diff --git a/README.md b/README.md index 54045d0..99b7452 100644 --- a/README.md +++ b/README.md @@ -1,18 +1,49 @@ # AWS HealthOmics Tools -Tools for working with the Amazon Omics Service. - -## Using the Omics Transfer Manager +SDK and CLI Tools for working with the AWS HealthOmics Service. + +- [AWS HealthOmics Tools](#aws-healthomics-tools) + - [Installation](#installation) + - [SDK Tools](#sdk-tools) + - [Omics Transfer Manager](#omics-transfer-manager) + - [Basic Usage](#basic-usage) + - [Download specific files](#download-specific-files) + - [Upload specific files](#upload-specific-files) + - [Subscribe to events](#subscribe-to-events) + - [Threads](#threads) + - [Omics URI Parser](#omics-uri-parser) + - [Readset file URI:](#readset-file-uri) + - [Reference file URI:](#reference-file-uri) + - [CLI Tools](#cli-tools) + - [Omics Rerun](#omics-rerun) + - [List runs from manifest](#list-runs-from-manifest) + - [Rerun a previously-executed run](#rerun-a-previously-executed-run) + - [Omics Run Analyzer](#omics-run-analyzer) + - [List completed runs](#list-completed-runs) + - [Analyze a specific workflow run](#analyze-a-specific-workflow-run) + - [Output workflow run manifest in JSON format](#output-workflow-run-manifest-in-json-format) + - [Security](#security) + - [License](#license) + +## Installation +AWS HealthOmics Tools is available through pypi. To install, type: + +```bash +pip install amazon-omics-tools +``` -### Installation -Installation -Amazon Omics Tools is available through pypi. To install, type: +To install from source: -```python -pip install amazon-omics-tools +``` +git clone https://github.com/awslabs/amazon-omics-tools.git +pip install ./amazon-omics-tools ``` -### Basic Usage +## SDK Tools + +### Omics Transfer Manager + +#### Basic Usage The `TransferManager` class makes it easy to download files for an Omics reference or read set. By default the files are saved to the current directory, or you can specify a custom location with the `directory` parameter. ```python @@ -34,7 +65,7 @@ manager.download_reference(REFERENCE_STORE_ID, "") manager.download_read_set(SEQUENCE_STORE_ID, "", "my-sequence-data") ``` -### Download specific files +#### Download specific files Specific files can be downloaded via the `download_reference_file` and `download_read_set_file` methods. The `client_fileobj` parameter can be either the name of a local file to create for storing the data, or a `TextIO` or `BinaryIO` object that supports write methods. @@ -55,7 +86,7 @@ manager.download_read_set_file( ) ``` -### Upload specific files +#### Upload specific files Specific files can be uploaded via the `upload_read_set` method. The `fileobjs` parameter can be either the name of a local file, or a `TextIO` or `BinaryIO` object that supports read methods. For paired end reads, you can define `fileobjs` as a list of files. @@ -84,7 +115,7 @@ read_set_id = manager.upload_read_set( ) ``` -### Subscribe to events +#### Subscribe to events Transfer events: `on_queued`, `on_progress`, and `on_done` can be observed by defining a subclass of `OmicsTransferSubscriber` and passing in an object which can receive events. ```python @@ -99,7 +130,7 @@ class ProgressReporter(OmicsTransferSubscriber): manager.download_read_set(SEQUENCE_STORE_ID, "", subscribers=[ProgressReporter()]) ``` -### Threads +#### Threads Transfer operations use threads to implement concurrency. Thread use can be disabled by setting the `use_threads` attribute to False. If thread use is disabled, transfer concurrency does not occur. Accordingly, the value of the `max_request_concurrency` attribute is ignored. @@ -111,33 +142,37 @@ manager = TransferManager(client, config) manager.download_read_set(SEQUENCE_STORE_ID, "") ``` -## Using the Omics URI Parser -### Basic Usage +### Omics URI Parser + The `OmicsUriParser` class makes it easy to parse omics readset and reference URIs to extract fields relevant for calling AWS omics APIs. #### Readset file URI: Readset file URIs come in the following format: -``` + +```text omics://.storage..amazonaws.com//readSet// ``` + For example: -``` +```text omics://123412341234.storage.us-east-1.amazonaws.com/5432154321/readSet/5346184667/source1 omics://123412341234.storage.us-east-1.amazonaws.com/5432154321/readSet/5346184667/source2 ``` #### Reference file URI: Reference file URIs come in the following format: -``` +```text omics://.storage..amazonaws.com//reference//source ``` For example: -``` +```text omics://123412341234.storage.us-east-1.amazonaws.com/5432154321/reference/5346184667/source ``` +To handle both Omics URI types, you would use code like the following: + ```python import boto3 from omics.uriparse.uri_parse import OmicsUriParser, OmicsUri @@ -169,14 +204,32 @@ manager.download_read_set_file( ) ``` -## Using the Omics Rerun tool -### Basic Usage +## CLI Tools +CLI tools are modules in this package that can be invoked from the command line with: + +```bash +python -m omics.cli. +``` + +### Omics Rerun + The `omics-rerun` tool makes it easy to start a new run execution from a CloudWatch Logs manifest. +For an overview of what it does and available options run: + +```bash +python -m omics.cli.rerun -h +``` + #### List runs from manifest The following example lists all workflow run ids which were completed on July 1st (UTC time): -```txt -> omics-rerun -s 2023-07-01T00:00:00 -e 2023-07-02T00:00:00 +```bash +python -m omics.cli.rerun -s 2023-07-01T00:00:00 -e 2023-07-02T00:00:00 +``` + +this returns something like: + +```text 1234567 (2023-07-01T12:00:00.000) 2345678 (2023-07-01T13:00:00.000) ``` @@ -184,8 +237,13 @@ The following example lists all workflow run ids which were completed on July 1s #### Rerun a previously-executed run To rerun a previously-executed run, specify the run id you would like to rerun: -```txt -> omics-rerun 1234567 +```bash +python -m omics.cli.rerun 1234567 +``` + +this returns something like: + +```text StartRun request: { "workflowId": "4974161", @@ -207,8 +265,14 @@ StartRun response: ``` It is possible to override a request parameter from the original run. The following example tags the new run, which is particularly useful as tags are not propagated from the original run. -```txt -> omics-rerun 1234567 --tag=myKey=myValue + +```bash +python -m omics.cli.rerun 1234567 --tag=myKey=myValue + +``` + +this returns something like: +```text StartRun request: { "workflowId": "4974161", @@ -235,8 +299,12 @@ StartRun response: ``` Before submitting a rerun request, it is possible to dry-run to view the new StartRun request: -```txt -> omics-rerun -d 1234567 +```bash +python -m omics.cli.rerun -d 1234567 +``` + +this returns something like: +```text StartRun request: { "workflowId": "4974161", @@ -250,22 +318,37 @@ StartRun request: } ``` -## Using the Omics Run Analyzer tool -### Basic Usage +### Omics Run Analyzer The `omics-run-analyzer` tool retrieves a workflow run manifest from CloudWatchLogs and generates statistics for the run, including CPU and memory utilization for each workflow task. +For an overview of what it does and available options run: + +```bash +python -m omics.cli.run_analyzer -h +``` + #### List completed runs The following example lists all workflow runs completed in the past 5 days: -```txt -> omics-run-analyzer -t5d +```bash +python -m omics.cli.run_analyzer -t5d +``` + +this returns something like: + +```text Workflow run IDs ( ): 1234567 (2024-02-01T12:00:00 12345678-1234-5678-9abc-123456789012) 2345678 (2024-02-03T13:00:00 12345678-1234-5678-9abc-123456789012) ``` #### Analyze a specific workflow run -```txt -> omics-run-analyzer 1234567 -o run-1234567.csv +```bash +python -m omics.cli.run_analyzer 1234567 -o run-1234567.csv +``` + +this returns something like: + +```text omics-run-analyzer: wrote run-1234567.csv ``` @@ -296,8 +379,13 @@ The CSV output by the command above includes the following columns: * __storageAverageGiB__ : Average gibibytes of storage used by the workflow run #### Output workflow run manifest in JSON format -```txt -> omics-run-analyzer 1234567 -s -o run-1234567.json + +```bash +python -m omics.cli.run_analyzer 1234567 -s -o run-1234567.json +``` + +this returns something like: +```text omics-run-analyzer: wrote run-1234567.json ``` diff --git a/omics/cli/__init__.py b/omics/cli/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/omics/cli/rerun/__init__.py b/omics/cli/rerun/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/omics/rerun/omics-rerun b/omics/cli/rerun/__main__.py similarity index 92% rename from omics/rerun/omics-rerun rename to omics/cli/rerun/__main__.py index a198642..bd9bc70 100755 --- a/omics/rerun/omics-rerun +++ b/omics/cli/rerun/__main__.py @@ -77,8 +77,9 @@ def stream_to_run(strm): m = re.match(r"^manifest/run/(\d+)/[a-f0-9-]+$", strm["logStreamName"]) if not m: return None - creation_time = datetime.datetime.fromtimestamp( - strm["creationTime"] / 1000.0).isoformat(timespec="milliseconds") + creation_time = datetime.datetime.fromtimestamp(strm["creationTime"] / 1000.0).isoformat( + timespec="milliseconds" + ) return { "id": m.group(1), "creationTime": creation_time, @@ -88,10 +89,12 @@ def stream_to_run(strm): def get_streams(logs, rqst, opts={}): """Get matching CloudWatch Log streams""" - start_time = dateutil.parser.parse( - opts["--start"]).timestamp() * 1000.0 if opts.get("--start") else None - end_time = dateutil.parser.parse( - opts["--end"]).timestamp() * 1000.0 if opts.get("--end") else None + start_time = ( + dateutil.parser.parse(opts["--start"]).timestamp() * 1000.0 if opts.get("--start") else None + ) + end_time = ( + dateutil.parser.parse(opts["--end"]).timestamp() * 1000.0 if opts.get("--end") else None + ) streams = [] while True: try: @@ -132,7 +135,7 @@ def get_runs(logs, runs, opts): # Get runs in time range rqst = { "logGroupName": "/aws/omics/WorkflowLog", - "logStreamNamePrefix": f"manifest/run/", + "logStreamNamePrefix": "manifest/run/", } streams.extend(get_streams(logs, rqst, opts)) runs = [stream_to_run(s) for s in streams] @@ -163,6 +166,7 @@ def get_run_resources(logs, run): def start_run_request(run, opts={}): """Build StartRun request""" + def set_param(rqst, key, key0, val=None): if not val and opts and key0: val = opts[key0] @@ -240,8 +244,7 @@ def set_param(rqst, key, key0, val=None): out.write(f"{r['id']} ({r['creationTime']})\n") else: resources = get_run_resources(logs, runs[0]) - run = [r for r in resources if r["arn"].endswith( - f"run/{runs[0]['id']}")] + run = [r for r in resources if r["arn"].endswith(f"run/{runs[0]['id']}")] run = run[0] if run else None if not resources: die("no workflow run resources") @@ -254,8 +257,7 @@ def set_param(rqst, key, key0, val=None): rqst0 = start_run_request(run) rqst = start_run_request(run, opts) if rqst != rqst0: - out.write( - f"Original request:\n{json.dumps(rqst0, indent=2)}\n") + out.write(f"Original request:\n{json.dumps(rqst0, indent=2)}\n") out.write(f"StartRun request:\n{json.dumps(rqst, indent=2)}\n") if not opts["--dry-run"]: try: @@ -263,11 +265,9 @@ def set_param(rqst, key, key0, val=None): resp = omics.start_run(**rqst) except Exception as e: die(f"StartRun failed: {e}") - del resp["ResponseMetadata"] - out.write( - f"StartRun response:\n{json.dumps(resp, indent=2)}\n") + del resp["ResponseMetadata"] # type: ignore + out.write(f"StartRun response:\n{json.dumps(resp, indent=2)}\n") if opts["--out"]: out.close() sys.stderr.write(f"{exename}: wrote {opts['--out']}\n") - diff --git a/omics/cli/run_analyzer/__init__.py b/omics/cli/run_analyzer/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/omics/analyzer/omics-run-analyzer b/omics/cli/run_analyzer/__main__.py similarity index 98% rename from omics/analyzer/omics-run-analyzer rename to omics/cli/run_analyzer/__main__.py index 8641390..e1ec533 100755 --- a/omics/analyzer/omics-run-analyzer +++ b/omics/cli/run_analyzer/__main__.py @@ -49,10 +49,11 @@ OMICS_SERVICE_CODE = "AmazonOmics" PRICING_AWS_REGION = "us-east-1" # Pricing service endpoint SECS_PER_HOUR = 3600.0 -STORAGE_TYPE_DYNAMIC_RUN_STORAGE="DYNAMIC" -STORAGE_TYPE_STATIC_RUN_STORAGE="STATIC" -PRICE_RESOURCE_TYPE_DYNAMIC_RUN_STORAGE="Dynamic Run Storage" -PRICE_RESOURCE_TYPE_STATIC_RUN_STORAGE="Run Storage" +STORAGE_TYPE_DYNAMIC_RUN_STORAGE = "DYNAMIC" +STORAGE_TYPE_STATIC_RUN_STORAGE = "STATIC" +PRICE_RESOURCE_TYPE_DYNAMIC_RUN_STORAGE = "Dynamic Run Storage" +PRICE_RESOURCE_TYPE_STATIC_RUN_STORAGE = "Run Storage" + def die(msg): """Show error message and terminate""" @@ -323,7 +324,7 @@ def add_metrics(res, resources, pricing): storage_type = res.get("storageType") if rtype == "run": - # Get capacity requested (static), capacity max. used (dynamic) and + # Get capacity requested (static), capacity max. used (dynamic) and # charged storage (the requested capacity for static or average used for dynamic) if storage_type == STORAGE_TYPE_STATIC_RUN_STORAGE: price_resource_type = PRICE_RESOURCE_TYPE_STATIC_RUN_STORAGE @@ -340,7 +341,7 @@ def add_metrics(res, resources, pricing): price = get_pricing(pricing, price_resource_type, region, gib_hrs) if price: metrics["estimatedUSD"] = price - + # Get price for optimal static storage if store_max: capacity = get_static_storage_gib(store_max) diff --git a/poetry.lock b/poetry.lock index cd443c0..39b2c90 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,4 +1,4 @@ -# This file is automatically @generated by Poetry 1.8.2 and should not be changed by hand. +# This file is automatically @generated by Poetry 1.8.3 and should not be changed by hand. 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+[package.dependencies] +urllib3 = ">=2" + [[package]] name = "types-s3transfer" version = "0.6.2" @@ -1156,13 +1598,13 @@ types-docutils = "*" [[package]] name = "typing-extensions" -version = "4.11.0" +version = "4.12.2" description = "Backported and Experimental Type Hints for Python 3.8+" optional = false python-versions = ">=3.8" files = [ - {file = "typing_extensions-4.11.0-py3-none-any.whl", hash = "sha256:c1f94d72897edaf4ce775bb7558d5b79d8126906a14ea5ed1635921406c0387a"}, - {file = "typing_extensions-4.11.0.tar.gz", hash = "sha256:83f085bd5ca59c80295fc2a82ab5dac679cbe02b9f33f7d83af68e241bea51b0"}, + {file = "typing_extensions-4.12.2-py3-none-any.whl", hash = "sha256:04e5ca0351e0f3f85c6853954072df659d0d13fac324d0072316b67d7794700d"}, + {file = "typing_extensions-4.12.2.tar.gz", hash = "sha256:1a7ead55c7e559dd4dee8856e3a88b41225abfe1ce8df57b7c13915fe121ffb8"}, ] [[package]] @@ -1196,4 +1638,4 @@ files = [ [metadata] lock-version = "2.0" python-versions = "^3.10" -content-hash = "c6da20e97c3cd526b90904ead5ad2811f9b7c2056735db19e22877c16cea8f84" +content-hash = "2dce2a7363341ea79c4fa9e52a1875e6266af2a6c188305da9769ccca3e8a67b" diff --git a/pyproject.toml b/pyproject.toml index f04e03d..8ed4b2f 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -6,7 +6,7 @@ build-backend = "poetry.core.masonry.api" name = "amazon-omics-tools" version = "0.3.0" license = "Apache-2.0" -description = "Tools for working with the Amazon Omics Service" +description = "Tools for working with the AWS HealthOmics Service" repository = "https://github.com/awslabs/amazon-omics-tools" authors = ["Amazon Web Services"] readme = "README.md" @@ -17,6 +17,7 @@ python = "^3.10" s3transfer = "^0.7.0" boto3 = "^1.28.83" mypy-boto3-omics = "^1.28.83" +boto3-stubs = "^1.34.124" botocore-stubs = "^1.31.83" docopt = "^0.6.2" python-dateutil = "^2.8.2" @@ -24,7 +25,7 @@ python-dateutil = "^2.8.2" [tool.poetry.group.dev.dependencies] black = ">=22.8,<25.0" pytest = "^7.1.3" -mypy = "^0.971" +mypy = "^0.981" flake8 = "^5.0.4" flake8-docstrings = "^1.6.0" isort = "^5.10.1" @@ -32,6 +33,9 @@ pytest-cov = "^4.0.0" pytest-rerunfailures = "^10.2" types-s3transfer = "^0.6.0.post4" types-setuptools = "^65.4.0.0" +types-requests = "^2.32.0.20240602" +types-python-dateutil = "^2.9.0.20240316" +types-docopt = "^0.6.11.4" pip-audit = "^2.7.2" idna = "3.7" diff --git a/setup.cfg b/setup.cfg index bf5edbc..02a0095 100644 --- a/setup.cfg +++ b/setup.cfg @@ -2,11 +2,14 @@ ignore = E501, # E501 is line length. Let Black deal with this (sometimes it can't split lines). E203, # whitespace before ‘:’ (https://black.readthedocs.io/en/stable/compatible_configs.html#flake8) D100,D104, # don't require module or package-level docstrings + D400, # ignore first line punctuation per-file-ignores = # don't require docstrings in tests tests/*:D101,D102,D103,D107 # public type aliases are used but flake8 doesn't know it omics_tools/data_transfer/__init__.py:F401 + # ignore docstring here + omics/cli/run_analyzer/__main__.py:D103 [mypy] # Re-enable 'attr-defined' and 'arg-type' after refactoring the way call_args are passed in