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Replace StudyMetaData object with Map in StudyAccessService and FENCE…
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…AuthenticationService

Reverting change. Attempting to determine if there is a parsing issue.
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@Gcolon021
Gcolon021 committed May 25, 2024
1 parent b7b00ea commit f30b491
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Showing 7 changed files with 4,224 additions and 49 deletions.
8 changes: 4 additions & 4 deletions ...th-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/rest/StudyAccessService.java
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Original file line number Diff line number Diff line change
Expand Up @@ -53,9 +53,9 @@ public Response addStudyAccess(@ApiParam(value="The Study Identifier of the new
return Response.status(Response.Status.BAD_REQUEST).entity("Study identifier cannot be blank").build();
}

StudyMetaData fenceMappingForStudy;
Map fenceMappingForStudy;
try {
Map<String, StudyMetaData> fenceMapping = fenceMappingUtility.getFENCEMapping();
Map<String, Map> fenceMapping = fenceMappingUtility.getFENCEMapping();
if (fenceMapping == null) {
throw new Exception("Fence mapping is null");
}
Expand All @@ -70,8 +70,8 @@ public Response addStudyAccess(@ApiParam(value="The Study Identifier of the new
return Response.status(Response.Status.BAD_REQUEST).entity("Could not find study with the provided identifier").build();
}

String projectId = fenceMappingForStudy.getStudy_identifier();
String consentCode = fenceMappingForStudy.getConsent_group_code();
String projectId = (String) fenceMappingForStudy.get("study_identifier");
String consentCode = (String) fenceMappingForStudy.get("consent_group_code");
String newRoleName = StringUtils.isNotBlank(consentCode) ? MANUAL+projectId+"_"+consentCode : MANUAL+projectId;

logger.debug("addStudyAccess - New manual PSAMA role name: {}", newRoleName);
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34 changes: 13 additions & 21 deletions ...main/java/edu/harvard/hms/dbmi/avillach/auth/service/auth/FENCEAuthenticationService.java
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Original file line number Diff line number Diff line change
Expand Up @@ -330,15 +330,16 @@ private Set<String> getProjectAccessNames(JsonNode fence_user_profile) {
// Loop over the project access names and convert them to database fence role names
while (project_access_names.hasNext()) {
String access_role_name = project_access_names.next();
StudyMetaData studyMetadata = fenceMappingUtility.getFenceMappingByAuthZ().get(access_role_name);
Map studyMetadata = fenceMappingUtility.getFenceMappingByAuthZ().get(access_role_name);

if (studyMetadata == null) {
logger.info("getFENCEProfile() -> Could not find study in FENCE mapping SKIPPING: {}", access_role_name);
continue;
}

String projectId = studyMetadata.getStudy_identifier();
String consentCode = studyMetadata.getConsent_group_code();
String projectId = (String) studyMetadata.get("study_identifier");
String consentCode = (String) studyMetadata.get("consent_group_code");

String newRoleName = StringUtils.isNotBlank(consentCode) ? "FENCE_" + projectId + "_" + consentCode : "FENCE_" + projectId;

project_access_set.add(newRoleName);
Expand Down Expand Up @@ -470,7 +471,7 @@ private Set<Privilege> addFENCEPrivileges(User u, Role r) {
logger.info("addFENCEPrivileges() project name: " + project_name + " consent group: " + consent_group);

// Look up the metadata by consent group.
StudyMetaData studyMetadata = getFENCEMappingforProjectAndConsent(project_name, consent_group);
Map studyMetadata = getFENCEMappingforProjectAndConsent(project_name, consent_group);
if (studyMetadata == null) {
//no privileges means no access to this project. just return existing set of privs.
logger.warn("No metadata available for project {}.{}", project_name, consent_group);
Expand All @@ -479,19 +480,18 @@ private Set<Privilege> addFENCEPrivileges(User u, Role r) {

logger.info("addPrivileges() This is a new privilege");

String dataType = studyMetadata.getData_type();
Boolean isHarmonized = "Y".equals(studyMetadata.getIs_harmonized());
String concept_path = studyMetadata.getTop_level_path();
String projectAlias = studyMetadata.getAbbreviated_name();
String dataType = (String) studyMetadata.get("data_type");
Boolean isHarmonized = "Y".equals(studyMetadata.get("is_harmonized"));
String concept_path = (String) studyMetadata.get("top_level_path");
String projectAlias = (String) studyMetadata.get("abbreviated_name");

//we need to add escape sequence back in to the path for parsing later (also need to double escape the regex)
//
// OK... so, we need to do this for the query Template and scopes, but should NOT do this for the rules.
//
// NOTE: I'm leaving this in here for now and removing the escaped values later. TODO: fix me!
if (concept_path != null) {
// This shouldn't be necessary, but it is. The double escape is necessary for the regex to work.
concept_path = concept_path.replace("\\", "\\\\");
// This shouldn't be necessary, but it is. The double escape is necessary for the regex to work.
concept_path = concept_path.replaceAll("\\\\", "\\\\\\\\");
}

Expand Down Expand Up @@ -1163,14 +1163,6 @@ private AccessRule upsertHarmonizedAccessRule(String project_name, String consen
private AccessRule upsertConsentGate(String gateName, String rule, boolean is_present, String description) {
gateName = "GATE_" + gateName + "_" + (is_present ? "PRESENT" : "MISSING");
AccessRule gate = accessruleRepo.getUniqueResultByColumn("name", gateName);

// jws will not parse the json if the rule contains a single backslash
if (!rule.contains("\\\\")) {
//these have to be escaped again so that jaxson can convert it correctly
rule = rule.replaceAll("\\\\", "\\\\\\\\");
logger.debug("upsertConsentGate(): escaped rule {}", rule);
}

if (gate != null) {
logger.info("upsertConsentGate() AccessRule {} already exists.", gateName);
return gate;
Expand All @@ -1192,12 +1184,12 @@ private AccessRule upsertConsentGate(String gateName, String rule, boolean is_pr
return gate;
}

private StudyMetaData getFENCEMappingforProjectAndConsent(String projectId, String consent_group) {
private Map getFENCEMappingforProjectAndConsent(String projectId, String consent_group) {
String consentVal = (consent_group != null && !consent_group.isEmpty()) ? projectId + "." + consent_group : projectId;
logger.info("getFENCEMappingforProjectAndConsent() looking up {}", consentVal);

StudyMetaData studyMetadata = fenceMappingUtility.getFENCEMapping().get(consentVal);
if (studyMetadata != null) {
Map studyMetadata = fenceMappingUtility.getFENCEMapping().get(consentVal);
if (studyMetadata instanceof Map) {
return studyMetadata;
} else {
logger.info("getFENCEMappingforProjectAndConsent() no mapping found for {}", consentVal);
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35 changes: 17 additions & 18 deletions ...-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/utils/FenceMappingUtility.java
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Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,6 @@

import com.fasterxml.jackson.databind.ObjectMapper;
import edu.harvard.hms.dbmi.avillach.auth.model.StudyMetaData;
import edu.harvard.hms.dbmi.avillach.auth.model.FenceMapping;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;

Expand All @@ -21,8 +20,8 @@
public class FenceMappingUtility {

private final Logger logger = LoggerFactory.getLogger(this.getClass());
private Map<String, StudyMetaData> fenceMappingByConsent;
private Map<String, StudyMetaData> fenceMappingByAuthZ;
private Map<String, Map> fenceMappingByConsent;
private Map<String, Map> fenceMappingByAuthZ;
private static String templatePath;
private ObjectMapper objectMapper;

Expand All @@ -43,43 +42,43 @@ public void init() {
}

private void initializeFENCEMapping() throws IOException {
ArrayList<StudyMetaData> studies = loadBioDataCatalystFenceMappingData();
ArrayList<Map> studies = loadBioDataCatalystFenceMappingData();
fenceMappingByConsent = new HashMap<>(studies.size());
for (StudyMetaData study : studies) {
String consentVal = (study.getConsent_group_code() != null && !study.getConsent_group_code().isEmpty()) ?
study.getStudy_identifier() + "." + study.getConsent_group_code() :
study.getStudy_identifier();
for (Map study : studies) {
String consentVal = (study.get("consent_group_code") != null && study.get("consent_group_code") != "") ?
"" + study.get("study_identifier") + "." + study.get("consent_group_code") :
"" + study.get("study_identifier");
fenceMappingByConsent.put(consentVal, study);
}
}

private void initializeFenceMappingByAuthZ() throws IOException {
ArrayList<StudyMetaData> studies = loadBioDataCatalystFenceMappingData();
ArrayList<Map> studies = loadBioDataCatalystFenceMappingData();
fenceMappingByAuthZ = new HashMap<>(studies.size());
for (StudyMetaData study : studies) {
fenceMappingByAuthZ.put(study.getAuthZ().replace("\\/", "/"), study);
for (Map study : studies) {
fenceMappingByAuthZ.put(((String) study.get("authZ")).replace("\\/", "/"), study);
}
}

public Map<String, StudyMetaData> getFENCEMapping() {
public Map<String, Map> getFENCEMapping() {
return fenceMappingByConsent;
}

public Map<String, StudyMetaData> getFenceMappingByAuthZ() {
public Map<String, Map> getFenceMappingByAuthZ() {
return fenceMappingByAuthZ;
}

private ArrayList<StudyMetaData> loadBioDataCatalystFenceMappingData() {
FenceMapping fenceMapping;
ArrayList<StudyMetaData> studies;
private ArrayList<Map> loadBioDataCatalystFenceMappingData() {
Map fenceMapping;
ArrayList<Map> studies;
try {
logger.debug("getFENCEMapping: loading FENCE mapping from {}", templatePath);
fenceMapping = objectMapper.readValue(
new File(String.join(File.separator,
new String[]{templatePath, "fence_mapping.json"}))
, FenceMapping.class);
, Map.class);

studies = fenceMapping.getBio_data_catalyst();
studies = (ArrayList<Map>) fenceMapping.get("bio_data_catalyst");
logger.debug("getFENCEMapping: found FENCE mapping with {} entries", studies.size());
} catch (Exception e) {
logger.error("loadFenceMappingData: Non-fatal error parsing fence_mapping.json: {}", templatePath, e);
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