diff --git a/src/runcrate/cli.py b/src/runcrate/cli.py index 5567a2f..e8010d2 100644 --- a/src/runcrate/cli.py +++ b/src/runcrate/cli.py @@ -20,6 +20,7 @@ from . import __version__ from .convert import ProvCrateBuilder from .report import dump_crate_actions +from .run import run_crate @click.group() @@ -86,6 +87,28 @@ def report(crate): dump_crate_actions(crate) +@cli.command() +@click.argument( + "crate", + metavar="RO_CRATE", + type=click.Path(exists=True, readable=True, path_type=Path), +) +@click.option("--executable", help="workflow runner executable") +@click.option("--keep-wd", help="keep working directory", is_flag=True) +@click.option( + "--dry-run", + help="do not actually run the workflow (implies --keep-wd)", + is_flag=True +) +def run(crate, executable, keep_wd, dry_run): + """\ + Run the workflow from a Workflow Run RO-Crate. + + RO_CRATE: RO-Crate directory or zip file. + """ + run_crate(crate, executable=executable, keep_wd=keep_wd, dry_run=dry_run) + + @cli.command() def version(): """\ diff --git a/src/runcrate/run.py b/src/runcrate/run.py new file mode 100644 index 0000000..7c6ad13 --- /dev/null +++ b/src/runcrate/run.py @@ -0,0 +1,207 @@ +# Copyright 2023 CRS4. +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. + +"""\ +Run the workflow from a Workflow Run RO-Crate. + +Only CWL is supported for now. +""" + +import json +import shutil +import subprocess +import sys +import tempfile +from pathlib import Path + +from rocrate.rocrate import ROCrate + +from .utils import as_list + + +CWL_ID = "https://w3id.org/workflowhub/workflow-ro-crate#cwl" +PARAMS_FILENAME = "params.json" +EXECUTABLE = "cwl-runner" +STREAMFLOW_FILE = "streamflow.yml" + + +def check_runnable(crate): + wf = crate.mainEntity + if not wf: + raise RuntimeError("crate does not have a mainEntity") + if "ComputationalWorkflow" not in as_list(wf.type): + raise RuntimeError("mainEntity is not a ComputationalWorkflow") + lang = wf.get("programmingLanguage") + if not lang or getattr(lang, "id", None) != CWL_ID: + raise RuntimeError(f"workflow language must be {CWL_ID}") + actions = [_ for _ in crate.get_entities() + if "CreateAction" in as_list(_.type) and _.get("instrument") is wf] + if not actions: + raise RuntimeError(f"no CreateAction associated to {wf.id}") + return wf, actions[0] + + +def auto_convert(value): + if not isinstance(value, str): # should not happen + return value + if value.lower() in {"true", "false"}: + return value.lower() == "true" + try: + return int(value) + except ValueError: + try: + return float(value) + except ValueError: + return value + + +def convert_file(fp, obj): + retval = {"class": "File"} + alt_name = obj.get("alternateName") + retval["location"] = alt_name or obj.id + format_ = fp.get("encodingFormat", obj.get("encodingFormat")) + if format_: + retval["format"] = format_ + return retval + + +def convert_dataset(fp, obj): + retval = {"class": "Directory"} + alt_name = obj.get("alternateName") + retval["location"] = alt_name or obj.id + return retval + + +def convert_value(fp, value): + if fp is None: + return auto_convert(value) + type_ = fp.get("additionalType") + if type_ == "PropertyValue": + return {_["name"]: convert_value(None, _["value"]) for _ in as_list(value)} + if isinstance(value, list): + return [convert_value(fp, _) for _ in value] + if not type_ or isinstance(type_, list) or type_ == "DataType": + return auto_convert(value) + if type_ == "Text": + return value + if type_ == "Integer": + return int(value) + if type_ == "Float": + return float(value) + if type_ == "Boolean": + return value.lower() == "true" + + +def convert_obj(fp, obj): + if "Collection" in as_list(obj.type): + main_entity = obj.get("mainEntity") + if not main_entity: + parts = obj.get("hasPart") + if not parts: + raise ValueError(f"collection {obj.id} has no parts") + main_entity = parts[0] + if "File" in as_list(main_entity.type): + return convert_file(fp, main_entity) + if "Dataset" in as_list(main_entity.type): + return convert_dataset(fp, main_entity) + raise ValueError(f"{main_entity.id} should be a File or Dataset") + elif "File" in as_list(obj.type): + return convert_file(fp, obj) + elif "Dataset" in as_list(obj.type): + return convert_dataset(fp, obj) + elif "PropertyValue" not in as_list(obj.type): + raise RuntimeError(f"object {obj.id} should be a File, Dataset, Collection or PropertyValue") + value = obj.get("value") + if not value: + raise RuntimeError(f"object {obj.id} has no value") + return convert_value(fp, value) + + +def gen_params(wf, action): + params = {} + wf_inputs = set(wf.get("input", [])) + for obj in action.get("object", []): + sel = [_ for _ in as_list(obj.get("exampleOfWork")) if _ in wf_inputs] + if not sel: + continue + fp = sel[0] # there should be only one of these + name = fp.get("name", obj.get("name")) + if not name: + continue + params[name] = convert_obj(fp, obj) + return params + + +def rename_data_entities(obj, workdir): + if "Collection" in as_list(obj.type): + parts = set(as_list(obj.get("hasPart", []))) + main_entity = obj.get("mainEntity") + if main_entity: + parts.add(main_entity) # should already be in parts + for p in parts: + rename_data_entities(p, workdir) + alt_name = obj.get("alternateName") + if alt_name: + dst_path = workdir / alt_name + if "Dataset" in as_list(obj.type): + (dst_path).mkdir(parents=True, exist_ok=True) + for p in set(as_list(obj.get("hasPart", []))): + rename_data_entities(p, workdir) + if "File" in as_list(obj.type): + (dst_path.parent).mkdir(parents=True, exist_ok=True) + src_path = workdir / obj.id + shutil.copy(src_path, dst_path) + + +def find_streamflow_file(crate): + for e in crate.get_entities(): + if "File" not in as_list(e.type): + continue + candidates = e.id, e.get("alternateName", "") + for c in candidates: + if c.lower().rsplit("/", 1)[-1] == STREAMFLOW_FILE: + return e.id + + +def run_crate(crate, executable=None, keep_wd=False, dry_run=False): + if executable is None: + executable = EXECUTABLE + if not isinstance(crate, ROCrate): + crate = ROCrate(crate) + wf, action = check_runnable(crate) + sys.stdout.write(f"workflow: {wf.id}; action: {action.id}\n") + workdir = Path(tempfile.mkdtemp(prefix="runcrate_")) + sys.stdout.write(f"working dir: {workdir}\n") + params = gen_params(wf, action) + crate.write(workdir) + params_path = Path(workdir / PARAMS_FILENAME) + with open(params_path, "w") as f: + json.dump(params, f, indent=4) + for obj in action.get("object", []): + rename_data_entities(obj, workdir) + if dry_run: + return + wf_path = workdir / wf.id + streamflow_relpath = find_streamflow_file(crate) + if streamflow_relpath: + streamflow_file = workdir / streamflow_relpath + args = [executable, "--streamflow-file", streamflow_file, wf_path, params_path] + else: + args = [executable, wf_path, params_path] + sys.stdout.write(f"running {args}\n") + try: + subprocess.check_call(args) + finally: + if not keep_wd: + shutil.rmtree(workdir) diff --git a/tests/data/revsort-provenance-crate-minimal/ro-crate-metadata.json b/tests/data/revsort-provenance-crate-minimal/ro-crate-metadata.json index 8f45fbb..05f4b7b 100644 --- a/tests/data/revsort-provenance-crate-minimal/ro-crate-metadata.json +++ b/tests/data/revsort-provenance-crate-minimal/ro-crate-metadata.json @@ -1,10 +1,33 @@ { - "@context": "https://w3id.org/ro/crate/1.1/context", + "@context": [ + "https://w3id.org/ro/crate/1.1/context", + { + "ParameterConnection": "https://w3id.org/ro/terms/workflow-run#ParameterConnection", + "connection": "https://w3id.org/ro/terms/workflow-run#connection", + "sha1": "https://w3id.org/ro/terms/workflow-run#sha1", + "sourceParameter": "https://w3id.org/ro/terms/workflow-run#sourceParameter", + "targetParameter": "https://w3id.org/ro/terms/workflow-run#targetParameter" + } + ], "@graph": [ { "@id": "./", "@type": "Dataset", - "datePublished": "2022-10-07T10:01:24+00:00", + "conformsTo": [ + { + "@id": "https://w3id.org/ro/wfrun/process/0.1" + }, + { + "@id": "https://w3id.org/ro/wfrun/workflow/0.1" + }, + { + "@id": "https://w3id.org/ro/wfrun/provenance/0.1" + }, + { + "@id": "https://w3id.org/workflowhub/workflow-ro-crate/1.0" + } + ], + "datePublished": "2023-03-23T14:39:57+00:00", "hasPart": [ { "@id": "packed.cwl" @@ -19,12 +42,13 @@ "@id": "97fe1b50b4582cebc7d853796ebd62e3e163aa3f" } ], + "license": "Apache-2.0", "mainEntity": { "@id": "packed.cwl" }, "mentions": [ { - "@id": "#7aeba0c9-78f6-4fb7-85d9-fcbe18fce057" + "@id": "#654421a2-66b7-47c0-889a-4047fd22aace" } ] }, @@ -43,13 +67,36 @@ } ] }, + { + "@id": "https://w3id.org/ro/wfrun/process/0.1", + "@type": "CreativeWork", + "name": "Process Run Crate", + "version": "0.1" + }, + { + "@id": "https://w3id.org/ro/wfrun/workflow/0.1", + "@type": "CreativeWork", + "name": "Workflow Run Crate", + "version": "0.1" + }, + { + "@id": "https://w3id.org/ro/wfrun/provenance/0.1", + "@type": "CreativeWork", + "name": "Provenance Run Crate", + "version": "0.1" + }, + { + "@id": "https://w3id.org/workflowhub/workflow-ro-crate/1.0", + "@type": "CreativeWork", + "name": "Workflow RO-Crate", + "version": "1.0" + }, { "@id": "packed.cwl", "@type": [ "File", "SoftwareSourceCode", - "ComputationalWorkflow", - "HowTo" + "ComputationalWorkflow" ], "hasPart": [ { @@ -94,28 +141,22 @@ "@id": "packed.cwl#main/input", "@type": "FormalParameter", "additionalType": "File", - "connectedTo": { - "@id": "packed.cwl#revtool.cwl/input" - }, "defaultValue": "file:///home/stain/src/cwltool/tests/wf/hello.txt", "encodingFormat": "https://www.iana.org/assignments/media-types/text/plain", - "name": "main/input" + "name": "input" }, { "@id": "packed.cwl#main/reverse_sort", "@type": "FormalParameter", "additionalType": "Boolean", - "connectedTo": { - "@id": "packed.cwl#sorttool.cwl/reverse" - }, "defaultValue": "True", - "name": "main/reverse_sort" + "name": "reverse_sort" }, { "@id": "packed.cwl#main/output", "@type": "FormalParameter", "additionalType": "File", - "name": "main/output" + "name": "output" }, { "@id": "packed.cwl#revtool.cwl", @@ -137,16 +178,13 @@ "@id": "packed.cwl#revtool.cwl/input", "@type": "FormalParameter", "additionalType": "File", - "name": "revtool.cwl/input" + "name": "input" }, { "@id": "packed.cwl#revtool.cwl/output", "@type": "FormalParameter", "additionalType": "File", - "connectedTo": { - "@id": "packed.cwl#sorttool.cwl/input" - }, - "name": "revtool.cwl/output" + "name": "output" }, { "@id": "packed.cwl#sorttool.cwl", @@ -171,25 +209,22 @@ "@id": "packed.cwl#sorttool.cwl/reverse", "@type": "FormalParameter", "additionalType": "Boolean", - "name": "sorttool.cwl/reverse" + "name": "reverse" }, { "@id": "packed.cwl#sorttool.cwl/input", "@type": "FormalParameter", "additionalType": "File", - "name": "sorttool.cwl/input" + "name": "input" }, { "@id": "packed.cwl#sorttool.cwl/output", "@type": "FormalParameter", "additionalType": "File", - "connectedTo": { - "@id": "packed.cwl#main/output" - }, - "name": "sorttool.cwl/output" + "name": "output" }, { - "@id": "#7aeba0c9-78f6-4fb7-85d9-fcbe18fce057", + "@id": "#654421a2-66b7-47c0-889a-4047fd22aace", "@type": "CreateAction", "endTime": "2018-10-25T15:46:43.020168", "instrument": { @@ -214,6 +249,7 @@ { "@id": "327fc7aedf4f6b69a42a7c8b808dc5a7aff61376", "@type": "File", + "alternateName": "whale.txt", "exampleOfWork": [ { "@id": "packed.cwl#main/input" @@ -221,7 +257,8 @@ { "@id": "packed.cwl#revtool.cwl/input" } - ] + ], + "sha1": "327fc7aedf4f6b69a42a7c8b808dc5a7aff61376" }, { "@id": "#pv-main/reverse_sort", @@ -229,12 +266,13 @@ "exampleOfWork": { "@id": "packed.cwl#main/reverse_sort" }, - "name": "main/reverse_sort", + "name": "reverse_sort", "value": "True" }, { "@id": "b9214658cc453331b62c2282b772a5c063dbd284", "@type": "File", + "alternateName": "output.txt", "exampleOfWork": [ { "@id": "packed.cwl#main/output" @@ -242,10 +280,11 @@ { "@id": "packed.cwl#sorttool.cwl/output" } - ] + ], + "sha1": "b9214658cc453331b62c2282b772a5c063dbd284" }, { - "@id": "#a439c61f-2378-49fb-a7e5-7258248daaeb", + "@id": "#1b0a99b0-bff6-486f-b9d9-50e89f9f8cc0", "@type": "CreateAction", "endTime": "2018-10-25T15:46:36.967359", "instrument": { @@ -267,6 +306,7 @@ { "@id": "97fe1b50b4582cebc7d853796ebd62e3e163aa3f", "@type": "File", + "alternateName": "output.txt", "exampleOfWork": [ { "@id": "packed.cwl#revtool.cwl/output" @@ -274,10 +314,11 @@ { "@id": "packed.cwl#sorttool.cwl/input" } - ] + ], + "sha1": "97fe1b50b4582cebc7d853796ebd62e3e163aa3f" }, { - "@id": "#4377b674-1c08-4afe-b3a6-df827c03b1c4", + "@id": "#4d406f10-e4a8-4767-8b91-fc0631825b3a", "@type": "CreateAction", "endTime": "2018-10-25T15:46:38.069110", "instrument": { @@ -305,7 +346,7 @@ "exampleOfWork": { "@id": "packed.cwl#sorttool.cwl/reverse" }, - "name": "main/sorted/reverse", + "name": "reverse", "value": "True" } ] diff --git a/tests/data/type-zoo-run-1-crate/4bd8e7e358488e833bf32cf5028695292cecb05b b/tests/data/type-zoo-run-1-crate/4bd8e7e358488e833bf32cf5028695292cecb05b new file mode 100644 index 0000000..4be05b7 --- /dev/null +++ b/tests/data/type-zoo-run-1-crate/4bd8e7e358488e833bf32cf5028695292cecb05b @@ -0,0 +1 @@ +--in-any tar --in-bool --in-double 3.142 --in-enum B --in-float 3.14 --in-int 42 --in-long 420 --in-multi 9.99 --in-record-A Tom --in-record-B Jerry --in-str spam foo bar diff --git a/tests/data/type-zoo-run-1-crate/index.html b/tests/data/type-zoo-run-1-crate/index.html new file mode 120000 index 0000000..a33a179 --- /dev/null +++ b/tests/data/type-zoo-run-1-crate/index.html @@ -0,0 +1 @@ +ro-crate-preview.html \ No newline at end of file diff --git a/tests/data/type-zoo-run-1-crate/packed.cwl b/tests/data/type-zoo-run-1-crate/packed.cwl new file mode 100644 index 0000000..2536d64 --- /dev/null +++ b/tests/data/type-zoo-run-1-crate/packed.cwl @@ -0,0 +1,125 @@ +{ + "class": "CommandLineTool", + "baseCommand": "echo", + "stdout": "output.txt", + "inputs": [ + { + "type": "Any", + "inputBinding": { + "prefix": "--in-any" + }, + "id": "#main/in_any" + }, + { + "type": { + "type": "array", + "items": "string" + }, + "inputBinding": { + "position": 1 + }, + "id": "#main/in_array" + }, + { + "type": "boolean", + "inputBinding": { + "prefix": "--in-bool" + }, + "id": "#main/in_bool" + }, + { + "type": "double", + "inputBinding": { + "prefix": "--in-double" + }, + "id": "#main/in_double" + }, + { + "type": { + "type": "enum", + "symbols": [ + "#main/in_enum/A", + "#main/in_enum/B" + ] + }, + "inputBinding": { + "prefix": "--in-enum" + }, + "id": "#main/in_enum" + }, + { + "type": "float", + "inputBinding": { + "prefix": "--in-float" + }, + "id": "#main/in_float" + }, + { + "type": "int", + "inputBinding": { + "prefix": "--in-int" + }, + "id": "#main/in_int" + }, + { + "type": "long", + "inputBinding": { + "prefix": "--in-long" + }, + "id": "#main/in_long" + }, + { + "type": [ + "int", + "float", + "null" + ], + "default": 9.99, + "inputBinding": { + "prefix": "--in-multi" + }, + "id": "#main/in_multi" + }, + { + "type": { + "type": "record", + "name": "#main/in_record/in_record", + "fields": [ + { + "type": "string", + "inputBinding": { + "prefix": "--in-record-A" + }, + "name": "#main/in_record/in_record/in_record_A" + }, + { + "type": "string", + "inputBinding": { + "prefix": "--in-record-B" + }, + "name": "#main/in_record/in_record/in_record_B" + } + ] + }, + "id": "#main/in_record" + }, + { + "type": "string", + "inputBinding": { + "prefix": "--in-str" + }, + "id": "#main/in_str" + } + ], + "id": "#main", + "outputs": [ + { + "type": "File", + "id": "#main/cl_dump", + "outputBinding": { + "glob": "output.txt" + } + } + ], + "cwlVersion": "v1.0" +} \ No newline at end of file diff --git a/tests/data/type-zoo-run-1-crate/ro-crate-metadata.json b/tests/data/type-zoo-run-1-crate/ro-crate-metadata.json new file mode 100644 index 0000000..70448b1 --- /dev/null +++ b/tests/data/type-zoo-run-1-crate/ro-crate-metadata.json @@ -0,0 +1,432 @@ +{ + "@context": [ + "https://w3id.org/ro/crate/1.1/context", + { + "ParameterConnection": "https://w3id.org/ro/terms/workflow-run#ParameterConnection", + "connection": "https://w3id.org/ro/terms/workflow-run#connection", + "sha1": "https://w3id.org/ro/terms/workflow-run#sha1", + "sourceParameter": "https://w3id.org/ro/terms/workflow-run#sourceParameter", + "targetParameter": "https://w3id.org/ro/terms/workflow-run#targetParameter" + } + ], + "@graph": [ + { + "@id": "./", + "@type": "Dataset", + "conformsTo": [ + { + "@id": "https://w3id.org/ro/wfrun/process/0.1" + }, + { + "@id": "https://w3id.org/ro/wfrun/workflow/0.1" + }, + { + "@id": "https://w3id.org/ro/wfrun/provenance/0.1" + }, + { + "@id": "https://w3id.org/workflowhub/workflow-ro-crate/1.0" + } + ], + "datePublished": "2023-03-24T07:53:37+00:00", + "hasPart": [ + { + "@id": "packed.cwl" + }, + { + "@id": "4bd8e7e358488e833bf32cf5028695292cecb05b" + } + ], + "license": "Apache-2.0", + "mainEntity": { + "@id": "packed.cwl" + }, + "mentions": [ + { + "@id": "#f4a43df6-8216-4b72-abf2-8beab8ca9894" + } + ] + }, + { + "@id": "ro-crate-metadata.json", + "@type": "CreativeWork", + "about": { + "@id": "./" + }, + "conformsTo": [ + { + "@id": "https://w3id.org/ro/crate/1.1" + }, + { + "@id": "https://w3id.org/workflowhub/workflow-ro-crate/1.0" + } + ] + }, + { + "@id": "https://w3id.org/ro/wfrun/process/0.1", + "@type": "CreativeWork", + "name": "Process Run Crate", + "version": "0.1" + }, + { + "@id": "https://w3id.org/ro/wfrun/workflow/0.1", + "@type": "CreativeWork", + "name": "Workflow Run Crate", + "version": "0.1" + }, + { + "@id": "https://w3id.org/ro/wfrun/provenance/0.1", + "@type": "CreativeWork", + "name": "Provenance Run Crate", + "version": "0.1" + }, + { + "@id": "https://w3id.org/workflowhub/workflow-ro-crate/1.0", + "@type": "CreativeWork", + "name": "Workflow RO-Crate", + "version": "1.0" + }, + { + "@id": "packed.cwl", + "@type": [ + "File", + "SoftwareSourceCode", + "ComputationalWorkflow", + "HowTo" + ], + "input": [ + { + "@id": "packed.cwl#main/in_any" + }, + { + "@id": "packed.cwl#main/in_array" + }, + { + "@id": "packed.cwl#main/in_bool" + }, + { + "@id": "packed.cwl#main/in_double" + }, + { + "@id": "packed.cwl#main/in_enum" + }, + { + "@id": "packed.cwl#main/in_float" + }, + { + "@id": "packed.cwl#main/in_int" + }, + { + "@id": "packed.cwl#main/in_long" + }, + { + "@id": "packed.cwl#main/in_multi" + }, + { + "@id": "packed.cwl#main/in_record" + }, + { + "@id": "packed.cwl#main/in_str" + } + ], + "name": "packed.cwl", + "output": [ + { + "@id": "packed.cwl#main/cl_dump" + } + ], + "programmingLanguage": { + "@id": "https://w3id.org/workflowhub/workflow-ro-crate#cwl" + } + }, + { + "@id": "https://w3id.org/workflowhub/workflow-ro-crate#cwl", + "@type": "ComputerLanguage", + "alternateName": "CWL", + "identifier": { + "@id": "https://w3id.org/cwl/v1.0/" + }, + "name": "Common Workflow Language", + "url": { + "@id": "https://www.commonwl.org/" + }, + "version": "v1.0" + }, + { + "@id": "packed.cwl#main/in_any", + "@type": "FormalParameter", + "additionalType": "DataType", + "name": "in_any" + }, + { + "@id": "packed.cwl#main/in_array", + "@type": "FormalParameter", + "additionalType": "Text", + "multipleValues": "True", + "name": "in_array" + }, + { + "@id": "packed.cwl#main/in_bool", + "@type": "FormalParameter", + "additionalType": "Boolean", + "name": "in_bool" + }, + { + "@id": "packed.cwl#main/in_double", + "@type": "FormalParameter", + "additionalType": "Float", + "name": "in_double" + }, + { + "@id": "packed.cwl#main/in_enum", + "@type": "FormalParameter", + "additionalType": "Text", + "name": "in_enum", + "valuePattern": "A|B" + }, + { + "@id": "packed.cwl#main/in_float", + "@type": "FormalParameter", + "additionalType": "Float", + "name": "in_float" + }, + { + "@id": "packed.cwl#main/in_int", + "@type": "FormalParameter", + "additionalType": "Integer", + "name": "in_int" + }, + { + "@id": "packed.cwl#main/in_long", + "@type": "FormalParameter", + "additionalType": "Integer", + "name": "in_long" + }, + { + "@id": "packed.cwl#main/in_multi", + "@type": "FormalParameter", + "additionalType": [ + "Float", + "Integer" + ], + "defaultValue": "9.99", + "name": "in_multi", + "valueRequired": "False" + }, + { + "@id": "packed.cwl#main/in_record", + "@type": "FormalParameter", + "additionalType": "PropertyValue", + "multipleValues": "True", + "name": "in_record" + }, + { + "@id": "packed.cwl#main/in_str", + "@type": "FormalParameter", + "additionalType": "Text", + "name": "in_str" + }, + { + "@id": "packed.cwl#main/cl_dump", + "@type": "FormalParameter", + "additionalType": "File", + "name": "cl_dump" + }, + { + "@id": "#011ba6cb-9622-4cec-bb95-da634b2ffc5e", + "@type": "SoftwareApplication", + "name": "cwltool 3.1.20220224085855" + }, + { + "@id": "#74481571-11f4-493c-8edf-3eb9bd5994e0", + "@type": "OrganizeAction", + "instrument": { + "@id": "#011ba6cb-9622-4cec-bb95-da634b2ffc5e" + }, + "name": "Run of cwltool 3.1.20220224085855", + "result": { + "@id": "#f4a43df6-8216-4b72-abf2-8beab8ca9894" + }, + "startTime": "2022-04-22T12:27:13.313333" + }, + { + "@id": "#f4a43df6-8216-4b72-abf2-8beab8ca9894", + "@type": "CreateAction", + "endTime": "2022-04-22T12:27:13.328912", + "instrument": { + "@id": "packed.cwl" + }, + "name": "Run of workflow/packed.cwl#main", + "object": [ + { + "@id": "#pv-main/in_array" + }, + { + "@id": "#pv-main/in_any" + }, + { + "@id": "#pv-main/in_str" + }, + { + "@id": "#pv-main/in_bool" + }, + { + "@id": "#pv-main/in_int" + }, + { + "@id": "#pv-main/in_long" + }, + { + "@id": "#pv-main/in_float" + }, + { + "@id": "#pv-main/in_double" + }, + { + "@id": "#pv-main/in_enum" + }, + { + "@id": "#pv-main/in_record" + }, + { + "@id": "#pv-main/in_multi" + } + ], + "result": [ + { + "@id": "4bd8e7e358488e833bf32cf5028695292cecb05b" + } + ], + "startTime": "2022-04-22T12:27:13.313422" + }, + { + "@id": "#pv-main/in_array", + "@type": "PropertyValue", + "exampleOfWork": { + "@id": "packed.cwl#main/in_array" + }, + "name": "in_array", + "value": [ + "foo", + "bar" + ] + }, + { + "@id": "#pv-main/in_any", + "@type": "PropertyValue", + "exampleOfWork": { + "@id": "packed.cwl#main/in_any" + }, + "name": "in_any", + "value": "tar" + }, + { + "@id": "#pv-main/in_str", + "@type": "PropertyValue", + "exampleOfWork": { + "@id": "packed.cwl#main/in_str" + }, + "name": "in_str", + "value": "spam" + }, + { + "@id": "#pv-main/in_bool", + "@type": "PropertyValue", + "exampleOfWork": { + "@id": "packed.cwl#main/in_bool" + }, + "name": "in_bool", + "value": "True" + }, + { + "@id": "#pv-main/in_int", + "@type": "PropertyValue", + "exampleOfWork": { + "@id": "packed.cwl#main/in_int" + }, + "name": "in_int", + "value": "42" + }, + { + "@id": "#pv-main/in_long", + "@type": "PropertyValue", + "exampleOfWork": { + "@id": "packed.cwl#main/in_long" + }, + "name": "in_long", + "value": "420" + }, + { + "@id": "#pv-main/in_float", + "@type": "PropertyValue", + "exampleOfWork": { + "@id": "packed.cwl#main/in_float" + }, + "name": "in_float", + "value": "3.14" + }, + { + "@id": "#pv-main/in_double", + "@type": "PropertyValue", + "exampleOfWork": { + "@id": "packed.cwl#main/in_double" + }, + "name": "in_double", + "value": "3.142" + }, + { + "@id": "#pv-main/in_enum", + "@type": "PropertyValue", + "exampleOfWork": { + "@id": "packed.cwl#main/in_enum" + }, + "name": "in_enum", + "value": "B" + }, + { + "@id": "#pv-main/in_record/in_record_B", + "@type": "PropertyValue", + "name": "in_record_B", + "value": "Jerry" + }, + { + "@id": "#pv-main/in_record/in_record_A", + "@type": "PropertyValue", + "name": "in_record_A", + "value": "Tom" + }, + { + "@id": "#pv-main/in_record", + "@type": "PropertyValue", + "exampleOfWork": { + "@id": "packed.cwl#main/in_record" + }, + "name": "in_record", + "value": [ + { + "@id": "#pv-main/in_record/in_record_B" + }, + { + "@id": "#pv-main/in_record/in_record_A" + } + ] + }, + { + "@id": "#pv-main/in_multi", + "@type": "PropertyValue", + "exampleOfWork": { + "@id": "packed.cwl#main/in_multi" + }, + "name": "in_multi", + "value": "9.99" + }, + { + "@id": "4bd8e7e358488e833bf32cf5028695292cecb05b", + "@type": "File", + "alternateName": "output.txt", + "exampleOfWork": { + "@id": "packed.cwl#main/cl_dump" + }, + "sha1": "4bd8e7e358488e833bf32cf5028695292cecb05b" + } + ] +} \ No newline at end of file diff --git a/tests/data/type-zoo-run-1-crate/ro-crate-preview.html b/tests/data/type-zoo-run-1-crate/ro-crate-preview.html new file mode 100644 index 0000000..22df055 --- /dev/null +++ b/tests/data/type-zoo-run-1-crate/ro-crate-preview.html @@ -0,0 +1,1175 @@ + + + + + + + + + + + + + + + + + + + + + + + + +
+
+

+

+ + +⬇️🏷️ Download all the metadata for in JSON-LD format + + +
+ + +
+ + + +
+
+
+

./

+ + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
@id./
@typeDataset
datePublished [?]2023-03-24T07:53:37+00:00
conformsTo [?]
hasPart [?]
license [?]Apache-2.0
mainEntity [?]packed.cwl
mentions [?]Run of workflow/packed.cwl#main
Items that reference this one
about [?]ro-crate-metadata.json
+
+ +
+


+
+

Go to: Process Run Crate

+ + + + +
+ + + + + + + + + + + + + + + + + + +
@idhttps://w3id.org/ro/wfrun/process/0.1
name [?]Process Run Crate
@typeCreativeWork
version [?]0.1
Items that reference this one
conformsTo [?]./
+
+ +
+


+
+

Go to: Workflow Run Crate

+ + + + +
+ + + + + + + + + + + + + + + + + + +
@idhttps://w3id.org/ro/wfrun/workflow/0.1
name [?]Workflow Run Crate
@typeCreativeWork
version [?]0.1
Items that reference this one
conformsTo [?]./
+
+ +
+


+
+

Go to: Provenance Run Crate

+ + + + +
+ + + + + + + + + + + + + + + + + + +
@idhttps://w3id.org/ro/wfrun/provenance/0.1
name [?]Provenance Run Crate
@typeCreativeWork
version [?]0.1
Items that reference this one
conformsTo [?]./
+
+ +
+


+
+

Go to: Workflow RO-Crate

+ + + + +
+ + + + + + + + + + + + + + + + + + +
@idhttps://w3id.org/workflowhub/workflow-ro-crate/1.0
name [?]Workflow RO-Crate
@typeCreativeWork
version [?]1.0
Items that reference this one
conformsTo [?]
+
+ +
+


+
+

⬇️ Download: packed.cwl

+ + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
@idpacked.cwl
name [?]packed.cwl
@type
    +
  • File
    • + +
  • SoftwareSourceCode
    • + +
  • ComputationalWorkflow
    • + +
  • HowTo
    • +
input [?]
output [?]cl_dump
programmingLanguage [?]Common Workflow Language
Items that reference this one
hasPart [?]./
mainEntity [?]./
instrument [?]Run of workflow/packed.cwl#main
+
+ +
+


+
+

⬇️ Download: 4bd8e7e358488e833bf32cf5028695292cecb05b

+ + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + +
@id4bd8e7e358488e833bf32cf5028695292cecb05b
@typeFile
alternateName [?]output.txt
exampleOfWork [?]cl_dump
sha1 [?]4bd8e7e358488e833bf32cf5028695292cecb05b
Items that reference this one
hasPart [?]./
result [?]Run of workflow/packed.cwl#main
+
+ +
+


+
+

Run of workflow/packed.cwl#main

+ + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
@id#f4a43df6-8216-4b72-abf2-8beab8ca9894
name [?]Run of workflow/packed.cwl#main
@typeCreateAction
endTime [?]2022-04-22T12:27:13.328912
instrument [?]packed.cwl
object [?]
    +
  • in_array: foo,bar
    • + +
  • in_any: tar
    • + +
  • in_str: spam
    • + +
  • in_bool: True
    • + +
  • in_int: 42
    • + +
  • in_long: 420
    • + +
  • in_float: 3.14
    • + +
  • in_double: 3.142
    • + +
  • in_enum: B
    • + +
  • in_record: [object Object],[object Object]
    • + +
  • in_multi: 9.99
    • +
result [?]4bd8e7e358488e833bf32cf5028695292cecb05b
startTime [?]2022-04-22T12:27:13.313422
Items that reference this one
mentions [?]./
result [?]Run of cwltool 3.1.20220224085855
+
+ +
+


+
+ + + + + + + diff --git a/tests/test_cli.py b/tests/test_cli.py index 6419b6b..0c59129 100644 --- a/tests/test_cli.py +++ b/tests/test_cli.py @@ -12,6 +12,8 @@ # See the License for the specific language governing permissions and # limitations under the License. +from pathlib import Path + from click.testing import CliRunner from rocrate.rocrate import ROCrate @@ -107,3 +109,16 @@ def test_cli_version(): result = runner.invoke(cli, ["version"]) assert result.exit_code == 0 assert result.stdout.strip() == __version__ + + +def test_cli_run(data_dir, tmpdir, monkeypatch): + crate_dir = data_dir / "type-zoo-run-1-crate" + runner = CliRunner() + args = ["run", str(crate_dir)] + monkeypatch.chdir(str(tmpdir)) + result = runner.invoke(cli, args) + assert result.exit_code == 0 + out_path = Path("output.txt") + assert out_path.is_file() + crate_out_path = crate_dir / "4bd8e7e358488e833bf32cf5028695292cecb05b" + assert out_path.read_text() == crate_out_path.read_text() diff --git a/tox.ini b/tox.ini index cfc2be2..7729758 100644 --- a/tox.ini +++ b/tox.ini @@ -11,6 +11,8 @@ skip_install = true deps = -r{toxinidir}/requirements.txt coverage + cwltool + cwlref-runner pytest pytest-cov hypothesis