Mercurial > repos > shellac > sam_consensus_v3
annotate env/lib/python3.9/site-packages/cwltool/tests/test_subgraph.py @ 0:4f3585e2f14b draft default tip
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
author | shellac |
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date | Mon, 22 Mar 2021 18:12:50 +0000 |
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1 import json |
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2 from pathlib import Path |
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3 from typing import Any |
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4 |
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5 from schema_salad.utils import convert_to_dict |
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6 |
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7 from cwltool.context import LoadingContext |
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8 from cwltool.load_tool import load_tool |
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9 from cwltool.subgraph import get_step, get_subgraph |
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10 from cwltool.workflow import Workflow, default_make_tool |
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11 |
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12 from .test_fetch import norm |
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13 from .util import get_data |
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14 |
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15 |
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16 def test_get_subgraph() -> None: |
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17 loadingContext = LoadingContext({"construct_tool_object": default_make_tool}) |
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18 wf = norm(Path(get_data("tests/subgraph/count-lines1-wf.cwl")).as_uri()) |
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19 loadingContext.do_update = False |
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20 tool = load_tool(wf, loadingContext) |
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21 |
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22 sg = norm(Path(get_data("tests/subgraph")).as_uri()) |
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23 |
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24 def clean(val: Any) -> Any: |
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25 if isinstance(val, str): |
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26 if val.startswith(sg): |
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27 return val[len(sg) + 1 :] |
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28 if isinstance(val, dict): |
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29 return {k: clean(v) for k, v in val.items()} |
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30 if isinstance(val, list): |
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31 return [clean(v) for v in val] |
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32 return val |
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33 |
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34 for a in ( |
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35 "file1", |
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36 "file2", |
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37 "file3", |
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38 "count_output", |
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39 "output3", |
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40 "output4", |
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41 "output5", |
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42 "step1", |
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43 "step2", |
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44 "step3", |
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45 "step4", |
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46 "step5", |
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47 ): |
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48 assert isinstance(tool, Workflow) |
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49 extracted = get_subgraph([wf + "#" + a], tool) |
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50 with open(get_data("tests/subgraph/extract_" + a + ".json")) as f: |
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51 assert json.load(f) == clean(convert_to_dict(extracted)) |
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52 |
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53 |
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54 def test_get_step() -> None: |
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55 loadingContext = LoadingContext({"construct_tool_object": default_make_tool}) |
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56 wf = norm(Path(get_data("tests/subgraph/count-lines1-wf.cwl")).as_uri()) |
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57 loadingContext.do_update = False |
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58 tool = load_tool(wf, loadingContext) |
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59 assert isinstance(tool, Workflow) |
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60 |
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61 sg = norm(Path(get_data("tests/subgraph")).as_uri()) |
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62 |
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63 def clean(val: Any) -> Any: |
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64 if isinstance(val, str): |
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65 if val.startswith(sg): |
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66 return val[len(sg) + 1 :] |
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67 if isinstance(val, dict): |
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68 return {k: clean(v) for k, v in val.items()} |
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69 if isinstance(val, list): |
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70 return [clean(v) for v in val] |
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71 return val |
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72 |
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73 for a in ( |
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74 "step1", |
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75 "step2", |
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76 "step3", |
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77 "step4", |
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78 "step5", |
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79 ): |
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80 extracted = get_step(tool, wf + "#" + a) |
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81 with open(get_data("tests/subgraph/single_" + a + ".json")) as f: |
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82 assert json.load(f) == clean(convert_to_dict(extracted)) |