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Rename status to more appropriate export to nahima
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@GenieTim
GenieTim committed Sep 29, 2021
1 parent c825449 commit dde752b
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Showing 3 changed files with 97 additions and 22 deletions.
85 changes: 66 additions & 19 deletions src/main/java/edu/harvard/mcz/imagecapture/data/NahimaManager.java
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Original file line number Diff line number Diff line change
Expand Up @@ -3,6 +3,7 @@
import com.github.mizosoft.methanol.MediaType;
import com.github.mizosoft.methanol.MultipartBodyPublisher;
import com.github.mizosoft.methanol.MutableRequest;
import edu.harvard.mcz.imagecapture.ImageCaptureApp;
import edu.harvard.mcz.imagecapture.ImageCaptureProperties;
import edu.harvard.mcz.imagecapture.entity.ICImage;
import edu.harvard.mcz.imagecapture.entity.Specimen;
Expand All @@ -24,8 +25,8 @@ public class NahimaManager extends AbstractRestClient {
private final String url;
private final String username;
private final String password;
private String token;
private final Map<String, Map<String, JSONObject>> resolveCache = new HashMap<>();
private String token;

public NahimaManager(String url, String username, String password) throws IOException, InterruptedException, RuntimeException {
// normalize URL
Expand All @@ -46,7 +47,6 @@ public NahimaManager(String url, String username, String password) throws IOExce

/**
* Start a Nahima session
*
*/
protected void startSessionAndRetrieveToken() throws RuntimeException {
String queryUrl = this.url + "session";
Expand All @@ -61,7 +61,6 @@ protected void startSessionAndRetrieveToken() throws RuntimeException {

/**
* Do login to Nahima
*
*/
protected void login() throws IOException, InterruptedException, RuntimeException {
String queryUrl = this.url + "session/authenticate?method=easydb&token=" + this.token;
Expand Down Expand Up @@ -121,14 +120,14 @@ public Object[] uploadImagesForSpecimen(Specimen specimen) throws IOException, I
/**
* Run the query to create an object in Nahima
*
* @param object the object to create
* @param pool the pool to create the object in
* @param object the object to create
* @param objType the pool to create the object in
* @return the created object as it is in Nahima
*/
public JSONObject createObjectInNahima(JSONObject object, String pool) throws IOException, InterruptedException {
public JSONObject createObjectInNahima(JSONObject object, String objType) throws IOException, InterruptedException {
// docs:
// https://docs.easydb.de/en/technical/api/db/
String queryURL = this.url + "db/" + pool + "?token=" + token;
String queryURL = this.url + "db/" + objType + "?token=" + token;
// EasyDB seems to have mixed up PUT & POST, but well, we don't care
String returnValue = this.putRequest(queryURL, (new JSONArray()).put(object).toString(), new HashMap<>() {{
put("Content-Type", "application/json");
Expand All @@ -145,6 +144,26 @@ public JSONObject createObjectInNahima(JSONObject object, String pool) throws IO
return (JSONObject) (new JSONArray(returnValue)).get(0);
}

protected JSONObject loadFromCache(String id, String objectType) {
Map<String, JSONObject> typeCache = resolveCache.get(objectType);
if (typeCache != null) {
JSONObject cacheLoaded = typeCache.get(id);
if (cacheLoaded != null) {
return cacheLoaded;
}
}
return null;
}

protected void storeInCache(String id, String objectType, JSONObject result) {
Map<String, JSONObject> typeCache = resolveCache.get(objectType);
if (typeCache == null) {
typeCache = new HashMap<>();
resolveCache.put(objectType, typeCache);
}
typeCache.put(id, result);
}

/**
* Search for a string in a Nahima objecttype
*
Expand All @@ -156,11 +175,10 @@ public JSONObject createObjectInNahima(JSONObject object, String pool) throws IO
*/
public JSONObject searchForString(String searchString, String objectType, String searchMode, boolean ignoreCache) throws IOException, InterruptedException {
// check cache for results
Map<String, JSONObject> typeCache = resolveCache.get(objectType);
if (typeCache != null) {
JSONObject cacheLoaded = typeCache.get(searchString);
if (cacheLoaded != null && !ignoreCache) {
return cacheLoaded;
if (!ignoreCache) {
JSONObject fromCache = loadFromCache(searchString, objectType);
if (fromCache != null) {
return fromCache;
}
}

Expand Down Expand Up @@ -190,11 +208,7 @@ public JSONObject searchForString(String searchString, String objectType, String

// store result in cache
JSONObject result = this.postRequest(queryURL, query);
if (typeCache == null) {
typeCache = new HashMap<>();
resolveCache.put(objectType, typeCache);
}
typeCache.put(searchString, result);
storeInCache(searchString, objectType, result);

return result;
}
Expand All @@ -218,13 +232,13 @@ public JSONObject searchForString(String searchString, String objectType, boolea
* @param objectType the object type that is searched
* @return the object if there is only one, null if not
*/
public JSONObject resolveStringSearchToOne(String search, String objectType) throws IOException, InterruptedException {
public JSONObject resolveStringSearchToOne(String search, String objectType, boolean ignoreCache) throws IOException, InterruptedException {
if (search == null || objectType == null) {
log.warn("Cannot search as search " + search + " or objectType " + objectType + " is null");
return null;
}

JSONObject results = this.searchForString(search, objectType);
JSONObject results = this.searchForString(search, objectType, ignoreCache);

if (results.has("code") && results.getString("code").startsWith("error")) {
throw new RuntimeException("Failed to resolve search. Error code: " + results.getString("code"));
Expand All @@ -240,6 +254,10 @@ public JSONObject resolveStringSearchToOne(String search, String objectType) thr
}
}

public JSONObject resolveStringSearchToOne(String search, String objectType) throws IOException, InterruptedException {
return resolveStringSearchToOne(search, objectType, false);
}

/**
* Find a person in Nahima
*
Expand Down Expand Up @@ -300,6 +318,35 @@ public JSONObject resolveUnitFor(String unit, String unitSubject) throws IOExcep
return results;
}

/**
* Find a typusstatus in Nahima
*
* @param nrType the search string
* @return the nahima returned object if only one
*/
public JSONObject resolveOtherNrType(String nrType) throws IOException, InterruptedException {
JSONObject results = this.resolveStringSearchToOne(nrType, "id_typen");
// TODO: create / select correct
if (results == null && nrType != null) {
// TODO: create
JSONObject toCreate = new JSONObject(new HashMap<>() {{
put("_idx_in_objects", 0);
put("_mask", "id_typen_all_fields");
put("_objecttype", "id_typen");
put("id_typen", new JSONObject(new HashMap<>() {{
put("_id", JSONObject.NULL);
put("_version", 1);
put("name", nrType);
put("bemerkung", "Created by " + ImageCaptureApp.APP_NAME + " " + ImageCaptureApp.getAppVersion());
}}));
}});
this.createObjectInNahima(toCreate, "id_typen");
// TODO: it would be simpler to store the created in cache. But well... current format does not allow
return this.resolveStringSearchToOne(nrType, "id_typen", true);
}
return results;
}

/**
* Find a unit in Nahima
*
Expand Down
2 changes: 1 addition & 1 deletion src/main/java/edu/harvard/mcz/imagecapture/entity/fixed/WorkFlowStatus.java
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Original file line number Diff line number Diff line change
Expand Up @@ -84,7 +84,7 @@ public class WorkFlowStatus {
* indicate further progress to complete load of all data into MCZbase. Record
* is now not editable in DataShot.
*/
public static final String STAGE_DONE = "Moved to MCZbase";
public static final String STAGE_DONE = "Moved to Nahima";

/**
* Specimen record has to be deleted.
Expand Down
32 changes: 30 additions & 2 deletions src/main/java/edu/harvard/mcz/imagecapture/serializer/nahima/Specimen2JSONSerializer.java
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Original file line number Diff line number Diff line change
@@ -1,6 +1,8 @@
package edu.harvard.mcz.imagecapture.serializer.nahima;

import edu.harvard.mcz.imagecapture.ImageCaptureApp;
import edu.harvard.mcz.imagecapture.data.NahimaManager;
import edu.harvard.mcz.imagecapture.entity.Number;
import edu.harvard.mcz.imagecapture.entity.*;
import edu.harvard.mcz.imagecapture.serializer.ToJSONSerializerInterface;
import org.apache.commons.lang3.time.DateUtils;
Expand Down Expand Up @@ -40,6 +42,32 @@ public JSONObject serialize2JSON(Object target) {
result.put("_id", JSONObject.NULL);
result.put("_pool", NahimaManager.defaultPool);
// here, it already starts to get complicated, fuu.
// first, other ids, incl. specimen ID
JSONArray otherIds = new JSONArray();
for (Number otherNr : toSerialize.getNumbers()) {
Map<String, Object> otherNrMap = new HashMap<>() {{
put("andereid", otherNr.getNumber());
put("bemerkung", String.join(" ", otherNr.getNumber(), String.valueOf(otherNr.getNumberId()), otherNr.getNumberType()));
}};
try {
otherNrMap.put("typ", nahimaManager.resolveOtherNrType(otherNr.getNumberType()));
} catch (IOException | InterruptedException e) {
log.error("Failed to resolve nr type", e);
}
otherIds.put(new JSONObject(otherNrMap));
}
// also add specimen id as other id
JSONObject dataShotId = new JSONObject(new HashMap<String, Object>() {{
put("andereid", String.valueOf(toSerialize.getSpecimenId()));
}});
try {
dataShotId.put("typ", nahimaManager.resolveOtherNrType(ImageCaptureApp.APP_NAME + "-ID"));
} catch (IOException | InterruptedException e) {
log.error("Failed to resolve nr type", e);
}
otherIds.put(dataShotId);
result.put("_nested:entomologie__andereids", otherIds);
//
JSONArray reverseNestedDeterminations = new JSONArray();
for (Determination det : toSerialize.getDeterminations()) {
Map<String, Object> reverseNestedCollectionMap = new HashMap<>() {{
Expand Down Expand Up @@ -77,15 +105,15 @@ public JSONObject serialize2JSON(Object target) {
identifierPersons.put(nahimaManager.reduceAssociateForAssociation(identifierPerson));
}
} catch (IOException | InterruptedException e) {
log.info("Failed to resolve person", e);
log.error("Failed to resolve person", e);
}
reverseNestedDetermination.put("_nested:bestimmung__bestimmer_person", identifierPersons);

try {
JSONObject resolvedTypeStatus = nahimaManager.resolveTypeStatus(det.getTypeStatus());
reverseNestedDetermination.put("typusstatus", resolvedTypeStatus);
} catch (IOException | InterruptedException e) {
log.info("Failed to resolve type status", e);
log.error("Failed to resolve type status", e);
}
// TODO: other fields

Expand Down

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