#6189

Committed 08 Jul 2025 08:49PM UTC coverage: 80.64% (+0.01%) from 80.63%

Build # #6189

Build Type

push

Committed by

Commit Message

DT-1936: New API to import allow list (#2601)

Coverage Stats

19 of 22 new or added lines in 1 file covered. (86.36%)

10430 of 12934 relevant lines covered (80.64%)

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92.31

/src/main/java/org/broadinstitute/consent/http/resources/InstitutionResource.java

package org.broadinstitute.consent.http.resources;

import com.google.gson.Gson;
import com.google.inject.Inject;
import io.dropwizard.auth.Auth;
import jakarta.annotation.security.PermitAll;
import jakarta.annotation.security.RolesAllowed;
import jakarta.ws.rs.Consumes;
import jakarta.ws.rs.DELETE;
import jakarta.ws.rs.GET;
import jakarta.ws.rs.PATCH;
import jakarta.ws.rs.POST;
import jakarta.ws.rs.PUT;
import jakarta.ws.rs.Path;
import jakarta.ws.rs.PathParam;
import jakarta.ws.rs.Produces;
import jakarta.ws.rs.core.Response;
import java.util.ArrayList;
import java.util.List;
import org.broadinstitute.consent.http.exceptions.ConsentConflictException;
import org.broadinstitute.consent.http.models.DuosUser;
import org.broadinstitute.consent.http.models.Institution;
import org.broadinstitute.consent.http.models.InstitutionDomainMap;
import org.broadinstitute.consent.http.service.InstitutionService;
import org.broadinstitute.consent.http.util.InstitutionUtil;
import org.broadinstitute.consent.http.util.gson.GsonUtil;

@Path("api/institutions")
public class InstitutionResource extends Resource {

  private final InstitutionService institutionService;
  /*
    NOTE: InstitutionUtil will provide a configured GsonBuilder to help format the JSON response.
    Response needs to be filtered based on user roles (Admins would see all, non-admins would not)
    As such, any @PermitAll route would require the entity (Institution) to be formatted with the GsonBuilder
    as opposed to being passed into the response directly.
  */
  private final InstitutionUtil institutionUtil = new InstitutionUtil();

  @Inject
  public InstitutionResource(InstitutionService institutionService) {
    this.institutionService = institutionService;
  }

  @GET
  @Produces("application/json")
  @PermitAll
  public Response getInstitutions(@Auth DuosUser duosUser) {
    try {
      Boolean isAdmin = institutionUtil.checkIfAdmin(duosUser.getUser());
      Gson gson = institutionUtil.getGsonBuilder(isAdmin);
      List<Institution> institutions = institutionService.findAllInstitutions();
      return Response.ok().entity(gson.toJson(institutions)).build();
    } catch (Exception e) {
      return createExceptionResponse(e);
    }
  }

  @GET
  @Produces("application/json")
  @Path("/{id}")
  @PermitAll
  public Response getInstitution(@Auth DuosUser duosUser, @PathParam("id") Integer id) {
    try {
      Boolean isAdmin = institutionUtil.checkIfAdmin(duosUser.getUser());
      Gson gson = institutionUtil.getGsonBuilder(isAdmin);
      Institution institution = institutionService.findInstitutionById(id);
      return Response.ok().entity(gson.toJson(institution)).build();
    } catch (Exception e) {
      return createExceptionResponse(e);
    }
  }

  @POST
  @Consumes("application/json")
  @Produces("application/json")
  @RolesAllowed(ADMIN)
  public Response createInstitution(@Auth DuosUser duosUser, String institution) {
    try {
      Institution payload = GsonUtil.getInstance().fromJson(institution, Institution.class);
      List<Institution> conflicts = institutionService.findAllInstitutionsByName(payload.getName());
      if (!conflicts.isEmpty()) {
        throw new ConsentConflictException(
            "An institution exists with the name of '" + payload.getName() + "'");
      }
      Institution newInstitution = institutionService.createInstitution(payload, duosUser.getUser().getUserId());
      return Response.ok().entity(newInstitution).build();
    } catch (Exception e) {
      return createExceptionResponse(e);
    }
  }

  @PATCH
  @Consumes("application/json")
  @Produces("application/json")
  @Path("/{id}")
  @RolesAllowed(ADMIN)
  public Response patchInstitution(@Auth DuosUser duosUser, @PathParam("id") Integer id,
      String institution) {
    try {
      Institution existingInstitution = institutionService.findInstitutionById(id);
      Institution payload = GsonUtil.getInstance().fromJson(institution, Institution.class);
      Institution mergedPayload = payload.mergeUpdatableFields(existingInstitution);
      Institution updatedInstitution = institutionService.updateInstitutionById(mergedPayload, id,
          duosUser.getUserId());
      return Response.ok().entity(updatedInstitution).build();
    } catch (Exception e) {
      return createExceptionResponse(e);
    }
  }

  @PUT
  @Consumes("application/json")
  @Produces("application/json")
  @Path("/{id}")
  @RolesAllowed(ADMIN)
  public Response updateInstitution(@Auth DuosUser duosUser, @PathParam("id") Integer id,
      String institution) {
    try {
      Institution payload = GsonUtil.getInstance().fromJson(institution, Institution.class);
      Institution updatedInstitution = institutionService.updateInstitutionById(payload, id,
          duosUser.getUserId());
      return Response.ok().entity(updatedInstitution).build();
    } catch (Exception e) {
      return createExceptionResponse(e);
    }
  }

  @DELETE
  @Produces("application/json")
  @Path("/{id}")
  @RolesAllowed(ADMIN)
  public Response deleteInstitution(@Auth DuosUser duosUser, @PathParam("id") Integer id) {
    try {
      institutionService.deleteInstitutionById(id);
      return Response.status(204).build();
    } catch (Exception e) {
      return createExceptionResponse(e);
    }
  }

  @POST
  @Consumes("application/json")
  @Produces("application/json")
  @Path("/domains")
  @RolesAllowed(ADMIN)
  public Response updateInstitutionDomains(@Auth DuosUser duosUser, String institutionDomainMap) {
    try {
      List<Institution> updatedInstitutions = new ArrayList<>();
      InstitutionDomainMap domainMap = GsonUtil.getInstance().fromJson(institutionDomainMap, InstitutionDomainMap.class);
      domainMap.getInstitutionDomainMap().forEach((institutionName, value) -> {
        List<String> domains = value.stream().toList();
        List<Institution> institutions = institutionService.findAllInstitutionsByName(
            institutionName);
        if (institutions.isEmpty()) {
          logWarn("No institution found with name: [%s]".formatted(institutionName));
        } else if (institutions.size() == 1) {
          Institution institution = institutions.get(0);
          institution.setDomains(domains);
          try {
            updatedInstitutions.add(institutionService.updateInstitutionById(
                institution,
                institution.getId(),
                duosUser.getUserId()));
          } catch (Exception e) {
            logException("Failed to update institution: [%s] with domains: %s".formatted(institutionName, domains), e);
          }
        } else {
          logWarn("Multiple institutions found with name: [%s]".formatted(institutionName));
        }
      });
      return Response.ok(updatedInstitutions).build();
    } catch (Exception e) {
      return createExceptionResponse(e);
    }
  }
}

1	package org.broadinstitute.consent.http.resources;
2
3	import com.google.gson.Gson;
4	import com.google.inject.Inject;
5	import io.dropwizard.auth.Auth;
6	import jakarta.annotation.security.PermitAll;
7	import jakarta.annotation.security.RolesAllowed;
8	import jakarta.ws.rs.Consumes;
9	import jakarta.ws.rs.DELETE;
10	import jakarta.ws.rs.GET;
11	import jakarta.ws.rs.PATCH;
12	import jakarta.ws.rs.POST;
13	import jakarta.ws.rs.PUT;
14	import jakarta.ws.rs.Path;
15	import jakarta.ws.rs.PathParam;
16	import jakarta.ws.rs.Produces;
17	import jakarta.ws.rs.core.Response;
18	import java.util.ArrayList;
19	import java.util.List;
20	import org.broadinstitute.consent.http.exceptions.ConsentConflictException;
21	import org.broadinstitute.consent.http.models.DuosUser;
22	import org.broadinstitute.consent.http.models.Institution;
23	import org.broadinstitute.consent.http.models.InstitutionDomainMap;
24	import org.broadinstitute.consent.http.service.InstitutionService;
25	import org.broadinstitute.consent.http.util.InstitutionUtil;
26	import org.broadinstitute.consent.http.util.gson.GsonUtil;
27
28	@Path("api/institutions")
29	public class InstitutionResource extends Resource {
30
31	private final InstitutionService institutionService;
32	/*
33	NOTE: InstitutionUtil will provide a configured GsonBuilder to help format the JSON response.
34	Response needs to be filtered based on user roles (Admins would see all, non-admins would not)
35	As such, any @PermitAll route would require the entity (Institution) to be formatted with the GsonBuilder
36	as opposed to being passed into the response directly.
37	*/
38	private final InstitutionUtil institutionUtil = new InstitutionUtil();	1✔
39
40	@Inject
41	public InstitutionResource(InstitutionService institutionService) {	1✔
42	this.institutionService = institutionService;	1✔
43	}	1✔
44
45	@GET
46	@Produces("application/json")
47	@PermitAll
48	public Response getInstitutions(@Auth DuosUser duosUser) {
49	try {
50	Boolean isAdmin = institutionUtil.checkIfAdmin(duosUser.getUser());	1✔
51	Gson gson = institutionUtil.getGsonBuilder(isAdmin);	1✔
52	List<Institution> institutions = institutionService.findAllInstitutions();	1✔
53	return Response.ok().entity(gson.toJson(institutions)).build();	1✔
54	} catch (Exception e) {	×
55	return createExceptionResponse(e);	×
56	}
57	}
58
59	@GET
60	@Produces("application/json")
61	@Path("/{id}")
62	@PermitAll
63	public Response getInstitution(@Auth DuosUser duosUser, @PathParam("id") Integer id) {
64	try {
65	Boolean isAdmin = institutionUtil.checkIfAdmin(duosUser.getUser());	1✔
66	Gson gson = institutionUtil.getGsonBuilder(isAdmin);	1✔
67	Institution institution = institutionService.findInstitutionById(id);	1✔
68	return Response.ok().entity(gson.toJson(institution)).build();	1✔
69	} catch (Exception e) {	1✔
70	return createExceptionResponse(e);	1✔
71	}
72	}
73
74	@POST
75	@Consumes("application/json")
76	@Produces("application/json")
77	@RolesAllowed(ADMIN)
78	public Response createInstitution(@Auth DuosUser duosUser, String institution) {
79	try {
80	Institution payload = GsonUtil.getInstance().fromJson(institution, Institution.class);	1✔
81	List<Institution> conflicts = institutionService.findAllInstitutionsByName(payload.getName());	1✔
82	if (!conflicts.isEmpty()) {	1✔
83	throw new ConsentConflictException(	1✔
84	"An institution exists with the name of '" + payload.getName() + "'");	1✔
85	}
86	Institution newInstitution = institutionService.createInstitution(payload, duosUser.getUser().getUserId());	1✔
87	return Response.ok().entity(newInstitution).build();	1✔
88	} catch (Exception e) {	1✔
89	return createExceptionResponse(e);	1✔
90	}
91	}
92
93	@PATCH
94	@Consumes("application/json")
95	@Produces("application/json")
96	@Path("/{id}")
97	@RolesAllowed(ADMIN)
98	public Response patchInstitution(@Auth DuosUser duosUser, @PathParam("id") Integer id,
99	String institution) {
100	try {
101	Institution existingInstitution = institutionService.findInstitutionById(id);	1✔
102	Institution payload = GsonUtil.getInstance().fromJson(institution, Institution.class);	1✔
103	Institution mergedPayload = payload.mergeUpdatableFields(existingInstitution);	1✔
104	Institution updatedInstitution = institutionService.updateInstitutionById(mergedPayload, id,	1✔
105	duosUser.getUserId());	1✔
106	return Response.ok().entity(updatedInstitution).build();	1✔
107	} catch (Exception e) {	1✔
108	return createExceptionResponse(e);	1✔
109	}
110	}
111
112	@PUT
113	@Consumes("application/json")
114	@Produces("application/json")
115	@Path("/{id}")
116	@RolesAllowed(ADMIN)
117	public Response updateInstitution(@Auth DuosUser duosUser, @PathParam("id") Integer id,
118	String institution) {
119	try {
120	Institution payload = GsonUtil.getInstance().fromJson(institution, Institution.class);	1✔
121	Institution updatedInstitution = institutionService.updateInstitutionById(payload, id,	1✔
122	duosUser.getUserId());	1✔
123	return Response.ok().entity(updatedInstitution).build();	1✔
124	} catch (Exception e) {	1✔
125	return createExceptionResponse(e);	1✔
126	}
127	}
128
129	@DELETE
130	@Produces("application/json")
131	@Path("/{id}")
132	@RolesAllowed(ADMIN)
133	public Response deleteInstitution(@Auth DuosUser duosUser, @PathParam("id") Integer id) {
134	try {
135	institutionService.deleteInstitutionById(id);	1✔
136	return Response.status(204).build();	1✔
137	} catch (Exception e) {	1✔
138	return createExceptionResponse(e);	1✔
139	}
140	}
141
142	@POST
143	@Consumes("application/json")
144	@Produces("application/json")
145	@Path("/domains")
146	@RolesAllowed(ADMIN)
147	public Response updateInstitutionDomains(@Auth DuosUser duosUser, String institutionDomainMap) {
148	try {
149	List<Institution> updatedInstitutions = new ArrayList<>();	1✔
150	InstitutionDomainMap domainMap = GsonUtil.getInstance().fromJson(institutionDomainMap, InstitutionDomainMap.class);	1✔
151	domainMap.getInstitutionDomainMap().forEach((institutionName, value) -> {	1✔
152	List<String> domains = value.stream().toList();	1✔
153	List<Institution> institutions = institutionService.findAllInstitutionsByName(	1✔
154	institutionName);
155	if (institutions.isEmpty()) {	1✔
156	logWarn("No institution found with name: [%s]".formatted(institutionName));	1✔
157	} else if (institutions.size() == 1) {	1✔
158	Institution institution = institutions.get(0);	1✔
159	institution.setDomains(domains);	1✔
160	try {
161	updatedInstitutions.add(institutionService.updateInstitutionById(	1✔
162	institution,
163	institution.getId(),	1✔
164	duosUser.getUserId()));	1✔
NEW 165	} catch (Exception e) {	×
NEW 166	logException("Failed to update institution: [%s] with domains: %s".formatted(institutionName, domains), e);	×
167	}	1✔
168	} else {	1✔
NEW 169	logWarn("Multiple institutions found with name: [%s]".formatted(institutionName));	×
170	}
171	});	1✔
172	return Response.ok(updatedInstitutions).build();	1✔
173	} catch (Exception e) {	1✔
174	return createExceptionResponse(e);	1✔
175	}
176	}
177	}

DataBiosphere / consent / #6189

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