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1 #!/usr/bin/env python3
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2
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3 import json
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4 import os.path
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5
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6 from result import Result
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7 from exceptions import CGECoreOutTypeError, CGECoreOutInputError
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8 from template import CGEOutTemplate
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9 from translate import Translate
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10
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11
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12 try:
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13 CGEOutTemplate("nonsense")
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14 except CGECoreOutTypeError:
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15 print("Caught expected template error.")
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16
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17 soft_dict = CGEOutTemplate("software_result")
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18 soft_dict["software_name"] = "ResFinder"
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19 soft_dict["key"] = "soft_dict key"
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20 soft_dict["version"] = "3.2.0"
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21
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22 soft_result = Result(**soft_dict)
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23
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24 test_gene = {
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25 "type": "gene",
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26 "key": "some_gene_key",
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27 "name": "gen_name",
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28 "identity": "187",
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29 "alignment_length": "800",
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30 "ref_gene_lenght": "800",
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31 "coverage": "89",
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32 "ref_id": "some_ref_id"
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33 }
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34
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35 soft_result.add_class(cl="genes", **test_gene)
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36
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37 test_dict = {
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38 "type": "software_result",
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39 "software_name": "ResFinder",
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40 "software_version": "4.0",
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41 "run_date": "20200214",
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42 "key": "software_key"
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43 }
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44
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45 result = Result(result_type="software_result", **test_dict)
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46 result.add_class(cl="genes", **test_gene)
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47
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48 test_trans_table = {
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49 "primary": "key",
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50 "gene": "name",
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51 "id": "identity",
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52 "alignment": "alignment_length",
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53 "gene_lenght": "ref_gene_lenght",
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54 "cov": "coverage"
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55 }
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56
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57 translator = Translate("gene", test_trans_table)
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58
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59 test_gene2 = {
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60 "primary": "some_gene_key2",
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61 "gene": "gen_name2",
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62 "id": "97",
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63 "alignment": "800",
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64 "gene_lenght": "800",
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65 "cov": "99"
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66 }
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67
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68 result.add_class(cl="genes", result_type="gene",
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69 **translator.translate(test_gene2))
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70
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71 try:
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72 result.check_results()
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73 soft_result.check_results()
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74 except CGECoreOutInputError as e:
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75 print("Error dict:\n{}".format(e.errors))
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76
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77 print(json.dumps(result))
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78 print(json.dumps(soft_result))
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