#6225

Committed 28 Jul 2025 12:14PM UTC coverage: 81.088% (+0.4%) from 80.694%

Build # #6225

Build Type

push

Committed by

Commit Message

DT-2026: Bring feature branch into develop (#2621)

Co-authored-by: Elliot Otchet <otchet@broadinstitute.org>
Co-authored-by: Rachel Johanek <55256690+rjohanek@users.noreply.github.com>
Co-authored-by: rjohanek <rjohanek@broadinstitute.org>
Co-authored-by: Matt Bemis <MatthewBemis@users.noreply.github.com>
Co-authored-by: otchet-broad <111771148+otchet-broad@users.noreply.github.com>

Coverage Stats

397 of 437 new or added lines in 34 files covered. (90.85%)

10775 of 13288 relevant lines covered (81.09%)

0.81 hits per line

Source File
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98.85

/src/main/java/org/broadinstitute/consent/http/rules/RuleImplementationInterface.java

package org.broadinstitute.consent.http.rules;

import org.apache.commons.lang3.StringUtils;
import org.broadinstitute.consent.http.models.DataAccessRequest;
import org.broadinstitute.consent.http.models.DataAccessRequestData;
import org.broadinstitute.consent.http.models.DataUse;
import org.broadinstitute.consent.http.models.Dataset;

public interface RuleImplementationInterface {

  DACAutomationRuleType getRuleType();

  boolean compare(Dataset dataset, DataAccessRequest dataAccessRequest);
  default boolean hasNoModifiers(DataUse data) {
    if (Boolean.TRUE.equals(data.getCollaboratorRequired())) {
      return false;
    }
    if (Boolean.TRUE.equals(data.getSexualDiseases())) {
      return false;
    }
    if (Boolean.TRUE.equals(data.getEthicsApprovalRequired())) {
      return false;
    }
    if (Boolean.TRUE.equals(data.getMethodsResearch())) {
      return false;
    }
    if (Boolean.TRUE.equals(data.getNonProfitUse())) {
      return false;
    }
    if (Boolean.TRUE.equals(data.getGeneticStudiesOnly())) {
      return false;
    }
    if (Boolean.TRUE.equals(data.getPopulationOriginsAncestry())) {
      return false;
    }
    if (Boolean.TRUE.equals(data.getPublicationResults())) {
      return false;
    }
    if (Boolean.TRUE.equals(data.getIllegalBehavior())) {
      return false;
    }
    if (Boolean.TRUE.equals(data.getControls())) {
      return false;
    }
    if (Boolean.TRUE.equals(data.getNotHealth())) {
      return false;
    }
    if (Boolean.TRUE.equals(data.getPopulation())) {
      return false;
    }
    if (Boolean.TRUE.equals(data.getPediatric())) {
      return false;
    }
    if (Boolean.TRUE.equals(data.getPsychologicalTraits())) {
      return false;
    }
    if (Boolean.TRUE.equals(data.getStigmatizeDiseases())) {
      return false;
    }
    if (Boolean.TRUE.equals(data.getVulnerablePopulations())) {
      return false;
    }
    if (!Boolean.TRUE.equals(data.getDiseaseRestrictions() == (null))
        && !Boolean.TRUE.equals(data.getDiseaseRestrictions().isEmpty())) {
      return false;
    }
    if (Boolean.TRUE.equals(!StringUtils.isBlank(data.getPublicationMoratorium()))) {
      return false;
    }
    if (Boolean.TRUE.equals(!StringUtils.isBlank(data.getOther()))) {
      return false;
    }
    if (Boolean.TRUE.equals(!StringUtils.isBlank(data.getGeographicalRestrictions()))) {
      return false;
    }
    if (Boolean.TRUE.equals(!StringUtils.isBlank(data.getSecondaryOther()))) {
      return false;
    }
    return !Boolean.TRUE.equals(!StringUtils.isBlank(data.getGender()));
  }

  default boolean secondaryConditionChecks(DataAccessRequestData data) {
    // Secondary condition checks, part 1
    if (Boolean.TRUE.equals(data.getControls())) {
      return false;
    }
    if (Boolean.TRUE.equals(data.getPopulation())) {
      return false;
    }
    if (Boolean.TRUE.equals(data.getForProfit())) {
      return false;
    }

    // Secondary condition checks, part 2
    if (!StringUtils.isBlank(data.getGender())) {
      return false;
    }
    if (Boolean.TRUE.equals(data.getPediatric())) {
      return false;
    }
    if (Boolean.TRUE.equals(data.getVulnerablePopulation())) {
      return false;
    }

    // Secondary condition checks, part 3
    if (Boolean.TRUE.equals(data.getIllegalBehavior())) {
      return false;
    }
    if (Boolean.TRUE.equals(data.getSexualDiseases())) {
      return false;
    }
    if (Boolean.TRUE.equals(data.getPsychiatricTraits())) {
      return false;
    }
    if (Boolean.TRUE.equals(data.getNotHealth())) {
      return false;
    }
    if (Boolean.TRUE.equals(data.getStigmatizedDiseases())) {
      return false;
    }
    if (Boolean.TRUE.equals(data.getAddiction())) {
      return false;
    }
    return true;
  }

  default boolean requestIsOnlyHMB(DataAccessRequestData data) {
    // Primary condition checks
    if (Boolean.TRUE.equals(data.getDiseases())) {
      return false;
    }
    if (!StringUtils.isBlank(data.getOtherText())) {
      return false;
    }
    if (Boolean.TRUE.equals(data.getOther())) {
      return false;
    }

    if (!secondaryConditionChecks(data)) {
      return false;
    }

    return Boolean.TRUE.equals(data.getHmb());
  }

  default boolean requestHasDiseases(DataAccessRequestData data) {
    if (!Boolean.TRUE.equals(data.getDiseases())) {
      return false;
    }

    if (!StringUtils.isBlank(data.getOtherText())) {
      return false;
    }
    if (Boolean.TRUE.equals(data.getOther())) {
      return false;
    }

    if (!secondaryConditionChecks(data)) {
      return false;
    }

    return Boolean.TRUE.equals(!data.getOntologies().isEmpty());
  }
}

1	package org.broadinstitute.consent.http.rules;
2
3	import org.apache.commons.lang3.StringUtils;
4	import org.broadinstitute.consent.http.models.DataAccessRequest;
5	import org.broadinstitute.consent.http.models.DataAccessRequestData;
6	import org.broadinstitute.consent.http.models.DataUse;
7	import org.broadinstitute.consent.http.models.Dataset;
8
9	public interface RuleImplementationInterface {
10
11	DACAutomationRuleType getRuleType();
12
13	boolean compare(Dataset dataset, DataAccessRequest dataAccessRequest);
14	default boolean hasNoModifiers(DataUse data) {
15	if (Boolean.TRUE.equals(data.getCollaboratorRequired())) {	1✔
16	return false;	1✔
17	}
18	if (Boolean.TRUE.equals(data.getSexualDiseases())) {	1✔
19	return false;	1✔
20	}
21	if (Boolean.TRUE.equals(data.getEthicsApprovalRequired())) {	1✔
22	return false;	1✔
23	}
24	if (Boolean.TRUE.equals(data.getMethodsResearch())) {	1✔
25	return false;	1✔
26	}
27	if (Boolean.TRUE.equals(data.getNonProfitUse())) {	1✔
28	return false;	1✔
29	}
30	if (Boolean.TRUE.equals(data.getGeneticStudiesOnly())) {	1✔
31	return false;	1✔
32	}
33	if (Boolean.TRUE.equals(data.getPopulationOriginsAncestry())) {	1✔
34	return false;	1✔
35	}
36	if (Boolean.TRUE.equals(data.getPublicationResults())) {	1✔
37	return false;	1✔
38	}
39	if (Boolean.TRUE.equals(data.getIllegalBehavior())) {	1✔
40	return false;	1✔
41	}
42	if (Boolean.TRUE.equals(data.getControls())) {	1✔
43	return false;	1✔
44	}
45	if (Boolean.TRUE.equals(data.getNotHealth())) {	1✔
46	return false;	1✔
47	}
48	if (Boolean.TRUE.equals(data.getPopulation())) {	1✔
49	return false;	1✔
50	}
51	if (Boolean.TRUE.equals(data.getPediatric())) {	1✔
52	return false;	1✔
53	}
54	if (Boolean.TRUE.equals(data.getPsychologicalTraits())) {	1✔
55	return false;	1✔
56	}
57	if (Boolean.TRUE.equals(data.getStigmatizeDiseases())) {	1✔
58	return false;	1✔
59	}
60	if (Boolean.TRUE.equals(data.getVulnerablePopulations())) {	1✔
61	return false;	1✔
62	}
63	if (!Boolean.TRUE.equals(data.getDiseaseRestrictions() == (null))	1✔
64	&& !Boolean.TRUE.equals(data.getDiseaseRestrictions().isEmpty())) {	1✔
65	return false;	1✔
66	}
67	if (Boolean.TRUE.equals(!StringUtils.isBlank(data.getPublicationMoratorium()))) {	1✔
68	return false;	1✔
69	}
70	if (Boolean.TRUE.equals(!StringUtils.isBlank(data.getOther()))) {	1✔
71	return false;	1✔
72	}
73	if (Boolean.TRUE.equals(!StringUtils.isBlank(data.getGeographicalRestrictions()))) {	1✔
74	return false;	1✔
75	}
76	if (Boolean.TRUE.equals(!StringUtils.isBlank(data.getSecondaryOther()))) {	1✔
77	return false;	1✔
78	}
79	return !Boolean.TRUE.equals(!StringUtils.isBlank(data.getGender()));	1✔
80	}
81
82	default boolean secondaryConditionChecks(DataAccessRequestData data) {
83	// Secondary condition checks, part 1
84	if (Boolean.TRUE.equals(data.getControls())) {	1✔
85	return false;	1✔
86	}
87	if (Boolean.TRUE.equals(data.getPopulation())) {	1✔
88	return false;	1✔
89	}
90	if (Boolean.TRUE.equals(data.getForProfit())) {	1✔
91	return false;	1✔
92	}
93
94	// Secondary condition checks, part 2
95	if (!StringUtils.isBlank(data.getGender())) {	1✔
96	return false;	1✔
97	}
98	if (Boolean.TRUE.equals(data.getPediatric())) {	1✔
99	return false;	1✔
100	}
101	if (Boolean.TRUE.equals(data.getVulnerablePopulation())) {	1✔
102	return false;	1✔
103	}
104
105	// Secondary condition checks, part 3
106	if (Boolean.TRUE.equals(data.getIllegalBehavior())) {	1✔
107	return false;	1✔
108	}
109	if (Boolean.TRUE.equals(data.getSexualDiseases())) {	1✔
110	return false;	1✔
111	}
112	if (Boolean.TRUE.equals(data.getPsychiatricTraits())) {	1✔
113	return false;	1✔
114	}
115	if (Boolean.TRUE.equals(data.getNotHealth())) {	1✔
116	return false;	1✔
117	}
118	if (Boolean.TRUE.equals(data.getStigmatizedDiseases())) {	1✔
119	return false;	1✔
120	}
121	if (Boolean.TRUE.equals(data.getAddiction())) {	1✔
122	return false;	1✔
123	}
124	return true;	1✔
125	}
126
127	default boolean requestIsOnlyHMB(DataAccessRequestData data) {
128	// Primary condition checks
129	if (Boolean.TRUE.equals(data.getDiseases())) {	1✔
130	return false;	1✔
131	}
132	if (!StringUtils.isBlank(data.getOtherText())) {	1✔
133	return false;	1✔
134	}
135	if (Boolean.TRUE.equals(data.getOther())) {	1✔
136	return false;	1✔
137	}
138
139	if (!secondaryConditionChecks(data)) {	1✔
140	return false;	1✔
141	}
142
143	return Boolean.TRUE.equals(data.getHmb());	1✔
144	}
145
146	default boolean requestHasDiseases(DataAccessRequestData data) {
147	if (!Boolean.TRUE.equals(data.getDiseases())) {	1✔
148	return false;	1✔
149	}
150
151	if (!StringUtils.isBlank(data.getOtherText())) {	1✔
152	return false;	1✔
153	}
154	if (Boolean.TRUE.equals(data.getOther())) {	1✔
155	return false;	1✔
156	}
157
158	if (!secondaryConditionChecks(data)) {	1✔
NEW 159	return false;	×
160	}
161
162	return Boolean.TRUE.equals(!data.getOntologies().isEmpty());	1✔
163	}
164	}

DataBiosphere / consent / #6225

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