}]} -{"type": "biolink:Cell", "ic": "100", "identifiers": [{"i": "UMLS:C1135969", "l": "Large Luteal Cells"}, {"i": "NCIT:C32693", "l": "Granulosa Lutein Cell"}]} -{"type": "biolink:Cell", "ic": "100", "identifiers": [{"i": "UMLS:C1518620", "l": "Orthochromatophilic Erythroblast"}, {"i": "NCIT:C13132", "l": "Orthochromatic Erythroblast"}]} -{"type": "biolink:Cell", "ic": "94.920724062801384", "identifiers": [{"i": "UMLS:C1709198", "l": "Neoplastic Sebocyte"}, {"i": "NCIT:C43338", "l": "Neoplastic Sebocyte"}]} -{"type": "biolink:Cell", "identifiers": [{"i": "UMLS:C1267871", "l": "Lymphoblast positive for CD13 antigen"}, {"i": "SNOMEDCT:117550007"}]} -{"type": "biolink:Cell", "ic": "100", "identifiers": [{"i": "UMLS:C1512490", "l": "Horizontal Cell of Cajal"}, {"i": "NCIT:C32745", "l": "Horizontal Cell of Cajal"}]} -{"type": "biolink:Cell", "ic": "91.94953810872488", "identifiers": [{"i": "UMLS:C1519458", "l": "Neoplastic Spindle-Shaped Fibroblast"}, {"i": "NCIT:C36955", "l": "Neoplastic Spindle-Shaped Fibroblast"}]} -{"type": "biolink:Cell", "ic": "100", "identifiers": [{"i": "UMLS:C4049868", "l": "Gitter Cell"}, {"i": "NCIT:C123738", "l": "Gitter Cell"}]} -{"type": "biolink:Cell", "identifiers": [{"i": "UMLS:C4510889", "l": "Blast cell positive for CD7 antigen"}, {"i": "SNOMEDCT:724315001"}]} -{"type": "biolink:Cell", "ic": "100", "identifiers": [{"i": "UMLS:C1708645", "l": "Large Multinucleated Malignant Histiocyte"}, {"i": "NCIT:C43256", "l": "Large Multinucleated Malignant Histiocyte"}]} -{"type": "biolink:Cell", "ic": "85.740669697216731", "identifiers": [{"i": "UMLS:C1514023", "l": "Neoplastic Meningothelial Cell"}, {"i": "NCIT:C37155", "l": "Neoplastic Meningothelial Cell"}]} -{"type": "biolink:Cell", "ic": "100", "identifiers": [{"i": "UMLS:C3899239", "l": "Exhausted T-Cell"}, {"i": "NCIT:C120000", "l": "Exhausted T-Cell"}]} -{"type": "biolink:Cell", "ic": "94.920724062801384", "identifiers": [{"i": "UMLS:C1882961", "l": "Round Adenocarcinoma Cell"}, {"i": "NCIT:C54417", "l": "Round Adenocarcinoma Cell"}]} -{"type": "biolink:Cell", "ic": "89.841448125602781", "identifiers": [{"i": "UMLS:C1522406", "l": "interstitial cell"}, {"i": "NCIT:C32870", "l": "Interstitial Cell"}]} -{"type": "biolink:Cell", "ic": "85.740669697216731", "identifiers": [{"i": "UMLS:C1708878", "l": "Malignant Germ Cell"}, {"i": "NCIT:C54110", "l": "Malignant Germ Cell"}]} -{"type": "biolink:Cell", "identifiers": [{"i": "UMLS:C1267859", "l": "Lymphocyte positive for both CD8 antigen and HLA-DR antigen"}, {"i": "SNOMEDCT:116815002"}]} -{"type": "biolink:Cell", "identifiers": [{"i": "UMLS:C4518169", "l": "Population of all band eosinophils in portion of fluid"}, {"i": "SNOMEDCT:725233000"}]} -{"type": "biolink:Cell", "ic": "100", "identifiers": [{"i": "UMLS:C1709102", "l": "Myopericyte"}, {"i": "NCIT:C51141", "l": "Myopericyte"}]} -{"type": "biolink:Cell", "identifiers": [{"i": "UMLS:C0228078", "l": "Partly differentiated neural cell"}, {"i": "SNOMEDCT:71609000"}]} -{"type": "biolink:Cell", "ic": "100", "identifiers": [{"i": "UMLS:C3642320", "l": "Immature Malignant Mast Cell"}, {"i": "NCIT:C37063", "l": "Immature Malignant Mast Cell"}]} -{"type": "biolink:Cell", "ic": "76.125169645393314", "identifiers": [{"i": "UMLS:C1522639", "l": "Leukocyte (WBC) (MMHCC)"}, {"i": "NCIT:C22570", "l": "Mouse Leukocyte"}]} -{"type": "biolink:Cell", "ic": "100", "identifiers": [{"i": "UMLS:C0333805", "l": "Macrocytic erythrocyte"}, {"i": "NCIT:C13112", "l": "Macrocytic Red Blood Cell"}, {"i": "SNOMEDCT:259681001"}]} -{"type": "biolink:Cell", "ic": "74.378130331796413", "identifiers": [{"i": "UMLS:C0027882", "l": "Neurons"}, {"i": "NCIT:C12623", "l": "Neuron"}]} -{"type": "biolink:Cell", "identifiers": [{"i": "UMLS:C4511163", "l": "Blast cell positive for cytoplasmic CD3 antigen"}, {"i": "SNOMEDCT:725483008"}]} -{"type": "biolink:Cell", "ic": "100", "identifiers": [{"i": "UMLS:C3896611", "l": "ROR1 CAR-specific Autologous T-Lymphocytes"}, {"i": "NCIT:C117237", "l": "ROR1 CAR-specific Autologous T-Lymphocytes"}]} -{"type": "biolink:Cell", "ic": "100", "identifiers": [{"i": "UMLS:C1516963", "l": "Glandular cell of esophagus"}, {"i": "NCIT:C32537", "l": "Esophageal Glandular Cell"}]} -{"type": "biolink:Cell", "ic": "82.428592223071533", "identifiers": [{"i": "UMLS:C0023516", "l": "Leukocytes"}, {"i": "NCIT:C12529", "l": "Leukocyte"}, {"i": "MESH:D007962", "l": "Leukocytes"}, {"i": "SNOMEDCT:52501007"}]} -{"type": "biolink:Cell", "ic": "94.920724062801384", "identifiers": [{"i": "UMLS:C2985477", "l": "Exocrine Pancreas Cell"}, {"i": "NCIT:C93173", "l": "Exocrine Pancreas Cell"}]} -{"type": "biolink:Cell", "identifiers": [{"i": "UMLS:C2331651", "l": "Polar Bodies"}, {"i": "MESH:D059705", "l": "Polar Bodies"}]} -{"type": "biolink:Cell", "ic": "85.740669697216731", "identifiers": [{"i": "UMLS:C1510728", "l": "Abnormal Keratinocyte"}, {"i": "NCIT:C36766", "l": "Abnormal Keratinocyte"}]} -{"type": "biolink:Cell", "ic": "100", "identifiers": [{"i": "UMLS:C4727694", "l": "Autologous Anti-Claudin18.2-transduced T Lymphocytes"}, {"i": "NCIT:C150382", "l": "Autologous Anti-Claudin18.2-transduced T Lymphocytes CT041"}]} -{"type": "biolink:Cell", "ic": "100", "identifiers": [{"i": "UMLS:C4725105", "l": "CD33-specific CAR Lentiviral Vector-transduced Autologous T-lymphocytes"}, {"i": "NCIT:C148530", "l": "CD33-specific CAR Lentiviral Vector-transduced Autologous T-lymphocytes"}]} -{"type": "biolink:Cell", "ic": "94.920724062801384", "identifiers": [{"i": "UMLS:C1513945", "l": "Neoplastic Cuboidal Cell"}, {"i": "NCIT:C42082", "l": "Neoplastic Cuboidal Cell"}]} -{"type": "biolink:Cell", "ic": "83.127010562534593", "identifiers": [{"i": "UMLS:C1440938", "l": "Immature Lymphocyte"}, {"i": "NCIT:C13118", "l": "Immature Lymphocyte"}]} -{"type": "biolink:Cell", "ic": "94.920724062801384", "identifiers": [{"i": "UMLS:C1514738", "l": "Reactive Glandular Cell"}, {"i": "NCIT:C36811", "l": "Reactive Glandular Cell"}]} -{"type": "biolink:Cell", "ic": "94.920724062801384", "identifiers": [{"i": "UMLS:C1514047", "l": "Neoplastic Neuroendocrine Spindle Cell"}, {"i": "NCIT:C36935", "l": "Neoplastic Neuroendocrine Spindle Cell"}]} -{"type": "biolink:Cell", "ic": "100", "identifiers": [{"i": "UMLS:C4725101", "l": "Autologous CD20-4SCAR-expressing T-cells 4SCAR20"}, {"i": "NCIT:C148525", "l": "Autologous CD20-4SCAR-expressing T-cells 4SCAR20"}]} -{"type": "biolink:Cell", "ic": "100", "identifiers": [{"i": "UMLS:C4724905", "l": "Autologous PD-L1/CD80/CD86-targeted CAR-T Cells"}, {"i": "NCIT:C148216", "l": "Autologous PD-L1/CD80/CD86-targeted CAR-T Cells"}]} -{"type": "biolink:Cell", "identifiers": [{"i": "UMLS:C2325623", "l": "Pyramidal cell of precentral gyrus of cerebral hemisphere"}, {"i": "SNOMEDCT:89416001"}]} -{"type": "biolink:Cell", "identifiers": [{"i": "UMLS:C1721028", "l": "Blastocyst Inner Cell Mass"}, {"i": "MESH:D053624", "l": "Blastocyst Inner Cell Mass"}]} -{"type": "biolink:Cell", "ic": "77.02358060617253", "identifiers": [{"i": "UMLS:C1514039", "l": "Neoplastic Myeloid Cell"}, {"i": "NCIT:C41063", "l": "Neoplastic Myeloid Cell"}]} -{"type": "biolink:Cell", "ic": "100", "identifiers": [{"i": "UMLS:C1515140", "l": "T-Lymphocyte with a Post-Thymic Immunophenotype"}, {"i": "NCIT:C39573", "l": "T-Lymphocyte with a Post-Thymic Immunophenotype"}]} -{"type": "biolink:Cell", "ic": "100", "identifiers": [{"i": "UMLS:C1517543", "l": "Giant Cell with Myoblastic Differentiation"}, {"i": "NCIT:C36828", "l": "Giant Cell with Myoblastic Differentiation"}]} -{"type": "biolink:Cell", "ic": "100", "identifiers": [{"i": "UMLS:C3641631", "l": "FAP-specific CD8-positive T Cells"}, {"i": "NCIT:C103829", "l": "FAP-specific CD8-positive T Cells"}]} -{"type": "biolink:Cell", "ic": "100", "identifiers": [{"i": "UMLS:C1171322", "l": "Adult Stem Cells"}, {"i": "NCIT:C43420", "l": "Adult Stem Cell"}, {"i": "MESH:D053687", "l": "Adult Stem Cells"}, {"i": "SNOMEDCT:417904004"}]} -{"type": "biolink:Cell", "ic": "55.861102409464458", "identifiers": [{"i": "UMLS:C4727509", "l": "Genetically-engineered Immune Cell"}, {"i": "NCIT:C154231", "l": "Genetically-engineered Immune Cell"}]} -{"type": "biolink:Cell", "identifiers": [{"i": "UMLS:C0008010", "l": "Chemoreceptor Cells"}, {"i": "MESH:D002628", "l": "Chemoreceptor Cells"}]} -{"type": "biolink:Cell", "ic": "100", "identifiers": [{"i": "UMLS:C1513747", "l": "Multinucleated Reed-Sternberg Cell"}, {"i": "NCIT:C36813", "l": "Multinucleated Reed-Sternberg Cell"}]} -{"type": "biolink:Cell", "identifiers": [{"i": "UMLS:C1267838", "l": "Lymphocyte negative for CD3 antigen and positive for 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"biolink:Cell", "ic": "100", "identifiers": [{"i": "UMLS:C4289974", "l": "Anti-CD22 CAR-expressing T Lymphocytes"}, {"i": "NCIT:C128556", "l": "Anti-CD22 CAR-expressing T Lymphocytes"}]} -{"type": "biolink:Cell", "identifiers": [{"i": "UMLS:C1267843", "l": "Lymphocyte positive for both CD4 antigen and CD8 antigen"}, {"i": "SNOMEDCT:117530008"}]} -{"type": "biolink:Cell", "ic": "100", "identifiers": [{"i": "UMLS:C4524459", "l": "Autologous EGFRt/19-28z/4-1BBL CAR T-Lymphocytes"}, {"i": "NCIT:C133189", "l": "Autologous EGFRt/19-28z/4-1BBL CAR T-Lymphocytes"}]} -{"type": "biolink:Cell", "ic": "100", "identifiers": [{"i": "UMLS:C1524102", "l": "Leukocyte - Myelocyte (Granulocyte) - Neutrophil (MMHCC)"}, {"i": "NCIT:C22593", "l": "Mouse Neutrophil"}]} -{"type": "biolink:Cell", "ic": "77.349316285872916", "identifiers": [{"i": "UMLS:C0017526", "l": "Giant Cells"}, {"i": "NCIT:C12607", "l": "Giant Cell"}, {"i": "MESH:D015726", "l": "Giant Cells"}, {"i": "SNOMEDCT:60401004"}, {"i": "SNOMEDCT:81480003"}]} -{"type": "biolink:Cell", "identifiers": [{"i": "UMLS:C0524456", "l": "Structure of endocervical glandular cell"}, {"i": "SNOMEDCT:91767003"}]} -{"type": "biolink:Cell", "identifiers": [{"i": "UMLS:C1135926", "l": "Satellite Cells, Skeletal Muscle"}, {"i": "MESH:D032496", "l": "Satellite Cells, Skeletal Muscle"}]} -{"type": "biolink:Cell", "ic": "100", "identifiers": [{"i": "UMLS:C1518995", "l": "Peripheral B-Lymphocyte of Inner Mantle Zone"}, {"i": "NCIT:C38332", "l": "Peripheral B-Lymphocyte of Inner Mantle Zone"}]} -{"type": "biolink:Cell", "identifiers": [{"i": "UMLS:C1978414", "l": "Blast cell positive for CD22 antigen"}, {"i": "SNOMEDCT:724266008"}]} -{"type": "biolink:Cell", "ic": "100", "identifiers": [{"i": "UMLS:C1515151", "l": "TE33"}, {"i": "NCIT:C20298", "l": "TE33"}]} -{"type": "biolink:Cell", "ic": "100", "identifiers": [{"i": "UMLS:C1514107", "l": "Neoplastic T-Immunoblast"}, {"i": "NCIT:C37012", "l": "Neoplastic T-Immunoblast"}]} -{"type": "biolink:Cell", "ic": "100", "identifiers": [{"i": "UMLS:C3640055", "l": "IGF-1R Antisense Oligodeoxynucleotide-treated Autologous Glioma Cells"}, {"i": "NCIT:C101257", "l": "IGF-1R Antisense Oligodeoxynucleotide-treated Autologous Glioma Cells IGV-001"}]} -{"type": "biolink:Cell", "ic": "91.94953810872488", "identifiers": [{"i": "UMLS:C0225698", "l": "Alveolar Epithelial Cells"}, {"i": "NCIT:C32053", "l": "Alveolar Cell"}, {"i": "MESH:D056809", "l": "Alveolar Epithelial Cells"}, {"i": "SNOMEDCT:47438009"}]} -{"type": "biolink:Cell", "ic": "100", "identifiers": [{"i": "UMLS:C1519120", "l": "SA01"}, {"i": "NCIT:C20264", "l": "SA01"}]} -{"type": "biolink:Cell", "ic": "100", "identifiers": [{"i": "UMLS:C1510956", "l": "Atypical Histiocyte"}, {"i": "NCIT:C40999", "l": "Atypical Histiocyte"}]} -{"type": "biolink:Cell", "identifiers": [{"i": "UMLS:C0333722", "l": "Tadpole cell"}, {"i": "SNOMEDCT:112657009"}]} -{"type": "biolink:Cell", "ic": "94.920724062801384", "identifiers": [{"i": "UMLS:C3896693", "l": "Bone Marrow-Derived Cell"}, {"i": "NCIT:C116388", "l": "Bone Marrow-Derived Cell"}]} -{"type": "biolink:Cell", "ic": "100", "identifiers": [{"i": "UMLS:C1511439", "l": "CH01"}, {"i": "NCIT:C20285", "l": "CH01"}]} -{"type": "biolink:Cell", "ic": "100", "identifiers": [{"i": "UMLS:C1517807", "l": "Leukemic Hematopoietic Stem Cell"}, {"i": "NCIT:C41069", "l": "Leukemic Hematopoietic Stem Cell"}]} -{"type": "biolink:Cell", "ic": "100", "identifiers": [{"i": "UMLS:C4725117", "l": "Anti-CD3/MUC1 Antibody-armed PD-1 Inhibitor-induced Cytokine-induced Killer Cells"}, {"i": "NCIT:C148543", "l": "Anti-CD3/MUC1 Antibody-armed PD-1 Inhibitor-induced Cytokine-induced Killer Cells"}]} -{"type": "biolink:Cell", "ic": "100", "identifiers": [{"i": "UMLS:C1515968", "l": "Anaplastic Melanocyte"}, {"i": "NCIT:C37110", "l": "Anaplastic Melanocyte"}]} -{"type": "biolink:Cell", "ic": "83.127010562534593", "identifiers": [{"i": "UMLS:C1510733", "l": "Abnormal Neutrophil"}, {"i": "NCIT:C37029", "l": "Abnormal Neutrophil"}]} -{"type": "biolink:Cell", "ic": "100", "identifiers": [{"i": "UMLS:C1708911", "l": "Malignant Spindle-Shaped Fibroblast"}, {"i": "NCIT:C49021", "l": "Malignant Spindle-Shaped Fibroblast"}]} -{"type": "biolink:Cell", "ic": "100", "identifiers": [{"i": "UMLS:C1515108", "l": "Syncytiotrophoblast cell"}, {"i": "NCIT:C38574", "l": "Syncytiotrophoblastic Cell"}]} -{"type": "biolink:Cell", "ic": "100", "identifiers": [{"i": "UMLS:C1514086", "l": "Neoplastic Small Cleaved Follicle Center Cell"}, {"i": "NCIT:C37002", "l": "Neoplastic Small Cleaved Follicle Center Cell"}]} -{"type": "biolink:Cell", "ic": "100", "identifiers": [{"i": "UMLS:C1517690", "l": "LH Cells"}, {"i": "NCIT:C32985", "l": "LH Cell"}]} -{"type": "biolink:Cell", "identifiers": [{"i": "UMLS:C1267996", "l": "Lymphocyte positive for CD117 antigen"}, {"i": "SNOMEDCT:117436000"}]} -{"type": "biolink:Cell", "identifiers": [{"i": "UMLS:C0229543", "l": "Pituitary hypertrophic amphophil 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"identifiers": [{"i": "UMLS:C1516727", "l": "Common Thymocyte"}, {"i": "NCIT:C32360", "l": "Common Thymocyte"}]} diff --git a/tests/resources/Disease.txt b/tests/resources/Disease.txt new file mode 100644 index 0000000..d545aa9 --- /dev/null +++ b/tests/resources/Disease.txt @@ -0,0 +1,3000 @@ +{"type": "biolink:Disease", "ic": "100", "identifiers": [{"i": "MONDO:0033558", "l": "autoinflammation, immune dysregulation, and eosinophilia"}, {"i": "OMIM:618999"}, {"i": "UMLS:C5436572", "l": "AUTOINFLAMMATION, IMMUNE DYSREGULATION, AND EOSINOPHILIA"}]} +{"type": "biolink:Disease", "ic": "73.946956196949927", "identifiers": [{"i": "UMLS:C4304995", "l": "Recurrent squamous cell carcinoma"}, {"i": "NCIT:C162652", "l": "Recurrent Squamous Cell Carcinoma"}, {"i": "SNOMEDCT:719052006"}]} +{"type": "biolink:Disease", "identifiers": [{"i": "UMLS:C0434322", "l": "Strain of rotator cuff of shoulder"}, {"i": "MEDDRA:10039224"}, {"i": "SNOMEDCT:789758005"}]} +{"type": "biolink:Disease", "ic": "100", "identifiers": [{"i": "MONDO:0013792", "l": "intracerebral hemorrhage"}, {"i": "OMIM:614519"}, {"i": "UMLS:C0472369", "l": "Hemorrhagic cerebral infarction"}, {"i": "UMLS:C0553692", "l": "Brain hemorrhage"}, {"i": "UMLS:C1862876", "l": "STROKE, HEMORRHAGIC, SUSCEPTIBILITY TO"}, {"i": "UMLS:C2937358", "l": "Cerebral Hemorrhage"}, {"i": "UMLS:C3281105", "l": "HEMORRHAGE, INTRACEREBRAL, SUSCEPTIBILITY TO"}, {"i": "UMLS:C5234922", "l": "Hemorrhagic Stroke"}, {"i": "MESH:D000083302", "l": "Hemorrhagic Stroke"}, {"i": "MESH:D002543", "l": "Cerebral Hemorrhage"}, {"i": "MEDDRA:10008111"}, {"i": "MEDDRA:10008114"}, {"i": "MEDDRA:10018972"}, {"i": "MEDDRA:10019005"}, {"i": "MEDDRA:10019016"}, {"i": "MEDDRA:10019529"}, {"i": "MEDDRA:10019531"}, {"i": "MEDDRA:10019551"}, {"i": "MEDDRA:10022737"}, {"i": "MEDDRA:10022751"}, {"i": "MEDDRA:10022753"}, {"i": "MEDDRA:10022754"}, {"i": "MEDDRA:10048863"}, {"i": "MEDDRA:10055278"}, {"i": "MEDDRA:10055293"}, {"i": "MEDDRA:10055800"}, {"i": 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alkaloid"}, {"i": "MEDDRA:10035890"}, {"i": "SNOMEDCT:74264003"}]} +{"type": "biolink:Disease", "ic": "100", "identifiers": [{"i": "MONDO:0008284", "l": "polyposis of gastric fundus without polyposis coli"}, {"i": "UMLS:C1868001", "l": "Polyposis Of Gastric Fundus Without Polyposis Coli"}, {"i": "MESH:C566775", "l": "Polyposis Of Gastric Fundus Without Polyposis Coli"}, {"i": "HP:0033769", "l": "Fundic gland polyposis"}]} +{"type": "biolink:Disease", "ic": "100", "identifiers": [{"i": "MONDO:0013567", "l": "atrial septal defect 3"}, {"i": "DOID:0110108", "l": "atrial heart septal defect 3"}, {"i": "OMIM:614089"}, {"i": "UMLS:C3279790", "l": "Atrial Septal Defect 3"}, {"i": "MESH:C563540", "l": "Atrial Septal Defect 3"}]} +{"type": "biolink:Disease", "identifiers": [{"i": "UMLS:C1532322", "l": "Infectious Endophthalmitis"}, {"i": "MEDDRA:10073350"}, {"i": "SNOMEDCT:414491002"}]} +{"type": "biolink:Disease", "ic": "100", "identifiers": [{"i": "MONDO:0020342", "l": "congenital myopathy 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AUTOSOMAL RECESSIVE 18B"}]} +{"type": "biolink:Disease", "identifiers": [{"i": "UMLS:C0149755", "l": "Fracture of phalanx of foot"}, {"i": "MEDDRA:10017314"}, {"i": "SNOMEDCT:21351003"}]} +{"type": "biolink:Disease", "identifiers": [{"i": "UMLS:C0862939", "l": "Esophageal adenocarcinoma thoracic stage II"}, {"i": "MEDDRA:10015349"}, {"i": "MEDDRA:10056011"}]} +{"type": "biolink:Disease", "ic": "80.661393760018115", "identifiers": [{"i": "MONDO:0003277", "l": "malignant ear neoplasm"}, {"i": "DOID:5101", "l": "ear cancer"}, {"i": "UMLS:C0013449", "l": "Ear Neoplasms"}, {"i": "UMLS:C0751094", "l": "Cancer of Ear Auricle"}, {"i": "UMLS:C2350059", "l": "Cancer of Ear"}, {"i": "MESH:D004428", "l": "Ear Neoplasms"}, {"i": "MEDDRA:10055016"}, {"i": "MEDDRA:10055017"}, {"i": "NCIT:C9337", "l": "Malignant Ear Neoplasm"}, {"i": "SNOMEDCT:363228008"}, {"i": "SNOMEDCT:443648003"}, {"i": "HP:0012780", "l": "Neoplasm of the ear"}]} +{"type": "biolink:Disease", "ic": "94.920724062801384", "identifiers": [{"i": "UMLS:C0278727", "l": "Small cell lung cancer recurrent"}, {"i": "MEDDRA:10041070"}, {"i": "NCIT:C9050", "l": "Recurrent Lung Small Cell Carcinoma"}]} +{"type": "biolink:Disease", "identifiers": [{"i": "UMLS:C0267667", "l": "Hernia, with gangrene"}, {"i": "MEDDRA:10019919"}, {"i": "MEDDRA:10019928"}, {"i": "MEDDRA:10061206"}, {"i": "SNOMEDCT:79990007"}]} +{"type": "biolink:Disease", "ic": "94.920724062801384", "identifiers": [{"i": "MONDO:0006351", "l": "parachordoma"}, {"i": "DOID:2647", "l": "parachordoma"}, {"i": "UMLS:C1266175", "l": "Parachordoma"}, {"i": "NCIT:C6581", "l": "Parachordoma"}, {"i": "SNOMEDCT:128786009"}, {"i": "SNOMEDCT:404086000"}]} +{"type": "biolink:Disease", "identifiers": [{"i": "UMLS:C2938931", "l": "Ischemic contracture of the left ventricle"}, {"i": "MEDDRA:10070589"}, {"i": "MEDDRA:10070590"}]} +{"type": "biolink:Disease", "ic": "100", "identifiers": [{"i": "MONDO:0010094", "l": "spondylocarpotarsal synostosis syndrome"}, {"i": 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+["NCBIGene:303135", "UniProtKB:G3V9Z6"] +["NCBIGene:191570", "UniProtKB:G3V782"] +["NCBIGene:101886961", "UniProtKB:A0A0R4IQ08"] +["NCBIGene:309441", "UniProtKB:D3ZA68"] +["NCBIGene:100312477", "UniProtKB:E9Q2N4"] +["NCBIGene:403066", "UniProtKB:F1Q5H5"] +["NCBIGene:100000880", "UniProtKB:X1WHE5"] +["NCBIGene:51435", "UniProtKB:Q6AZY7"] +["NCBIGene:290229", "UniProtKB:A0A0G2QC55"] +["NCBIGene:56996", "UniProtKB:Q9BXP2", "UniProtKB:Q9H7I6"] +["NCBIGene:38354", "UniProtKB:E1JIA4", "UniProtKB:E5AJE7", "UniProtKB:Q9VZW8"] +["NCBIGene:60344", "UniProtKB:Q9ERZ6"] +["NCBIGene:568668", "UniProtKB:F1QKJ0", "UniProtKB:G9JKB3"] +["NCBIGene:11247", "UniProtKB:O95158"] +["NCBIGene:566697", "UniProtKB:A0A0R4IJJ1"] +["NCBIGene:295741", "UniProtKB:D3ZNG2"] +["NCBIGene:10178906", "UniProtKB:A0A0B4JD30"] +["NCBIGene:680434", "UniProtKB:D4A474"] +["NCBIGene:67628", "UniProtKB:Q9EST5"] +["NCBIGene:300047", "UniProtKB:D3ZFQ8"] +["NCBIGene:690728", "UniProtKB:D4A6N9"] +["NCBIGene:100333424", "UniProtKB:F1Q4L4"] +["NCBIGene:245937", "UniProtKB:Q8NES8"] +["NCBIGene:57662", "UniProtKB:Q9P1Y5"] +["NCBIGene:244550", "UniProtKB:Q6P3Y9"] +["NCBIGene:2876", "UniProtKB:A0A2R8Y6B6", "UniProtKB:P07203", "UniProtKB:Q7L4Q3"] +["NCBIGene:42735", "UniProtKB:Q7KS50", "UniProtKB:Q9VCQ6"] +["NCBIGene:55599", "UniProtKB:Q96LT9"] +["NCBIGene:33171", "UniProtKB:Q8IPV3", "UniProtKB:Q9VPJ9"] +["NCBIGene:292894", "UniProtKB:A0A0G2JVL7", "UniProtKB:D3ZH12"] +["NCBIGene:246514", "UniProtKB:Q3ZAL6"] +["NCBIGene:67472", "UniProtKB:Q3TTQ5", "UniProtKB:Q99MB2"] +["NCBIGene:51172", "UniProtKB:Q9UK23"] +["NCBIGene:24553", "UniProtKB:P97523", "UniProtKB:Q2IBC7"] +["NCBIGene:37522", "UniProtKB:Q4V4U2"] +["NCBIGene:29940", "UniProtKB:A0A2R8YE23", "UniProtKB:A0A2U3TZJ0", "UniProtKB:B7Z1T3", "UniProtKB:B7Z765", "UniProtKB:Q9UL01"] +["NCBIGene:100526683", "UniProtKB:E3NZ06"] +["NCBIGene:767674", "UniProtKB:A2CEP8", "UniProtKB:Q08CL0"] +["NCBIGene:11332", "UniProtKB:O00154"] +["NCBIGene:51409", "UniProtKB:A0A140VK98", "UniProtKB:B2RA37", "UniProtKB:Q9Y5R4"] +["NCBIGene:100361529", "UniProtKB:D3ZXM2"] +["NCBIGene:92305", "UniProtKB:A0AVI4"] +["NCBIGene:320664", "UniProtKB:A0A0R4J199", "UniProtKB:Q08EC4"] +["NCBIGene:246048", "UniProtKB:Q9CXM0"] +["NCBIGene:64760", "UniProtKB:Q86V87"] +["NCBIGene:92667", "UniProtKB:Q5QPE7", "UniProtKB:Q9BQP7"] +["NCBIGene:2709", "UniProtKB:A0A654IE64", "UniProtKB:O95377"] +["NCBIGene:24161", "UniProtKB:B0BNC1", "UniProtKB:P41498"] +["NCBIGene:287970", "UniProtKB:M0R908", "UniProtKB:Q5USB7"] +["NCBIGene:112849", "UniProtKB:Q96EM0"] +["NCBIGene:17380", "UniProtKB:Q61391"] +["NCBIGene:50202", "UniProtKB:A1ZBP6"] +["NCBIGene:100132285", "UniProtKB:A0A0G2JPR7", "UniProtKB:A0A1W2PSB7", "UniProtKB:K7R1S5", "UniProtKB:O43755", "UniProtKB:O75579", "UniProtKB:P43631", "UniProtKB:Q14950", "UniProtKB:Q32MZ1"] +["NCBIGene:40637", "UniProtKB:Q9VNA3"] +["NCBIGene:5740605", "UniProtKB:A0A0C4DHH2", "UniProtKB:A8JR30"] +["NCBIGene:314442", "UniProtKB:Q6P7B0"] 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"UniProtKB:Q3UNC6", "UniProtKB:Q4LDG0"] +["NCBIGene:38813", "UniProtKB:Q9VS51"] +["NCBIGene:11477", "UniProtKB:P37172"] +["NCBIGene:12036", "UniProtKB:O35855", "UniProtKB:O88374", "UniProtKB:Q3ULU3"] +["NCBIGene:195555", "UniProtKB:A2A8M8", "UniProtKB:E9Q2S4"] +["NCBIGene:38818", "UniProtKB:Q8IQ80", "UniProtKB:Q8IQ82"] +["NCBIGene:64844", "UniProtKB:B7Z5K0", "UniProtKB:B7ZAR7", "UniProtKB:F5H6W4", "UniProtKB:Q9H992"] +["NCBIGene:3679", "UniProtKB:Q13683", "UniProtKB:Q4LE35"] +["NCBIGene:1983", "UniProtKB:A0A024R6Q1", "UniProtKB:P55010"] +["NCBIGene:558864", "UniProtKB:B8A507"] +["NCBIGene:16576", "UniProtKB:E9QMU1", "UniProtKB:J3QNW9"] +["NCBIGene:13043", "UniProtKB:Q60598", "UniProtKB:Q8BNA5", "UniProtKB:Q921L6"] +["NCBIGene:498971", "UniProtKB:Q5G5J2"] +["NCBIGene:567986", "UniProtKB:E7F984", "UniProtKB:F1QY53"] +["NCBIGene:499762", "UniProtKB:A0JPN6"] +["NCBIGene:277973", "UniProtKB:B2RXE2"] +["NCBIGene:327958", "UniProtKB:Q3UHE1"] +["NCBIGene:81729", "UniProtKB:P62907"] 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"UniProtKB:A0A0S2Z613", "UniProtKB:Q96NR8"] +["NCBIGene:11783", "UniProtKB:G3XA09", "UniProtKB:O88879", "UniProtKB:Q5DU30"] +["NCBIGene:553163", "UniProtKB:Q58T08"] +["NCBIGene:81749", "UniProtKB:Q64617"] +["NCBIGene:100537791", "UniProtKB:E7F670"] +["NCBIGene:7046", "UniProtKB:B4DXN7", "UniProtKB:B4DY26", "UniProtKB:P36897", "UniProtKB:Q5T7S2"] +["NCBIGene:393848", "UniProtKB:A0A0R4IKK1", "UniProtKB:Q6P4P5"] +["NCBIGene:7200", "UniProtKB:P20396"] +["NCBIGene:308908", "UniProtKB:D3ZHR1"] +["NCBIGene:302703", "UniProtKB:D3ZY10"] +["NCBIGene:258534", "UniProtKB:Q8VFH0"] +["NCBIGene:567675", "UniProtKB:F6NNU9"] +["NCBIGene:10598", "UniProtKB:G3V438", "UniProtKB:O95433"] +["NCBIGene:381626", "UniProtKB:D3Z5I9", "UniProtKB:Q9CXK9"] +["NCBIGene:14459", "UniProtKB:P48757"] +["NCBIGene:66848", "UniProtKB:Q505Q3", "UniProtKB:Q99KR8"] +["NCBIGene:20658", "UniProtKB:Q80TM4", "UniProtKB:Q8C9T5", "UniProtKB:Q9QX47"] +["NCBIGene:38168", "UniProtKB:P20350", "UniProtKB:Q540V7"] +["NCBIGene:35715", "UniProtKB:A0A0B4KEE7", "UniProtKB:A1Z734", "UniProtKB:E1JGZ7", "UniProtKB:E1JGZ8", "UniProtKB:Q6NND6", "UniProtKB:Q8IGL5"] +["NCBIGene:31404", "UniProtKB:Q9W4H8"] +["NCBIGene:565685", "UniProtKB:Q1X871"] +["NCBIGene:2298", "UniProtKB:Q12950"] +["NCBIGene:25461", "UniProtKB:P25102"] +["NCBIGene:258150", "UniProtKB:Q7TRH9"] +["NCBIGene:68066", "UniProtKB:Q14BQ5", "UniProtKB:Q9D8K8"] +["NCBIGene:66707", "UniProtKB:Q5SZT7"] +["NCBIGene:794053", "UniProtKB:B3IWZ9"] +["NCBIGene:335335", "UniProtKB:Q6PBJ8"] +["NCBIGene:78906", "UniProtKB:Q9D279"] +["NCBIGene:293597", "UniProtKB:A0A0G2K0L2"] +["NCBIGene:328108", "UniProtKB:Q6A070"] +["NCBIGene:307667", "UniProtKB:D4A2N0"] +["NCBIGene:445153", "UniProtKB:F1R0Z9", "UniProtKB:Q58EM8"] +["NCBIGene:381404", "UniProtKB:A2A5N3"] +["NCBIGene:261623", "UniProtKB:Q9Y168"] +["NCBIGene:25398", "UniProtKB:O70368", "UniProtKB:P54282"] +["NCBIGene:313038", "UniProtKB:D4A0M3"] +["NCBIGene:440345", "UniProtKB:A0A804HK81"] +["NCBIGene:115290", "UniProtKB:Q96EF6"] +["NCBIGene:246703", "UniProtKB:Q8K4Z3"] +["NCBIGene:218343", "UniProtKB:F8VPK0"] +["NCBIGene:544666", "UniProtKB:A5PM60", "UniProtKB:Q5IHX7"] +["NCBIGene:28984", "UniProtKB:Q9H4X1"] +["NCBIGene:384309", "UniProtKB:A0A0R4J0Q6", "UniProtKB:Q80VI1"] +["NCBIGene:9478", "UniProtKB:Q9NZU7"] +["NCBIGene:567041", "UniProtKB:A0A0R4IGM8", "UniProtKB:F1R5N2", "UniProtKB:Q5SP05"] +["NCBIGene:108100", "UniProtKB:B1AZ46", "UniProtKB:Q3UKP6", "UniProtKB:Q8BKX1"] +["NCBIGene:300191", "UniProtKB:B0BNL4"] +["NCBIGene:25714", "UniProtKB:P19335"] +["NCBIGene:317575", "UniProtKB:D3ZIE5"] +["NCBIGene:621430", "UniProtKB:E9Q067"] +["NCBIGene:194655", "UniProtKB:Q8K1S5"] +["NCBIGene:207667", "UniProtKB:D3YX64", "UniProtKB:Q8BX46"] +["NCBIGene:2245", "UniProtKB:A0A024R9Y5", "UniProtKB:P98174"] +["NCBIGene:32939", "UniProtKB:M9NEP8", "UniProtKB:M9NFE1", "UniProtKB:Q9VWH5"] +["NCBIGene:560548", "UniProtKB:A0A1D5NSL5"] +["NCBIGene:294774", "UniProtKB:D3ZBZ9"] +["NCBIGene:34833", "UniProtKB:Q9VJT4"] +["NCBIGene:40534", "UniProtKB:Q9VMZ5"] +["NCBIGene:257872", "UniProtKB:Q7TRG7"] +["NCBIGene:43212", "UniProtKB:Q9VBD0"] +["NCBIGene:40267", "UniProtKB:Q9VPE9"] +["NCBIGene:8723", "UniProtKB:O95219"] +["NCBIGene:26067071", "UniProtKB:A0A0S0X9R6"] +["NCBIGene:302507", "UniProtKB:D3ZKF6"] +["NCBIGene:537", "UniProtKB:A0A0C4DGX8", "UniProtKB:A0A384MQW4", "UniProtKB:Q15904"] +["NCBIGene:100034402", "UniProtKB:Q7T011"] +["NCBIGene:1791", "UniProtKB:P04053"] +["NCBIGene:9923", "UniProtKB:B3KR52", "UniProtKB:F8WAI8", "UniProtKB:Q1RMZ5", "UniProtKB:Q9NUA8"] +["NCBIGene:243377", "UniProtKB:Q6WIZ7", "UniProtKB:Q8BZI2"] +["NCBIGene:100332028", "UniProtKB:E7F5X2"] +["NCBIGene:295425", "UniProtKB:D3ZYY9"] +["NCBIGene:31539", "UniProtKB:E4NKK1", "UniProtKB:Q8SYT8", "UniProtKB:Q9W442"] +["NCBIGene:56196", "UniProtKB:Q9JJX7"] +["NCBIGene:13168", "UniProtKB:O09035", "UniProtKB:Q545L5"] +["NCBIGene:68250", "UniProtKB:Q9DCL2"] +["NCBIGene:405208", "UniProtKB:D4ACK2"] 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"UniProtKB:D3ZV54"] +["NCBIGene:29285", "UniProtKB:P62845"] +["NCBIGene:559001", "UniProtKB:E7F5V3"] +["NCBIGene:678527", "UniProtKB:Q5PNN8"] +["NCBIGene:12372", "UniProtKB:O09165", "UniProtKB:Q6P3C3", "UniProtKB:Q8C7M8"] +["NCBIGene:50274", "UniProtKB:Q9VV03"] +["NCBIGene:406260", "UniProtKB:A0A2R8Q670", "UniProtKB:A0A2R8QLP1", "UniProtKB:E7F1U7", "UniProtKB:X1WFM4"] +["NCBIGene:314436", "UniProtKB:A4GTP4"] +["NCBIGene:563725", "UniProtKB:A0A140LH23"] +["NCBIGene:136242", "UniProtKB:A4D1T9", "UniProtKB:B7ZMK3"] +["NCBIGene:94189", "UniProtKB:Q62931"] +["NCBIGene:26010", "UniProtKB:A0A024R3V0", "UniProtKB:B8ZZZ7", "UniProtKB:Q9NUQ6"] +["NCBIGene:386675", "UniProtKB:P60409"] +["NCBIGene:74519", "UniProtKB:Q924D1"] +["NCBIGene:436854", "UniProtKB:F6NGJ3", "UniProtKB:Q6DGX6"] +["NCBIGene:17347", "UniProtKB:A0A0R4IZX7", "UniProtKB:Q3TPM2", "UniProtKB:Q8CDB0"] +["NCBIGene:25695", "UniProtKB:Q03484"] +["NCBIGene:402987", "UniProtKB:Q6QX43", "UniProtKB:X1WBA5"] +["NCBIGene:100271927", "UniProtKB:F5GXT2"] +["NCBIGene:241289", "UniProtKB:Q6A025"] +["NCBIGene:678604", "UniProtKB:Q1RLP9"] +["NCBIGene:3355123", "UniProtKB:Q8SYC3"] +["NCBIGene:254042", "UniProtKB:Q6UB28"] +["NCBIGene:33406", "UniProtKB:Q9VQ97"] +["NCBIGene:56525", "UniProtKB:Q499D5"] +["NCBIGene:565165", "UniProtKB:E9QB44"] +["NCBIGene:52202", "UniProtKB:A0A1D5RLR3", "UniProtKB:Q8C5L7"] +["NCBIGene:403000", "UniProtKB:Q6NZV1"] +["NCBIGene:79800", "UniProtKB:A0A024R405", "UniProtKB:B4DIA7", "UniProtKB:C9JI92", "UniProtKB:Q8N187"] +["NCBIGene:8490", "UniProtKB:A0A024R8X9", "UniProtKB:O15539"] +["NCBIGene:58839", "UniProtKB:Q9QYK3"] +["NCBIGene:32178", "UniProtKB:Q9VYP6"] +["NCBIGene:67804", "UniProtKB:Q9CWK8"] diff --git a/tests/resources/Protein.txt b/tests/resources/Protein.txt new file mode 100644 index 0000000..f4820fa --- /dev/null +++ b/tests/resources/Protein.txt @@ -0,0 +1,3000 @@ +{"type": "biolink:Protein", "identifiers": [{"i": "UniProtKB:A0A3B4TC59", "l": "A0A3B4TC59_SERDU Perforin-1-like (trembl)"}, {"i": "ENSEMBL:ENSSDUP00000003635"}, {"i": "ENSEMBL:ENSSDUP00000003635.1"}]} +{"type": "biolink:Protein", "identifiers": [{"i": "UniProtKB:A0A673VP59", "l": "A0A673VP59_SURSU Uncharacterized protein (trembl)"}, {"i": "ENSEMBL:ENSSSUP00005035241"}]} +{"type": "biolink:Protein", "identifiers": [{"i": "UniProtKB:A0A8C0XH88", "l": "A0A8C0XH88_CASCN DOP1 leucine zipper like protein A (trembl)"}, {"i": "ENSEMBL:ENSCCNP00000028400"}, {"i": "ENSEMBL:ENSCCNP00000028400.1"}]} +{"type": "biolink:Protein", "identifiers": [{"i": "UniProtKB:A0A8C1II68", "l": "A0A8C1II68_CYPCA E3 ubiquitin-protein ligase (trembl)"}, {"i": "ENSEMBL:ENSCCRP00010017938"}, {"i": "ENSEMBL:ENSCCRP00010017938.1"}]} +{"type": "biolink:Protein", "identifiers": [{"i": "UniProtKB:A0A2K5XE63", "l": "A0A2K5XE63_MANLE IF rod domain-containing protein (trembl)"}, {"i": "ENSEMBL:ENSMLEP00000001592"}, {"i": "ENSEMBL:ENSMLEP00000001592.1"}]} +{"type": "biolink:Protein", "identifiers": [{"i": "UniProtKB:A0A8C6NT13", "l": 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"UMLS:CN202575", - "NCIT:C121945", - "SNOMEDCT:697897003" - ], - "description": null, - "value_type_id": "EDAM:data_0006", - "attributes": null - } - ], - "categories": [ - "biolink:Disease", - "biolink:DiseaseOrPhenotypicFeature", - "biolink:BiologicalEntity", - "biolink:NamedThing" - ], - "name": "heritable pulmonary arterial hypertension" - } - }, - "edges": { - "044a7916-fba9-4b4f-ae48-f0815b0b222d": { - "subject": "NCBIGene:9496", - "object": "MONDO:0017148", - "predicate": "biolink:related_to", - "attributes": null, - "qualifiers": null - }, - "a8575c4e-61a6-428a-bf09-fcb3e8d1644d": { - "subject": "NCBIGene:9496", - "object": "MONDO:0005002", - "predicate": "biolink:related_to", - "attributes": null, - "qualifiers": null - } - } - }, - "results": [ - { - "node_bindings": { - "n1": [ - { - "id": "NCBIGene:9496", - "query_id": null, - "attributes": null - } - ], - "n3": [ - { - "id": "MONDO:0005002", - "query_id": null, - "attributes": null - } - ] - }, - "edge_bindings": { - "e1": [ - { - "id": "a8575c4e-61a6-428a-bf09-fcb3e8d1644d", - "attributes": null - } - ] - }, - "score": null - }, - { - "node_bindings": { - "n2": [ - { - "id": "NCBIGene:9496", - "query_id": null, - "attributes": null - } - ], - "n4": [ - { - "id": "MONDO:0005002", - "query_id": null, - "attributes": null - } - ] - }, - "edge_bindings": { - "e2": [ - { - "id": "a8575c4e-61a6-428a-bf09-fcb3e8d1644d", - "attributes": null - } - ] - }, - "score": null - }, - { - "node_bindings": { - "n1": [ - { - "id": "NCBIGene:9496", - "query_id": null, - "attributes": null - } - ], - "n5": [ - { - "id": "MONDO:0017148", - "query_id": null, - "attributes": null - } - ] - }, - "edge_bindings": { - "e3": [ - { - "id": "044a7916-fba9-4b4f-ae48-f0815b0b222d", - "attributes": null - } - ] - }, - "score": null - } - ] - }, - "logs": null, - "status": null, - "log_level": null -} diff --git a/tests/resources/premerged_kgraph.json b/tests/resources/premerged_kgraph.json index b297204..2e1f934 100644 --- a/tests/resources/premerged_kgraph.json +++ b/tests/resources/premerged_kgraph.json @@ -1,62 +1,16 @@ { - "nodes": { - "HGNC:11603": { - "name": "TBX4", - "categories": [ - "biolink:Gene" - ] - }, - "NCBIGene:9496": { - "name": "T-box transcription factor 4", - "categories": [ - "biolink:Gene" - ] - }, - "MONDO:0005002": { - "name": "chronic obstructive pulmonary disease", - "categories": [ - "biolink:Disease" - ] - }, - "DOID:3083": { - "name": "chronic obstructive pulmonary disease", - "categories": [ - "biolink:Disease" - ] - }, - "OMIM:613355": { - "name": "CHROMOSOME 17q23.1-q23.2 DELETION SYNDROME", - "categories": [ - "biolink:Disease" - ] - }, - "UMLS:CN202575": { - "name": "heritable pulmonary arterial hypertension", - "categories": [ - "biolink:Disease" - ] - } - }, - "edges": { - "a8575c4e-61a6-428a-bf09-fcb3e8d1644d": { - "subject": "HGNC:11603", - "object": "MONDO:0005002", - "predicate": "biolink:related_to" - }, - "b4971c4e-61a6-428a-bf09-fcb31234gfbs": { - "subject": "NCBIGene:9496", - "object": "DOID:3083", - "predicate": "biolink:related_to" - }, - "2d38345a-e9bf-4943-accb-dccba351dd04": { - "subject": "NCBIGene:9496", - "object": "OMIM:613355", - "predicate": "biolink:related_to" - }, - "044a7916-fba9-4b4f-ae48-f0815b0b222d": { - "subject": "HGNC:11603", - "object": "UMLS:CN202575", - "predicate": "biolink:related_to" + "nodes": { + "HGNC:11603": {"name": "TBX4", "categories": ["biolink:Gene"]}, + "NCBIGene:9496": {"name": "T-box transcription factor 4", "categories": ["biolink:Gene"]}, + "MONDO:0005002": {"name": "chronic obstructive pulmonary disease", "categories": ["biolink:Disease"]}, + "DOID:3083": {"name": "chronic obstructive pulmonary disease", "categories": ["biolink:Disease"]}, + "OMIM:613355": {"name": "CHROMOSOME 17q23.1-q23.2 DELETION SYNDROME", "categories": ["biolink:Disease"]}, + "UMLS:CN202575": {"name": "heritable pulmonary arterial hypertension", "categories": ["biolink:Disease"]} + }, + "edges": { + "a8575c4e-61a6-428a-bf09-fcb3e8d1644d": {"subject": "HGNC:11603", "object": "MONDO:0005002", "predicate": "biolink:related_to"}, + "b4971c4e-61a6-428a-bf09-fcb31234gfbs": {"subject": "NCBIGene:9496", "object": "DOID:3083", "predicate": "biolink:related_to"}, + "2d38345a-e9bf-4943-accb-dccba351dd04": {"subject": "NCBIGene:9496", "object": "OMIM:613355", "predicate": "biolink:related_to"}, + "044a7916-fba9-4b4f-ae48-f0815b0b222d": {"subject": "HGNC:11603", "object": "UMLS:CN202575", "predicate": "biolink:related_to"} } - } } diff --git a/tests/resources/premerged_response.json b/tests/resources/premerged_response.json deleted file mode 100644 index 83398dc..0000000 --- a/tests/resources/premerged_response.json +++ /dev/null @@ -1,170 +0,0 @@ -{ - "message": { - "query_graph": { - "nodes": { - "n1": { - "ids": ["HGNC:11603"], - "categories": [ - "biolink:Gene" - ] - }, - "n2": { - "ids": ["NCBIGene:9496"], - "categories": [ - "biolink:Gene" - ] - }, - "n3": { - "ids": ["MONDO:0005002"], - "categories": [ - "biolink:Disease" - ] - }, - "n4": { - "ids": ["DOID:3083"], - "categories": [ - "biolink:Disease" - ] - }, - "n5": { - "categories": [ - "biolink:Disease" - ] - } - }, - "edges": { - "e1": { - "subject": "n1", - "object": "n3" - }, - "e2": { - "subject": "n2", - "object": "n4", - "predicates": ["biolink:related_to"] - }, - "e3": { - "subject": "n1", - "object": "n5" - } - } - }, - "knowledge_graph": { - "nodes": { - "HGNC:11603": { - "name": "TBX4", - "categories": [ - "biolink:Gene" - ] - }, - "NCBIGene:9496": { - "name": "T-box transcription factor 4", - "categories": [ - "biolink:Gene" - ] - }, - "MONDO:0005002": { - "name": "chronic obstructive pulmonary disease", - "categories": [ - "biolink:Disease" - ] - }, - "DOID:3083": { - "name": "chronic obstructive pulmonary disease", - "categories": [ - "biolink:Disease" - ] - }, - "UMLS:CN202575": { - "name": "heritable pulmonary arterial hypertension", - "categories": [ - "biolink:Disease" - ] - } - }, - "edges": { - "a8575c4e-61a6-428a-bf09-fcb3e8d1644d": { - "subject": "HGNC:11603", - "object": "MONDO:0005002", - "predicate": "biolink:related_to" - }, - "2d38345a-e9bf-4943-accb-dccba351dd04": { - "subject": "NCBIGene:9496", - "object": "DOID:3083", - "predicate": "biolink:related_to" - }, - "044a7916-fba9-4b4f-ae48-f0815b0b222d": { - "subject": "HGNC:11603", - "object": "UMLS:CN202575", - "predicate": "biolink:related_to" - } - } - }, - "results": [ - { - "node_bindings": { - "n1": [ - { - "id": "HGNC:11603" - } - ], - "n3": [ - { - "id": "MONDO:0005002" - } - ] - }, - "edge_bindings": { - "e1": [ - { - "id": "a8575c4e-61a6-428a-bf09-fcb3e8d1644d" - } - ] - } - }, - { - "node_bindings": { - "n2": [ - { - "id": "NCBIGene:9496" - } - ], - "n4": [ - { - "id": "DOID:3083" - } - ] - }, - "edge_bindings": { - "e2": [ - { - "id": "2d38345a-e9bf-4943-accb-dccba351dd04" - } - ] - } - }, - { - "node_bindings": { - "n1": [ - { - "id": "HGNC:11603" - } - ], - "n5": [ - { - "id": "UMLS:CN202575" - } - ] - }, - "edge_bindings": { - "e3": [ - { - "id": "044a7916-fba9-4b4f-ae48-f0815b0b222d" - } - ] - } - } - ] - }, - "logs": null, - "status": null -} diff --git a/tests/resources/redis-config.yaml b/tests/resources/redis-config.yaml deleted file mode 100644 index 3c2cccd..0000000 --- a/tests/resources/redis-config.yaml +++ /dev/null @@ -1,54 +0,0 @@ -"eq_id_to_id_db" : - "ssl_enabled": false - "is_cluster": false - "db": 0 - "hosts": - # list of cluster member ips and ports - - "host_name": "127.0.0.1" - "port": "6379" - "password": "" - -"id_to_eqids_db": - "ssl_enabled": false - "is_cluster": false - "db": 1 - "hosts": - - "host_name": "127.0.0.1" - "port": "6379" - "password": "" - -"id_to_type_db": - "ssl_enabled": false - "is_cluster": true - "db": 2 - "hosts": - - "host_name": "127.0.0.1" - "port": "6379" - "password": "" - -"curie_to_bl_type_db": - "ssl_enabled": true - "is_cluster": true - "db": 3 - "hosts": - - "host_name": "127.0.0.1" - "port": "6379" - "password": "" - -"info_content_db": - "ssl_enabled": true - "is_cluster": false - "db": 4 - "hosts": - - "host_name": "127.0.0.1" - "port": "6379" - "password": "" - -"gene_protein_db": - "ssl_enabled": true - "is_cluster": false - "db": 5 - "hosts": - - "host_name": "127.0.0.1" - "port": "6379" - "password": "" \ No newline at end of file diff --git a/tests/test_callback.py b/tests/test_callback.py deleted file mode 100644 index e81f246..0000000 --- a/tests/test_callback.py +++ /dev/null @@ -1,47 +0,0 @@ -"""Test node_normalizer server.py""" -import json -import time - -import reasoner_pydantic -import requests -import fastapi -from pathlib import Path - -from node_normalizer.util import LoggingUtil - -logger = LoggingUtil.init_logging() - -premerged_response = Path(__file__).parent / "resources" / "premerged_response.json" - - -def test_async_query_callback(session): - - # host_url = "http://r3:8080/asyncquery" - # host_url = f"{session[1]}/asyncquery" - host_url = "http://127.0.0.1:8080/asyncquery" - logger.info(f"host_url: {host_url}") - - # callback_url = f"http://callback-app:8008/receive_callback_query" - # callback_url = f"{session[2]}/receive_callback_query" - callback_url = f"http://callback-app:8008/receive_callback_query" - logger.info(f"callback_url: {callback_url}") - - with open(premerged_response, "r") as pre: - premerged_data = json.load(pre) - - premerged_data["callback"] = callback_url - - async_query = reasoner_pydantic.message.AsyncQuery.parse_obj(premerged_data) - - response = requests.post(url=host_url, headers={"Content-Type": "application/json", "Accept": "application/json"}, data=async_query.json()) - - # sleep here to allow the /asyncquery background task to run through - time.sleep(10) - - assert response.status_code == 200 - assert response.json() == {"description": f"Query commenced. Will send result to {callback_url}"} - - compose_stdout, compose_stderr = session[0].get_logs() - assert b'Successfully received message from "http://callback-app:8008/receive_callback_query"' in compose_stdout - - diff --git a/tests/test_endpoints.py b/tests/test_endpoints.py index 56ff680..b7df71c 100644 --- a/tests/test_endpoints.py +++ b/tests/test_endpoints.py @@ -1,131 +1,222 @@ """Test node_normalizer server.py""" +from deepdiff import DeepDiff import json +import time import reasoner_pydantic - -from node_normalizer.server import app -from starlette.testclient import TestClient +import requests from pathlib import Path -from unittest.mock import Mock, patch -from deepdiff import DeepDiff -import fastapi -# Need to add to sources root to avoid linter warnings -from .helpers.redis_mocks import mock_get_equivalent_curies -from .helpers.redis_mocks import mock_get_ic +HEADERS = {"Content-Type": "application/json", "Accept": "application/json"} -premerged_response = Path(__file__).parent / "resources" / "premerged_response.json" -postmerged_response = Path(__file__).parent / "resources" / "postmerged_response.json" -premerged_dupe_edge = Path(__file__).parent / "resources" / "premerged_dupe_edge.json" -postmerged_dupe_edge = Path(__file__).parent / "resources" / "postmerged_dupe_edge.json" +def test_get_conflations(session): + host_url = "http://127.0.0.1:8080/get_allowed_conflations" + print(f"host_url: {host_url}") + response = requests.get(url=host_url, headers=HEADERS) + assert response.status_code == 200 + response_json = response.json() + assert "gene_protein" in response_json['conflations'] -input_set = Path(__file__).parent / "resources" / "input_set.json" +def test_async_query_callback(session): + host_url = "http://127.0.0.1:8080/asyncquery" + print(f"host_url: {host_url}") -class TestServer: - @classmethod - def setup_class(self): - app.testing = True - self.test_client = TestClient(app) + callback_url = f"http://callback-app:8008/receive_callback_query" + print(f"callback_url: {callback_url}") - @classmethod - def teardown_class(self): - self.test_client = None + basic_query_file = Path(__file__).parent / "resources" / "basic_query.json" - @patch( - "node_normalizer.normalizer.get_equivalent_curies", - Mock(side_effect=mock_get_equivalent_curies), - ) - @patch( - "node_normalizer.normalizer.get_info_content_attribute", - Mock(side_effect=mock_get_ic), - ) - def test_message_normalize_endpoint(self): - """ - TODO turn this into a parametrized test for various cases - """ - with open(premerged_response, "r") as pre: - premerged_data = json.load(pre) - - with open(postmerged_response, "r") as post: - postmerged_from_file = json.load(post) - - response = self.test_client.post("/query", json=premerged_data) - postmerged_from_api = json.loads(response.text) - - # get the difference - diffs = DeepDiff(postmerged_from_file, postmerged_from_api, ignore_order=True) - # diffs = find_diffs(postmerged_from_api, postmerged_from_file) - - # no diffs, no problem - # assert diffs is None - assert len(diffs) == 0 - - # unless these nodes are added to the mock-redis, this won't run - def x_test_real_result(self): - with open("resources/ac_out_attributes.json", "r") as pre: - premerged_data = json.load(pre) - - response = self.test_client.post("/query", json=premerged_data) - postmerged_from_api = json.loads(response.text) - - assert len(postmerged_from_api["message"]["results"]) == len( - premerged_data["message"]["results"] - ) - - @patch( - "node_normalizer.normalizer.get_equivalent_curies", - Mock(side_effect=mock_get_equivalent_curies), - ) - @patch( - "node_normalizer.normalizer.get_info_content_attribute", - Mock(side_effect=mock_get_ic), - ) - def test_dupe_edge(self): - """ - TODO turn this into a parametrized test for various cases - """ - with open(premerged_dupe_edge, "r") as pre: - premerged_data = json.load(pre) + with open(basic_query_file, "r") as pre: + basic_query_data = json.load(pre) + + basic_query_data["callback"] = callback_url + + async_query = reasoner_pydantic.message.AsyncQuery.parse_obj(basic_query_data) + + response = requests.post(url=host_url, headers=HEADERS, data=async_query.json()) + + # sleep here to allow the /asyncquery background task to run through + time.sleep(10) + + assert response.status_code == 200 + assert response.json() == {"description": f"Query commenced. Will send result to {callback_url}"} + + compose_stdout, compose_stderr = session[0].get_logs() + assert b'Successfully received message from "http://callback-app:8008/receive_callback_query"' in compose_stdout - with open(postmerged_dupe_edge, "r") as post: - postmerged_from_file = json.load(post) - response = self.test_client.post("/query", json=premerged_data) - postmerged_from_api = json.loads(response.text) +def test_message_normalize_endpoint(session): + host_url = "http://127.0.0.1:8080/query" + print(f"host_url: {host_url}") - # print(f"{postmerged_from_api}") + basic_query_file = Path(__file__).parent / "resources" / "basic_query.json" + with open(basic_query_file, "r") as pre: + basic_query = json.load(pre) - # get the difference - diffs = DeepDiff(postmerged_from_file, postmerged_from_api, ignore_order=True) - # diffs = find_diffs(postmerged_from_api, postmerged_from_file) + query = reasoner_pydantic.message.Query.parse_obj(basic_query) - # no diffs, no problem - # assert diffs is None - assert len(diffs) == 0 + response = requests.post(url=host_url, headers=HEADERS, data=query.json()) + assert response.status_code == 200 + response_json = response.json() - @patch( - "node_normalizer.normalizer.get_equivalent_curies", - Mock(side_effect=mock_get_equivalent_curies), + # confirm that the used, non-canonical identifier is replaced with the canonical identifier + assert ( + response_json["message"]["query_graph"]["nodes"]["n1"]["ids"][0] == "NCBIGene:64109" + and response_json["message"]["query_graph"]["nodes"]["n1"]["ids"][0] != "HGNC:14281" ) - @patch( - "node_normalizer.normalizer.get_info_content_attribute", - Mock(side_effect=mock_get_ic), + assert ( + response_json["message"]["query_graph"]["nodes"]["n2"]["ids"][0] == "MONDO:0013985" + and response_json["message"]["query_graph"]["nodes"]["n2"]["ids"][0] != "DOID:0110474" ) - def test_input_has_set(self): - """ - Node normalizer is doing something bad with nodes when there are more than one knodes bound to a single qnode - """ - with open(input_set, "r") as pre: - premerged_data = json.load(pre) - response = self.test_client.post("/query", json=premerged_data) - postmerged_from_api = json.loads(response.text) - result = postmerged_from_api["message"]["results"][0] - # There are 2 coming in and no merging, so should be 2 going out - assert len(result["edge_bindings"]["treats"]) == 2 - assert len(result["node_bindings"]["drug"]) == 2 +def test_get_semantic_types(session): + host_url = "http://127.0.0.1:8080/get_semantic_types" + response = requests.get(url=host_url, headers=HEADERS) + assert response.status_code == 200 + response_json = response.json() + assert response_json["semantic_types"] is not None + # this is utterly idiotic...no idiomatic list contains list? There has to be a better way to do this. + assert all(elem in response_json["semantic_types"]["types"] for elem in ["biolink:Disease", "biolink:Gene", "biolink:Cell", "biolink:Protein"]) + + +def test_get_normalized_nodes_not_found(session): + host_url = "http://127.0.0.1:8080/get_normalized_nodes" + + # GET + response = requests.get(url=host_url, headers=HEADERS, params={"curie": ["UNKNOWN:000000"]}) + assert response.status_code == 200 + response_json = response.json() + assert response_json == {"UNKNOWN:000000": None} + + # POST + response = requests.post(url=host_url, headers=HEADERS, json={"curies": ["UNKNOWN:000000"]}) + assert response.status_code == 200 + response_json = response.json() + assert response_json == {"UNKNOWN:000000": None} + + +def test_get_normalized_nodes_one_missing(): + host_url = "http://127.0.0.1:8080/get_normalized_nodes" + + response = requests.get(url=host_url, headers=HEADERS, params={"curie": ["UNKNOWN:000000", "DOID:0110474"]}) + assert response.status_code == 200 + response_json = response.json() + assert len(response_json) == 2 + assert not response_json["UNKNOWN:000000"] + assert response_json["DOID:0110474"]["id"]["identifier"] == "MONDO:0013985" + + +def test_get_normalized_nodes_all_missing(): + """ + /get_normalized_nodes previously returned {} if none of the provided CURIEs are resolvable. + This test ensures that that bug has been fixed. + + Reported in https://github.com/TranslatorSRI/NodeNormalization/issues/113 + """ + + host_url = "http://127.0.0.1:8080/get_normalized_nodes" + + # GET + response = requests.get(url=host_url, headers=HEADERS, params={"curie": ["NCBIGene:ABCD", "NCBIGene:GENE:1017"]}) + assert response.status_code == 200 + response_json = response.json() + assert response_json == {"NCBIGene:ABCD": None, "NCBIGene:GENE:1017": None} + + # POST + response = requests.post(url=host_url, headers=HEADERS, json={"curies": ["NCBIGene:ABCD", "NCBIGene:GENE:1017"]}) + assert response.status_code == 200 + response_json = response.json() + assert response_json == {"NCBIGene:ABCD": None, "NCBIGene:GENE:1017": None} + + +def test_get_normalized_nodes_merge(): + host_url = "http://127.0.0.1:8080/get_normalized_nodes" + response = requests.get(url=host_url, headers=HEADERS, params={"curie": ["MONDO:0005002", "DOID:3812"]}) + assert response.status_code == 200 + response_json = response.json() + assert len(response_json) == 2 + assert "MONDO:0005002" in response_json + assert "DOID:3812" in response_json + + +def test_get_normalized_nodes_empty(): + host_url = "http://127.0.0.1:8080/get_normalized_nodes" + + # GET + response = requests.get(url=host_url, headers=HEADERS, params={"curie": []}) + assert response.status_code == 422 + assert response.reason == "Unprocessable Entity" + response_json = response.json() + assert response_json["detail"][0]["msg"] == "ensure this value has at least 1 items" + assert response_json["detail"][0]["loc"] == ["query", "curie"] + + # POST + response = requests.post(url=host_url, headers=HEADERS, json={"curies": []}) + assert response.status_code == 422 + assert response.reason == "Unprocessable Entity" + response_json = response.json() + assert response_json["detail"][0]["msg"] == "ensure this value has at least 1 items" + assert response_json["detail"][0]["loc"] == ["body", "curies"] + + +def x_test_real_result(session): + host_url = "http://127.0.0.1:8080/query" + print(f"host_url: {host_url}") + + ac_out_attributes_file = Path(__file__).parent / "resources" / "ac_out_attributes.json" + + with open(ac_out_attributes_file, "r") as pre: + ac_out_attributes_data = json.load(pre) + + query = reasoner_pydantic.message.Query.parse_obj(ac_out_attributes_data) + + response = requests.post(url=host_url, headers=HEADERS, data=query.json()) + assert response.status_code == 200 + post_merged_from_api = response.json() + + assert len(post_merged_from_api["message"]["results"]) == len(ac_out_attributes_data["message"]["results"]) + + +def test_dupe_edge(session): + host_url = "http://127.0.0.1:8080/query" + print(f"host_url: {host_url}") + + pre_merged_dupe_edge_file = Path(__file__).parent / "resources" / "premerged_dupe_edge.json" + with open(pre_merged_dupe_edge_file, "r") as pre: + pre_merged_dupe_edge_data = json.load(pre) + + post_merged_dupe_edge_file = Path(__file__).parent / "resources" / "postmerged_dupe_edge.json" + with open(post_merged_dupe_edge_file, "r") as pre: + post_merged_dupe_edge_data = json.load(pre) + + query = reasoner_pydantic.message.Query.parse_obj(pre_merged_dupe_edge_data) + + response = requests.post(url=host_url, headers=HEADERS, data=query.json()) + assert response.status_code == 200 + post_merged_from_api = response.json() + + diffs = DeepDiff(post_merged_dupe_edge_data, post_merged_from_api, ignore_order=True) + assert len(diffs) == 0 + + +def test_input_has_set(session): + host_url = "http://127.0.0.1:8080/query" + print(f"host_url: {host_url}") + + input_set_file = Path(__file__).parent / "resources" / "input_set.json" + with open(input_set_file, "r") as pre: + input_set_data = json.load(pre) + + query = reasoner_pydantic.message.Query.parse_obj(input_set_data) + response = requests.post(url=host_url, headers=HEADERS, data=query.json()) + assert response.status_code == 200 + post_merged_from_api = response.json() + result = post_merged_from_api["message"]["results"][0] + # There are 2 coming in and no merging, so should be 2 going out + assert len(result["edge_bindings"]["treats"]) == 2 + assert len(result["node_bindings"]["drug"]) == 2 diff --git a/tests/test_loader.py b/tests/test_loader.py deleted file mode 100644 index 85d3f26..0000000 --- a/tests/test_loader.py +++ /dev/null @@ -1,29 +0,0 @@ -from pathlib import Path - -import pytest - -from node_normalizer.loader import NodeLoader - - -good_json = Path(__file__).parent / "resources" / "datafile.json" -bad_json = Path(__file__).parent / "resources" / "datafile_with_errors.json" - - -def test_nn_load(): - node_loader: NodeLoader = NodeLoader() - - node_loader._test_mode = 1 - - assert node_loader.load_compendium(good_json, 5) - - -def test_nn_record_validation(): - node_loader: NodeLoader = NodeLoader() - - ret_val = node_loader.validate_compendia(good_json) - - assert ret_val - - ret_val = node_loader.validate_compendia(bad_json) - - assert not ret_val diff --git a/tests/test_norm.py b/tests/test_norm.py deleted file mode 100644 index aec287e..0000000 --- a/tests/test_norm.py +++ /dev/null @@ -1,109 +0,0 @@ -"""Test node_normalizer server.py""" -import json -from node_normalizer.server import app -from starlette.testclient import TestClient -from unittest.mock import Mock, patch -from .helpers.redis_mocks import mock_get_equivalent_curies, mock_get_ic -from pathlib import Path -import os - - -class MockRedis: - def __init__(self, data): - self.data = data - - async def mget(self, *args, **kwargs): - return [self.data[x] if x in self.data else None for x in args] - - -# Id -> Canonical -app.state.redis_connection0 = MockRedis( - {"DOID:3812": "MONDO:0005002", "MONDO:0005002": "MONDO:0005002"} -) -# Canonical->Equiv -app.state.redis_connection1 = MockRedis( - {"MONDO:0005002": json.dumps([{"i": "MONDO:0005002"}, {"i": "DOID:3812"}])} -) -app.state.redis_connection2 = MockRedis({"MONDO:0005002": "biolink:Disease"}) -app.state.redis_connection3 = MockRedis({}) -app.state.redis_connection4 = MockRedis({}) -app.state.redis_connection5 = MockRedis({}) -app.state.ancestor_map = {"biolink:Disease": ["biolink:Disease", "biolink:NamedThing"]} - - -def test_not_found(): - client = TestClient(app) - response = client.get("/get_normalized_nodes", params={"curie": ["UNKNOWN:000000"]}) - result = json.loads(response.text) - assert result == {"UNKNOWN:000000": None} - response = client.post("/get_normalized_nodes", json={"curies": ["UNKNOWN:000000"]}) - result = json.loads(response.text) - assert result == {"UNKNOWN:000000": None} - - -def test_one_missing(): - client = TestClient(app) - response = client.get( - "/get_normalized_nodes", params={"curie": ["UNKNOWN:000000", "DOID:3812"]} - ) - result = json.loads(response.text) - assert len(result) == 2 - assert result["UNKNOWN:000000"] == None - assert result["DOID:3812"]["id"]["identifier"] == "MONDO:0005002" - - -def test_all_missing(): - """ - /get_normalized_nodes previously returned {} if none of the provided CURIEs are resolvable. - This test ensures that that bug has been fixed. - - Reported in https://github.com/TranslatorSRI/NodeNormalization/issues/113 - """ - client = TestClient(app) - - # Test GET - response = client.get( - "/get_normalized_nodes", - params={"curie": ["NCBIGene:ABCD", "NCBIGene:GENE:1017"]}, - ) - result = json.loads(response.text) - assert result == {"NCBIGene:ABCD": None, "NCBIGene:GENE:1017": None} - - # Test POST - response = client.post( - "/get_normalized_nodes", - json={"curies": ["NCBIGene:ABCD", "NCBIGene:GENE:1017"]}, - ) - result = json.loads(response.text) - assert result == {"NCBIGene:ABCD": None, "NCBIGene:GENE:1017": None} - - -def test_merge(): - client = TestClient(app) - response = client.get( - "/get_normalized_nodes", params={"curie": ["MONDO:0005002", "DOID:3812"]} - ) - result = json.loads(response.text) - assert len(result) == 2 - assert "MONDO:0005002" in result - assert "DOID:3812" in result - - -def test_empty(): - client = TestClient(app) - - # GET - response = client.get("/get_normalized_nodes", params={"curie": []}) - assert response.status_code == 422 - assert response.reason == "Unprocessable Entity" - result = json.loads(response.text) - assert result["detail"][0]["msg"] == "ensure this value has at least 1 items" - assert result["detail"][0]["loc"] == ["query", "curie"] - - # POST - response = client.post("/get_normalized_nodes", json={"curies": []}) - assert response.status_code == 422 - assert response.reason == "Unprocessable Entity" - result = json.loads(response.text) - assert result["detail"][0]["msg"] == "ensure this value has at least 1 items" - assert result["detail"][0]["loc"] == ["body", "curies"] diff --git a/tests/test_normalizer.py b/tests/test_normalizer.py index 72cd0f0..831cd9b 100644 --- a/tests/test_normalizer.py +++ b/tests/test_normalizer.py @@ -104,8 +104,8 @@ def float_or_none(x): return None -premerged_graph = Path(__file__).parent / "resources" / "premerged_kgraph.json" -postmerged_graph = Path(__file__).parent / "resources" / "postmerged_kgraph.json" +pre_merged_graph = Path(__file__).parent / "resources" / "premerged_kgraph.json" +post_merged_graph = Path(__file__).parent / "resources" / "postmerged_kgraph.json" class TestNormalizer: @@ -120,13 +120,14 @@ class TestNormalizer: ) async def test_kg_normalize(self): app = None - with open(premerged_graph, "r") as pre: - premerged_data = KnowledgeGraph.parse_obj(json.load(pre)) + with open(pre_merged_graph, "r") as pre: + pre_merged_data = KnowledgeGraph.parse_obj(json.load(pre)) - with open(postmerged_graph, "r") as post: - postmerged_from_file = json.load(post) + with open(post_merged_graph, "r") as post: + post_merged_from_file = json.load(post) + print(f"post_merged_from_file: {post_merged_from_file}") - postmerged_from_api, nmap, emap = await normalize_kgraph(app, premerged_data) + postmerged_from_api, nmap, emap = await normalize_kgraph(app, pre_merged_data, None) nodes: dict = {} for code, node in postmerged_from_api.nodes.items(): @@ -138,8 +139,10 @@ async def test_kg_normalize(self): post = {"nodes": nodes, "edges": edges} + print(f"post_merged_from_api: {postmerged_from_api.json()}") # get the difference - diffs = DeepDiff(post, postmerged_from_file, ignore_order=True) + diffs = DeepDiff(post_merged_from_file, post, ignore_order=True) + print(diffs) # diffs = find_diffs(post, postmerged_from_file) # no diffs, no problem diff --git a/tests/test_redis_adapter.py b/tests/test_redis_adapter.py index 0a0d50b..1d5a5ac 100644 --- a/tests/test_redis_adapter.py +++ b/tests/test_redis_adapter.py @@ -1,10 +1,10 @@ import pytest, yaml -from node_normalizer.redis_adapter import ConnectionConfig, RedisInstance, RedisConnectionFactory, \ - RedisConnection, Resource +from node_normalizer.redis_adapter import ConnectionConfig, RedisInstance, RedisConnectionFactory, RedisConnection, Resource from pathlib import Path from unittest.mock import patch -REDIS_CONF_PATH = Path(__file__).parent / 'resources' / 'redis-config.yaml' +REDIS_CONF_PATH = Path(__file__).parent.parent / "redis_config.yaml" + @pytest.fixture def config_dict(): @@ -17,13 +17,13 @@ def test_connection_config_is_dynamic(config_dict): for key in config_dict: assert connection.__getattr__(key) assert isinstance(connection.__getattr__(key), RedisInstance) - config_dict.pop('gene_protein_db') + config_dict.pop("conflation_db") connection = ConnectionConfig(config_dict) for key in config_dict: assert connection.__getattr__(key) assert isinstance(connection.__getattr__(key), RedisInstance) try: - connection.__getattr__('gene_protein_db') + connection.__getattr__("conflation_db") except KeyError: error_raise = True @@ -33,27 +33,27 @@ def test_connection_config_is_dynamic(config_dict): def test_redis_instance_attributes(config_dict): connection = ConnectionConfig(config_dict) clusterd_db_name = "id_to_type_db" - ssl_db_name = "gene_protein_db" + ssl_db_name = "conflation_db" ssl_and_cluster_db_name = "curie_to_bl_type_db" config_instance: RedisInstance = connection.__getattr__(clusterd_db_name) assert isinstance(config_instance, RedisInstance) - assert config_instance.is_cluster + assert not config_instance.is_cluster assert not config_instance.ssl_enabled config_instance: RedisInstance = connection.__getattr__(ssl_db_name) assert isinstance(config_instance, RedisInstance) assert not config_instance.is_cluster - assert config_instance.ssl_enabled + assert not config_instance.ssl_enabled config_instance: RedisInstance = connection.__getattr__(ssl_and_cluster_db_name) assert isinstance(config_instance, RedisInstance) - assert config_instance.is_cluster - assert config_instance.ssl_enabled - + assert not config_instance.is_cluster + assert not config_instance.ssl_enabled class RedisConnectionMock: instances_list = [] + def __init__(self): self.connector = None @@ -66,7 +66,7 @@ async def create(cls, redis_instance: RedisInstance): @pytest.mark.asyncio async def test_redis_connectors_created(config_dict): - with patch('node_normalizer.redis_adapter.RedisConnection',RedisConnectionMock): + with patch("node_normalizer.redis_adapter.RedisConnection", RedisConnectionMock): redis_factory: RedisConnectionFactory = await RedisConnectionFactory.create_connection_pool(REDIS_CONF_PATH) connections = redis_factory.get_all_connections() config = redis_factory.get_config(REDIS_CONF_PATH) @@ -78,27 +78,26 @@ async def test_redis_connectors_created(config_dict): class RedisClusterMock: closed = False redis_instance: RedisInstance = None + def __init__(self, *args, **kwargs): pass rc = RedisClusterMock.redis_instance host = rc.hosts[0].host_name port = rc.hosts[0].port - start_up_nodes = [ {'host': host.host_name, 'port': host.port } for host in rc.hosts] - assert kwargs['startup_nodes'] == start_up_nodes - assert kwargs['decode_responses'] == True - assert kwargs['skip_full_coverage_check'] == True - assert kwargs['password'] == rc.password + start_up_nodes = [{"host": host.host_name, "port": host.port} for host in rc.hosts] + assert kwargs["startup_nodes"] == start_up_nodes + assert kwargs["decode_responses"] == True + assert kwargs["skip_full_coverage_check"] == True + assert kwargs["password"] == rc.password if rc.ssl_enabled: - assert kwargs['ssl'] - assert not kwargs['ssl_cert_reqs'] + assert kwargs["ssl"] + assert not kwargs["ssl_cert_reqs"] else: - assert 'ssl' not in kwargs - assert 'ssl_cert_reqs' not in kwargs + assert "ssl" not in kwargs + assert "ssl_cert_reqs" not in kwargs - self.k_v = { - "someKey": "some" - } + self.k_v = {"someKey": "some"} def get(self, name, encoding="utf-8"): return self.k_v.get(name) @@ -121,28 +120,27 @@ def connection(self): class aioredisMock: - - def __init__(self, ): - self.k_v = { - "someKey": "someValue" - } + def __init__( + self, + ): + self.k_v = {"someKey": "someValue"} async def get(self, key, encoding): - assert encoding == 'utf-8' + assert encoding == "utf-8" return self.k_v.get(key) async def pipeline(self): return "pipeline" async def mget(self, *keys, encoding): - assert encoding == 'utf-8' + assert encoding == "utf-8" response = {} for k in keys: response[k] = self.k_v.get(k) return response - async def lrange(self, key=0, start=0, stop=0, encoding='utf-8'): - assert encoding == 'utf-8' + async def lrange(self, key=0, start=0, stop=0, encoding="utf-8"): + assert encoding == "utf-8" return "called" def close(self): @@ -151,7 +149,6 @@ def close(self): async def wait_closed(self): self.close() - def __instancecheck__(self, *args, **kwargs): return True @@ -160,23 +157,21 @@ def __instancecheck__(self, *args, **kwargs): async def test_redis_aioredis_connection(): mocked_connection = aioredisMock() - redis_instance: RedisInstance = RedisInstance(ssl_enabled=True, - password='somepassword', - is_cluster=False, - db=0, - hosts=[Resource(host_name="127.0.0.1", port=6379)]) + redis_instance: RedisInstance = RedisInstance( + ssl_enabled=True, password="somepassword", is_cluster=False, db=0, hosts=[Resource(host_name="127.0.0.1", port=6379)] + ) + async def create_redis_mock(*args, **kwargs): - assert kwargs['password'] == redis_instance.password - assert kwargs['db'] == redis_instance.db + assert kwargs["password"] == redis_instance.password + assert kwargs["db"] == redis_instance.db host = redis_instance.hosts[0].host_name port = redis_instance.hosts[0].port assert args == (f"redis://{host}:{port}",) - assert kwargs['ssl'] == redis_instance.ssl_enabled + assert kwargs["ssl"] == redis_instance.ssl_enabled return mocked_connection - with patch('aioredis.create_redis_pool', create_redis_mock): - + with patch("aioredis.create_redis_pool", create_redis_mock): with patch("aioredis.commands.Redis", mocked_connection): connection = await RedisConnection.create(redis_instance) @@ -188,14 +183,9 @@ async def create_redis_mock(*args, **kwargs): assert await mocked_connection.pipeline() == await connection.pipeline() # test mget keys = ["someKey", "anotherKey"] - assert await mocked_connection.mget(*keys, encoding='utf-8') == await connection.mget(*keys) + assert await mocked_connection.mget(*keys, encoding="utf-8") == await connection.mget(*keys) # test lrange - kwargs = { - "key": 2, - "start": 1, - "stop": 2, - "encoding": 'utf-8' - } + kwargs = {"key": 2, "start": 1, "stop": 2, "encoding": "utf-8"} assert await mocked_connection.lrange(**kwargs) == await connection.lrange(**kwargs) # test close @@ -210,17 +200,18 @@ async def create_redis_mock(*args, **kwargs): @pytest.mark.asyncio - async def test_redis_rediscluster(): - redis_instance: RedisInstance = RedisInstance(ssl_enabled=True, - password='somepassword', - # it is a cluster - is_cluster=True, - db=0, - hosts=[Resource(host_name="127.0.0.1", port=6379)]) + redis_instance: RedisInstance = RedisInstance( + ssl_enabled=True, + password="somepassword", + # it is a cluster + is_cluster=True, + db=0, + hosts=[Resource(host_name="127.0.0.1", port=6379)], + ) RedisClusterMock.redis_instance = redis_instance # redisclustermock = RedisClusterMock("redis://127.0.0.1:6379") - with patch('node_normalizer.redis_adapter.RedisCluster', RedisClusterMock): + with patch("node_normalizer.redis_adapter.RedisCluster", RedisClusterMock): connection = await RedisConnection.create(redis_instance) # test ssl disabled redis_instance.ssl_enabled = False @@ -230,15 +221,10 @@ async def test_redis_rediscluster(): assert "some" == await connection.get("someKey") # test mget - assert {"someKey": "some", "another": None} == await connection.mget(*['someKey', 'another']) + assert {"someKey": "some", "another": None} == await connection.mget(*["someKey", "another"]) # test lrange - kwargs = { - "key": 2, - "start": 1, - "stop": 2, - "encoding": 'utf-8' - } + kwargs = {"key": 2, "start": 1, "stop": 2, "encoding": "utf-8"} assert "lrange called" == await connection.lrange(**kwargs) # test close