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Made all REST calls test with and without country code
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Depending on whether we are syncing with a national node or with the
central Directory, we may or may not need to incoporate the country
code into the URL for REST API calls. The changes test both
possibilities.
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@DavidCroftDKFZ
DavidCroftDKFZ committed Jan 30, 2025
1 parent 868e45c commit e110eed
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Showing 5 changed files with 61 additions and 43 deletions.
2 changes: 1 addition & 1 deletion pom.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -10,7 +10,7 @@
</parent>
<groupId>de.samply</groupId>
<artifactId>directory_sync_service</artifactId>
<version>1.5.10</version>
<version>1.5.11</version>
<name>directory_sync_service</name>
<description>Directory sync</description>
<url>https://github.com/samply/directory_sync_service</url>
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5 changes: 2 additions & 3 deletions src/main/java/de/samply/directory_sync_service/directory/DirectoryApi.java
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Expand Up @@ -155,7 +155,7 @@ protected boolean deleteStarModel(StarModelData starModelInputData) {
// We need to do things this way, because the Directory implements paging
// and a single pass may not get all facts.
do {
List<String> factIds = getNextPageOfFactIdsForCollection(countryCode, collectionId);
List<String> factIds = getNextPageOfFactIdsForCollection(collectionId);

if (factIds == null) {
logger.warn("deleteStarModel: Problem getting facts for collection: " + collectionId);
Expand Down Expand Up @@ -186,11 +186,10 @@ protected boolean deleteStarModel(StarModelData starModelInputData) {
/**
* Retrieves a list of fact IDs from the Directory associated with a specific collection.
*
* @param countryCode The country code, e.g. DE.
* @param collectionId The ID of the collection to retrieve fact IDs for.
* @return A list of fact IDs for the specified collection, or null if there is an issue retrieving the data. An empty list indicates that there are no more facts left to be retrieved.
*/
protected abstract List<String> getNextPageOfFactIdsForCollection(String countryCode, String collectionId);
protected abstract List<String> getNextPageOfFactIdsForCollection(String collectionId);

/**
* Deletes facts from the Directory service based on a list of fact IDs.
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4 changes: 2 additions & 2 deletions src/main/java/de/samply/directory_sync_service/directory/graphql/DirectoryApiGraphql.java
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Expand Up @@ -640,12 +640,12 @@ private String wrapValueInHashWithAttribute(String attributeName, String value)
/**
* Retrieves a list of fact IDs from the Directory associated with a specific collection.
*
* @param countryCode The country code, e.g. DE.
* @param collectionId The ID of the collection to retrieve fact IDs for.
* @return A list of fact IDs for the specified collection, or null if there is an issue retrieving the data. An empty list indicates that there are no more facts left to be retrieved.
*/
@Override
protected List<String> getNextPageOfFactIdsForCollection(String countryCode, String collectionId) {
protected List<String> getNextPageOfFactIdsForCollection(String collectionId) {
String countryCode = extractCountryCodeFromBbmriEricId(collectionId);
List<String> factIds = new ArrayList<>();

// Use getFactPageToggle to ensure that this method gets run only once.
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82 changes: 56 additions & 26 deletions src/main/java/de/samply/directory_sync_service/directory/rest/DirectoryApiRest.java
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Original file line number Diff line number Diff line change
Expand Up @@ -70,14 +70,20 @@ public Biobank fetchBiobank(BbmriEricId id) {
// Return a fake Biobank if we are mocking
return new Biobank();

Biobank biobank = (Biobank) directoryCallsRest.get(directoryEndpointsRest.getBiobankEndpoint(id.getCountryCode()) + "/" + id, Biobank.class);
Biobank biobank = fetchBiobank(id.getCountryCode(), id);
if (biobank == null) {
logger.warn("fetchBiobank: No Biobank in Directory with id: " + id);
return null;
logger.info("fetchBiobank: biobank is null, trying URL without country code");
biobank = fetchBiobank(null, id);
if (biobank == null)
logger.warn("fetchBiobank: No Biobank in Directory with id: " + id);
}
return biobank;
}

private Biobank fetchBiobank(String countryCode, BbmriEricId id) {
return (Biobank) directoryCallsRest.get(directoryEndpointsRest.getBiobankEndpoint(countryCode) + "/" + id, Biobank.class);
}

/**
* Make API calls to the Directory to fill a DirectoryCollectionGet object containing attributes
* for all of the collections listed in collectionIds. The countryCode is used solely for
Expand All @@ -97,17 +103,15 @@ public DirectoryCollectionGet fetchCollectionGetOutcomes(String countryCode, Lis
return directoryCollectionGet;
}

logger.debug("fetchCollectionGetOutcomes: ?????????????????????????????????????????????????????????????????????????????????????????????????????????????");
boolean warnFlag = false;
for (String collectionId: collectionIds) {
logger.debug("fetchCollectionGetOutcomes: collectionId: " + collectionId);
String commandUrl = directoryEndpointsRest.getCollectionEndpoint(countryCode) + "?q=id==%22" + collectionId + "%22";
logger.debug("fetchCollectionGetOutcomes: commandUrl: " + commandUrl);
DirectoryCollectionGet singleDirectoryCollectionGet = (DirectoryCollectionGet) directoryCallsRest.get(commandUrl, DirectoryCollectionGet.class);
if (singleDirectoryCollectionGet == null) {
logger.warn("fetchCollectionGetOutcomes: singleDirectoryCollectionGet is null, trying URL without country code");
logger.info("fetchCollectionGetOutcomes: singleDirectoryCollectionGet is null, trying URL without country code");
commandUrl = directoryEndpointsRest.getCollectionEndpoint(null) + "?q=id==%22" + collectionId + "%22";
logger.debug("fetchCollectionGetOutcomes: new commandUrl: " + commandUrl);
singleDirectoryCollectionGet = (DirectoryCollectionGet) directoryCallsRest.get(commandUrl, DirectoryCollectionGet.class);
if (singleDirectoryCollectionGet == null) {
logger.warn("fetchCollectionGetOutcomes: singleDirectoryCollectionGet is null, does the collection exist in the Directory: " + collectionId);
Expand All @@ -123,7 +127,6 @@ public DirectoryCollectionGet fetchCollectionGetOutcomes(String countryCode, Lis
}
directoryCollectionGet.getItems().add(item);
}
logger.debug("fetchCollectionGetOutcomes: ?????????????????????????????????????????????????????????????????????????????????????????????????????????????");

if (warnFlag && directoryCollectionGet.isEmpty()) {
logger.warn("fetchCollectionGetOutcomes: No entities retrieved from Directory");
Expand All @@ -145,15 +148,24 @@ public boolean updateEntities(DirectoryCollectionPut directoryCollectionPut) {
return true;
}

String response = directoryCallsRest.put(directoryEndpointsRest.getCollectionEndpoint(directoryCollectionPut.getCountryCode()), directoryCollectionPut);
String response = updateEntities(directoryCollectionPut.getCountryCode(), directoryCollectionPut);
if (response == null) {
logger.warn("entity update, PUT problem");
return false;
logger.info("updateEntities: PUT problem, trying URL without country code");
response = updateEntities(null, directoryCollectionPut);
if (response == null) {
logger.warn("updateEntities: PUT problem even without country code, aborting");
return false;
}
}

return true;
}

private String updateEntities(String countryCode, DirectoryCollectionPut directoryCollectionPut) {
return directoryCallsRest.put(directoryEndpointsRest.getCollectionEndpoint(countryCode), directoryCollectionPut);
}


/**
* Updates the fact tables block for a specific country with the provided data.
*
Expand All @@ -168,13 +180,22 @@ protected boolean updateFactTablesBlock(String countryCode, List<Map<String, Str
return true;
}

if (mockDirectory) {
// Dummy return if we're in mock mode
return true;
}

Map<String,Object> body = new HashMap<String,Object>();
body.put("entities", factTablesBlock);
String response = directoryCallsRest.post(directoryEndpointsRest.getFactEndpoint(countryCode), body);

String response = directoryCallsRest.post(directoryEndpointsRest.getFactEndpoint(countryCode), body);
if (response == null) {
logger.warn("updateFactTablesBlock: null response from REST call");
return false;
logger.info("updateFactTablesBlock: null response from REST call, trying URL without country code");
response = directoryCallsRest.post(directoryEndpointsRest.getFactEndpoint(null), body);
if (response == null) {
logger.warn("updateFactTablesBlock: null response from REST call even without country code, aborting");
return false;
}
}

return true;
Expand All @@ -183,23 +204,26 @@ protected boolean updateFactTablesBlock(String countryCode, List<Map<String, Str
/**
* Retrieves a list of fact IDs from the Directory associated with a specific collection.
*
* @param countryCode The country code, e.g. DE.
* @param collectionId The ID of the collection to retrieve fact IDs for.
* @return A list of fact IDs for the specified collection, or null if there is an issue retrieving the data. An empty list indicates that there are no more facts left to be retrieved.
*/
@Override
protected List<String> getNextPageOfFactIdsForCollection(String countryCode, String collectionId) {
String apiUrl = directoryEndpointsRest.getFactEndpoint(countryCode);

protected List<String> getNextPageOfFactIdsForCollection(String collectionId) {
// Get a list of fact IDs for this collection
String apiUrl = directoryEndpointsRest.getFactEndpoint(extractCountryCodeFromBbmriEricId(collectionId));
Map factWrapper = (Map) directoryCallsRest.get(apiUrl + "?q=collection==%22" + collectionId + "%22", Map.class);

if (factWrapper == null) {
logger.warn("deleteStarModel: Problem getting facts for collection, factWrapper == null, collectionId=" + collectionId);
return null;
logger.info("getNextPageOfFactIdsForCollection: Problem getting facts for collection, factWrapper == null, collectionId=" + collectionId + ", trying without country code");
apiUrl = directoryEndpointsRest.getFactEndpoint(extractCountryCodeFromBbmriEricId(null));
factWrapper = (Map) directoryCallsRest.get(apiUrl + "?q=collection==%22" + collectionId + "%22", Map.class);
if (factWrapper == null) {
logger.warn("getNextPageOfFactIdsForCollection: Problem getting facts for collection, factWrapper == null, collectionId=" + collectionId + " even without contry code, aborting");
return null;
}
}

if (!factWrapper.containsKey("items")) {
logger.warn("deleteStarModel: Problem getting facts for collection, no item key present: " + collectionId);
logger.warn("getNextPageOfFactIdsForCollection: Problem getting facts for collection, no item key present: " + collectionId);
return null;
}
List<Map<String, String>> facts = (List<Map<String, String>>) factWrapper.get("items");
Expand Down Expand Up @@ -227,14 +251,20 @@ protected boolean deleteFactsByIds(String countryCode, List<String> factIds) {
// Nothing to delete
return true;

String apiUrl = directoryEndpointsRest.getFactEndpoint(countryCode);
if (mockDirectory) {
// Dummy return if we're in mock mode
return true;
}

// Directory likes to have its delete data wrapped in a map with key "entityIds".
String result = directoryCallsRest.delete(apiUrl, new HashMap<>(Map.of("entityIds", factIds)));

String result = directoryCallsRest.delete(directoryEndpointsRest.getFactEndpoint(countryCode), new HashMap<>(Map.of("entityIds", factIds)));
if (result == null) {
logger.warn("deleteFactsByIds, Problem during delete of factIds");
return false;
logger.info("deleteFactsByIds, Problem during delete of factIds, trying without country code");
result = directoryCallsRest.delete(directoryEndpointsRest.getFactEndpoint(null), new HashMap<>(Map.of("entityIds", factIds)));
if (result == null) {
logger.warn("deleteFactsByIds, Problem during delete of factIds even without contry code, aborting");
return false;
}
}

return true;
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11 changes: 0 additions & 11 deletions src/main/java/de/samply/directory_sync_service/directory/rest/DirectoryCallsRest.java
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Original file line number Diff line number Diff line change
@@ -1,24 +1,13 @@
package de.samply.directory_sync_service.directory.rest;

import com.google.gson.Gson;
import de.samply.directory_sync_service.Util;
import de.samply.directory_sync_service.directory.DirectoryCalls;
import de.samply.directory_sync_service.directory.DirectoryCredentials;
import org.apache.http.HttpEntity;
import org.apache.http.HttpResponse;
import org.apache.http.client.methods.CloseableHttpResponse;
import org.apache.http.client.methods.HttpEntityEnclosingRequestBase;
import org.apache.http.client.methods.HttpGet;
import org.apache.http.client.methods.HttpOptions;
import org.apache.http.client.methods.HttpPost;
import org.apache.http.client.methods.HttpPut;
import org.apache.http.client.methods.HttpUriRequest;
import org.apache.http.entity.StringEntity;
import org.apache.http.impl.client.CloseableHttpClient;
import org.apache.http.impl.client.HttpClients;
import org.apache.http.util.EntityUtils;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;

import java.io.BufferedReader;
import java.io.IOException;
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