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Ezequiel-ValenciaEzequiel-Valencia
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Merge pull request #1512 from virtualcell/rename-quarkus-classes-to-services
Rename DB Classes to Services
2 parents 31a8124 + 639f434 commit bb1bb16

16 files changed

Lines changed: 130 additions & 135 deletions

‎vcell-rest/src/main/java/org/vcell/restq/handlers/AdminResource.java‎

Lines changed: 9 additions & 9 deletions
Original file line numberDiff line numberDiff line change
@@ -20,8 +20,8 @@
2020
import org.eclipse.microprofile.openapi.annotations.media.Schema;
2121
import org.eclipse.microprofile.openapi.annotations.responses.APIResponse;
2222
import org.jboss.resteasy.reactive.NoCache;
23-
import org.vcell.restq.db.AdminRestDB;
24-
import org.vcell.restq.db.UserRestDB;
23+
import org.vcell.restq.services.AdminRestService;
24+
import org.vcell.restq.services.UserRestService;
2525
import org.vcell.restq.errors.exceptions.DataAccessWebException;
2626
import org.vcell.restq.errors.exceptions.NotAuthenticatedWebException;
2727
import org.vcell.restq.errors.exceptions.PermissionWebException;
@@ -41,13 +41,13 @@ public class AdminResource {
4141
@Inject
4242
SecurityIdentity securityIdentity;
4343

44-
private final AdminRestDB adminRestDB;
45-
private final UserRestDB userRestDB;
44+
private final AdminRestService adminRestService;
45+
private final UserRestService userRestService;
4646

4747
@Inject
48-
public AdminResource(AdminRestDB adminRestDB, UserRestDB userRestDB) {
49-
this.adminRestDB = adminRestDB;
50-
this.userRestDB = userRestDB;
48+
public AdminResource(AdminRestService adminRestService, UserRestService userRestService) {
49+
this.adminRestService = adminRestService;
50+
this.userRestService = userRestService;
5151
}
5252

5353
@GET
@@ -65,9 +65,9 @@ public Response getUsage() throws DataAccessWebException, NotAuthenticatedWebExc
6565
if (securityIdentity.isAnonymous()){
6666
throw new NotAuthenticatedWebException("not authenticated");
6767
}
68-
User vcellUser = userRestDB.getUserFromIdentity(securityIdentity, UserRestDB.UserRequirement.REQUIRE_USER);
68+
User vcellUser = userRestService.getUserFromIdentity(securityIdentity, UserRestService.UserRequirement.REQUIRE_USER);
6969
try {
70-
String htmlString = adminRestDB.getUsageSummaryHtml(vcellUser);
70+
String htmlString = adminRestService.getUsageSummaryHtml(vcellUser);
7171
StreamingOutput fileStream = output -> {
7272
try {
7373
Document document = new Document();

‎vcell-rest/src/main/java/org/vcell/restq/handlers/BioModelResource.java‎

Lines changed: 15 additions & 15 deletions
Original file line numberDiff line numberDiff line change
@@ -13,8 +13,8 @@
1313
import jakarta.ws.rs.core.MediaType;
1414
import org.eclipse.microprofile.openapi.annotations.Operation;
1515
import org.vcell.restq.Main;
16-
import org.vcell.restq.db.BioModelRestDB;
17-
import org.vcell.restq.db.UserRestDB;
16+
import org.vcell.restq.services.BioModelRestService;
17+
import org.vcell.restq.services.UserRestService;
1818
import org.vcell.restq.errors.exceptions.*;
1919
import org.vcell.restq.errors.exceptions.NotFoundWebException;
2020
import org.vcell.restq.models.BioModel;
@@ -30,26 +30,26 @@ public class BioModelResource {
3030
@Inject
3131
SecurityIdentity securityIdentity;
3232

33-
private final BioModelRestDB bioModelRestDB;
34-
private final UserRestDB userRestDB;
33+
private final BioModelRestService bioModelRestService;
34+
private final UserRestService userRestService;
3535

3636
@Inject
37-
public BioModelResource(BioModelRestDB bioModelRestDB, UserRestDB userRestDB) {
38-
this.bioModelRestDB = bioModelRestDB;
39-
this.userRestDB = userRestDB;
37+
public BioModelResource(BioModelRestService bioModelRestService, UserRestService userRestService) {
38+
this.bioModelRestService = bioModelRestService;
39+
this.userRestService = userRestService;
4040
}
4141

4242
@GET
4343
@Path("{bioModelID}")
4444
@Operation(operationId = "getBioModel", summary = "Get BioModel.")
4545
@Produces(MediaType.APPLICATION_JSON)
4646
public BioModel getBioModelInfo(@PathParam("bioModelID") String bioModelID) throws DataAccessWebException, NotFoundWebException, PermissionWebException, NotAuthenticatedWebException {
47-
User vcellUser = userRestDB.getUserFromIdentity(securityIdentity, UserRestDB.UserRequirement.ALLOW_ANONYMOUS);
47+
User vcellUser = userRestService.getUserFromIdentity(securityIdentity, UserRestService.UserRequirement.ALLOW_ANONYMOUS);
4848
if (vcellUser == null) {
4949
vcellUser = Main.DUMMY_USER;
5050
}
5151
try {
52-
BioModelRep bioModelRep = bioModelRestDB.getBioModelRep(new KeyValue(bioModelID), vcellUser);
52+
BioModelRep bioModelRep = bioModelRestService.getBioModelRep(new KeyValue(bioModelID), vcellUser);
5353
return BioModel.fromBioModelRep(bioModelRep);
5454
}catch (ObjectNotFoundException e) {
5555
throw new NotFoundWebException(e.getMessage(), e);
@@ -63,12 +63,12 @@ public BioModel getBioModelInfo(@PathParam("bioModelID") String bioModelID) thro
6363
@Operation(operationId = "getBioModelVCML", summary = "Get the BioModel in VCML format.")
6464
@Produces(MediaType.TEXT_XML)
6565
public String getBioModelVCML(@PathParam("bioModelID") String bioModelID) throws DataAccessWebException, NotFoundWebException, PermissionWebException, NotAuthenticatedWebException {
66-
User vcellUser = userRestDB.getUserFromIdentity(securityIdentity, UserRestDB.UserRequirement.ALLOW_ANONYMOUS);
66+
User vcellUser = userRestService.getUserFromIdentity(securityIdentity, UserRestService.UserRequirement.ALLOW_ANONYMOUS);
6767
if (vcellUser == null) {
6868
vcellUser = Main.DUMMY_USER;
6969
}
7070
try {
71-
return bioModelRestDB.getBioModel(vcellUser, new KeyValue(bioModelID));
71+
return bioModelRestService.getBioModel(vcellUser, new KeyValue(bioModelID));
7272
}catch (ObjectNotFoundException e) {
7373
throw new NotFoundWebException(e.getMessage(), e);
7474
} catch (DataAccessException e) {
@@ -112,9 +112,9 @@ public void getBioModelDiagram(@PathParam("bioModelID") String bioModelID){
112112
@Path("{bioModelID}")
113113
@Operation(operationId = "deleteBioModel", summary = "Delete the BioModel from VCell's database.")
114114
public void deleteBioModel(@PathParam("bioModelID") String bioModelID) throws DataAccessWebException, PermissionWebException, NotAuthenticatedWebException {
115-
User user = userRestDB.getUserFromIdentity(securityIdentity, UserRestDB.UserRequirement.REQUIRE_USER);;
115+
User user = userRestService.getUserFromIdentity(securityIdentity, UserRestService.UserRequirement.REQUIRE_USER);;
116116
try {
117-
bioModelRestDB.deleteBioModel(user, new KeyValue(bioModelID));
117+
bioModelRestService.deleteBioModel(user, new KeyValue(bioModelID));
118118
} catch (DataAccessException e) {
119119
throw new DataAccessWebException(e.getMessage(), e);
120120
}
@@ -128,9 +128,9 @@ public void deleteBioModel(@PathParam("bioModelID") String bioModelID) throws Da
128128
@Operation(operationId = "saveBioModel", summary = "Save's the given BioModel. Optional parameters of name and simulations to update due to math changes." +
129129
" Returns saved BioModel as VCML.")
130130
public String save(@Valid SaveBioModel saveBioModel) throws DataAccessWebException, UnprocessableContentWebException, PermissionWebException, NotAuthenticatedWebException {
131-
User user = userRestDB.getUserFromIdentity(securityIdentity, UserRestDB.UserRequirement.REQUIRE_USER);
131+
User user = userRestService.getUserFromIdentity(securityIdentity, UserRestService.UserRequirement.REQUIRE_USER);
132132
try {
133-
cbit.vcell.biomodel.BioModel savedBioModel = bioModelRestDB.save(user, saveBioModel.bioModelXML,
133+
cbit.vcell.biomodel.BioModel savedBioModel = bioModelRestService.save(user, saveBioModel.bioModelXML,
134134
saveBioModel.name.orElse(null), saveBioModel.simsRequiringUpdates.orElse(null));
135135
return XmlHelper.bioModelToXML(savedBioModel);
136136
} catch (DataAccessException e) {

vcell-rest/src/main/java/org/vcell/restq/handlers/FieldData/FieldDataResource.java renamed to vcell-rest/src/main/java/org/vcell/restq/handlers/FieldDataResource.java

Lines changed: 27 additions & 27 deletions
Original file line numberDiff line numberDiff line change
@@ -1,4 +1,4 @@
1-
package org.vcell.restq.handlers.FieldData;
1+
package org.vcell.restq.handlers;
22

33
import cbit.image.ImageException;
44
import cbit.vcell.field.io.FieldDataSpec;
@@ -17,7 +17,8 @@
1717
import org.eclipse.microprofile.openapi.annotations.Operation;
1818
import org.jboss.resteasy.reactive.PartType;
1919
import org.jboss.resteasy.reactive.RestForm;
20-
import org.vcell.restq.db.UserRestDB;
20+
import org.vcell.restq.services.FieldDataService;
21+
import org.vcell.restq.services.UserRestService;
2122
import org.vcell.restq.errors.exceptions.*;
2223
import org.vcell.restq.errors.exceptions.NotFoundWebException;
2324
import org.vcell.util.DataAccessException;
@@ -28,7 +29,6 @@
2829
import org.vcell.util.document.KeyValue;
2930
import org.vcell.util.document.User;
3031
import org.vcell.util.document.VersionableType;
31-
import org.w3c.www.http.HTTP;
3232

3333
import java.io.File;
3434
import java.io.FileNotFoundException;
@@ -48,14 +48,14 @@ public class FieldDataResource {
4848
@Inject
4949
SecurityIdentity securityIdentity;
5050

51-
private final FieldDataDB fieldDataDB;
52-
private final UserRestDB userRestDB;
51+
private final FieldDataService fieldDataService;
52+
private final UserRestService userRestService;
5353
private final String allowedFieldDataNamesRegex = "^[a-zA-Z0-9_]*$";
5454

5555
@Inject
56-
public FieldDataResource(FieldDataDB fieldDataDB, UserRestDB userRestDB){
57-
this.fieldDataDB = fieldDataDB;
58-
this.userRestDB = userRestDB;
56+
public FieldDataResource(FieldDataService fieldDataService, UserRestService userRestService){
57+
this.fieldDataService = fieldDataService;
58+
this.userRestService = userRestService;
5959
}
6060

6161

@@ -65,7 +65,7 @@ public FieldDataResource(FieldDataDB fieldDataDB, UserRestDB userRestDB){
6565
@Operation(operationId = "getAllIDs", summary = "Get all of the ids used to identify, and retrieve field data.")
6666
public ArrayList<FieldDataReference> getAllFieldDataIDs() throws DataAccessWebException, PermissionWebException, NotAuthenticatedWebException {
6767
try {
68-
return fieldDataDB.getAllFieldDataIDs(userRestDB.getUserFromIdentity(securityIdentity, UserRestDB.UserRequirement.REQUIRE_USER));
68+
return fieldDataService.getAllFieldDataIDs(userRestService.getUserFromIdentity(securityIdentity, UserRestService.UserRequirement.REQUIRE_USER));
6969
} catch (DataAccessException e) {
7070
throw new DataAccessWebException("Can't get field data ID's: " + e.getMessage(), e);
7171
}
@@ -77,9 +77,9 @@ public ArrayList<FieldDataReference> getAllFieldDataIDs() throws DataAccessWebEx
7777
@Operation(operationId = "getShapeFromID", summary = "Get the shape of the field data. That is it's size, origin, extent, times, and data identifiers.")
7878
public FieldDataShape getFieldDataShapeFromID(@PathParam("fieldDataID") String fieldDataID) throws DataAccessWebException, NotFoundWebException, PermissionWebException, NotAuthenticatedWebException {
7979
try {
80-
User user = userRestDB.getUserFromIdentity(securityIdentity, UserRestDB.UserRequirement.REQUIRE_USER);
80+
User user = userRestService.getUserFromIdentity(securityIdentity, UserRestService.UserRequirement.REQUIRE_USER);
8181
KeyValue keyValue = new KeyValue(fieldDataID);
82-
cbit.vcell.field.io.FieldDataShape results = fieldDataDB.getFieldDataShapeFromID(user, keyValue, FieldDataSpec.JOBINDEX_DEFAULT);
82+
cbit.vcell.field.io.FieldDataShape results = fieldDataService.getFieldDataShapeFromID(user, keyValue, FieldDataSpec.JOBINDEX_DEFAULT);
8383
return new FieldDataShape(results.extent, results.origin, results.iSize, results.variableInformation,results.times);
8484
} catch (DataAccessException e) {
8585
if (e.getCause() instanceof FileNotFoundException){
@@ -96,8 +96,8 @@ public FieldDataShape getFieldDataShapeFromID(@PathParam("fieldDataID") String f
9696
@Operation(operationId = "createFromSimulation", summary = "Create new field data from existing simulation results.")
9797
public void createNewFieldDataFromSimulation(@RestForm String simKeyReference, @RestForm int jobIndex, @RestForm String newFieldDataName) throws DataAccessWebException, PermissionWebException, NotAuthenticatedWebException {
9898
try {
99-
User user = userRestDB.getUserFromIdentity(securityIdentity, UserRestDB.UserRequirement.REQUIRE_USER);
100-
fieldDataDB.saveFieldDataFromSimulation(user, new KeyValue(simKeyReference), jobIndex, newFieldDataName);
99+
User user = userRestService.getUserFromIdentity(securityIdentity, UserRestService.UserRequirement.REQUIRE_USER);
100+
fieldDataService.saveFieldDataFromSimulation(user, new KeyValue(simKeyReference), jobIndex, newFieldDataName);
101101
} catch (DataAccessException e) {
102102
throw new DataAccessWebException(e.getMessage(), e);
103103
}
@@ -119,12 +119,12 @@ public FieldDataSavedResults analyzeAndCreateFieldData(@RestForm @PartType(Media
119119
@RestForm("annotation") @PartType(MediaType.TEXT_PLAIN) String annotation,
120120
@RestForm("origin") @PartType(MediaType.APPLICATION_JSON) Origin origin) throws UnprocessableContentWebException, DataAccessWebException, PermissionWebException, NotAuthenticatedWebException {
121121
try{
122-
User user = userRestDB.getUserFromIdentity(securityIdentity, UserRestDB.UserRequirement.REQUIRE_USER);
122+
User user = userRestService.getUserFromIdentity(securityIdentity, UserRestService.UserRequirement.REQUIRE_USER);
123123
if (!Pattern.matches(allowedFieldDataNamesRegex, fileName) || fileName.length() > 100 || fileName.isEmpty()){
124124
throw new UnprocessableContentWebException("Invalid file name.");
125125
}
126-
FieldData fieldData = fieldDataDB.analyzeFieldDataFromFile(file, fileName);
127-
ExternalDataIdentifier edi = fieldDataDB.saveNewFieldDataFromFile(fileName,
126+
FieldData fieldData = fieldDataService.analyzeFieldDataFromFile(file, fileName);
127+
ExternalDataIdentifier edi = fieldDataService.saveNewFieldDataFromFile(fileName,
128128
channelNames, fieldData.shortSpecData, annotation,
129129
user, times, origin, extent, iSize);
130130
return new FieldDataSavedResults(edi.getName(), edi.getKey().toString());
@@ -146,12 +146,12 @@ public FieldDataSavedResults analyzeAndCreateFieldData(@RestForm @PartType(Media
146146
public FieldDataSavedResults createFromFileWithDefaults(@RestForm @PartType(MediaType.APPLICATION_OCTET_STREAM) File file,
147147
@RestForm String fieldDataName) throws UnprocessableContentWebException, DataAccessWebException, PermissionWebException, NotAuthenticatedWebException {
148148
try{
149-
User user = userRestDB.getUserFromIdentity(securityIdentity, UserRestDB.UserRequirement.REQUIRE_USER);
149+
User user = userRestService.getUserFromIdentity(securityIdentity, UserRestService.UserRequirement.REQUIRE_USER);
150150
if (!Pattern.matches(allowedFieldDataNamesRegex, fieldDataName) || fieldDataName.length() > 100 || fieldDataName.isEmpty()){
151151
throw new UnprocessableContentWebException("Invalid file name.");
152152
}
153-
FieldData fieldData = fieldDataDB.analyzeFieldDataFromFile(file, fieldDataName);
154-
ExternalDataIdentifier edi = fieldDataDB.saveNewFieldDataFromFile(fieldDataName, fieldData.varNames, fieldData.shortSpecData,
153+
FieldData fieldData = fieldDataService.analyzeFieldDataFromFile(file, fieldDataName);
154+
ExternalDataIdentifier edi = fieldDataService.saveNewFieldDataFromFile(fieldDataName, fieldData.varNames, fieldData.shortSpecData,
155155
fieldData.annotation, user, fieldData.times, fieldData.origin, fieldData.extent, fieldData.isize);
156156
return new FieldDataSavedResults(edi.getName(), edi.getKey().toString());
157157
} catch (DataFormatException e){
@@ -172,11 +172,11 @@ public FieldDataSavedResults createFromFileWithDefaults(@RestForm @PartType(Medi
172172
"Filenames must be lowercase alphanumeric, and can contain underscores.")
173173
public FieldData analyzeFile(@RestForm File file, @RestForm String fileName) throws UnprocessableContentWebException, DataAccessWebException, PermissionWebException, NotAuthenticatedWebException {
174174
try{
175-
userRestDB.getUserFromIdentity(securityIdentity, UserRestDB.UserRequirement.REQUIRE_USER);
175+
userRestService.getUserFromIdentity(securityIdentity, UserRestService.UserRequirement.REQUIRE_USER);
176176
if (!Pattern.matches(allowedFieldDataNamesRegex, fileName) || fileName.length() > 100 || fileName.isEmpty()){
177177
throw new UnprocessableContentWebException("Invalid file name.");
178178
}
179-
return fieldDataDB.analyzeFieldDataFromFile(file, fileName);
179+
return fieldDataService.analyzeFieldDataFromFile(file, fileName);
180180
} catch (DataFormatException e){
181181
throw new UnprocessableContentWebException(e.getMessage(), e);
182182
} catch (DataAccessException e){
@@ -196,8 +196,8 @@ public FieldData analyzeFile(@RestForm File file, @RestForm String fileName) thr
196196
public FieldDataSavedResults createNewFieldDataFromSpecification(FieldData saveFieldData) throws UnprocessableContentWebException, DataAccessWebException, PermissionWebException, NotAuthenticatedWebException {
197197
FieldDataSavedResults fieldDataSavedResults;
198198
try{
199-
User user = userRestDB.getUserFromIdentity(securityIdentity, UserRestDB.UserRequirement.REQUIRE_USER);
200-
ExternalDataIdentifier edi = fieldDataDB.saveNewFieldDataFromFile(saveFieldData.name,
199+
User user = userRestService.getUserFromIdentity(securityIdentity, UserRestService.UserRequirement.REQUIRE_USER);
200+
ExternalDataIdentifier edi = fieldDataService.saveNewFieldDataFromFile(saveFieldData.name,
201201
saveFieldData.varNames, saveFieldData.shortSpecData, saveFieldData.doubleSpecData, saveFieldData.annotation,
202202
user, saveFieldData.times, saveFieldData.origin, saveFieldData.extent, saveFieldData.isize);
203203
fieldDataSavedResults = new FieldDataSavedResults(edi.getName(), edi.getKey().toString());
@@ -219,8 +219,8 @@ public FieldDataSavedResults createNewFieldDataFromSpecification(FieldData saveF
219219
@Operation(operationId = "copyModelsFieldData", summary = "Copy all existing field data from a BioModel/MathModel that you have access to, but don't own.")
220220
public Hashtable<String, ExternalDataIdentifier> copyFieldData(SourceModel sourceModel) throws UnprocessableContentWebException, DataAccessWebException, PermissionWebException, NotAuthenticatedWebException {
221221
try {
222-
User user = userRestDB.getUserFromIdentity(securityIdentity, UserRestDB.UserRequirement.REQUIRE_USER);
223-
return fieldDataDB.copyModelsFieldData(user, new KeyValue(sourceModel.modelID()), sourceModel.modelType.getName());
222+
User user = userRestService.getUserFromIdentity(securityIdentity, UserRestService.UserRequirement.REQUIRE_USER);
223+
return fieldDataService.copyModelsFieldData(user, new KeyValue(sourceModel.modelID()), sourceModel.modelType.getName());
224224
} catch (MathException | XmlParseException | ExpressionException e){
225225
throw new UnprocessableContentWebException(e.getMessage(), e);
226226
} catch (DataAccessException e){
@@ -234,9 +234,9 @@ public Hashtable<String, ExternalDataIdentifier> copyFieldData(SourceModel sourc
234234
@Operation(operationId = "delete", summary = "Delete the selected field data.")
235235
public void deleteFieldData(@PathParam("fieldDataID") String fieldDataID) throws DataAccessWebException, PermissionWebException, NotAuthenticatedWebException {
236236
try{
237-
ExternalDataIdentifier edi = new ExternalDataIdentifier(new KeyValue(fieldDataID), userRestDB.getUserFromIdentity(securityIdentity, UserRestDB.UserRequirement.REQUIRE_USER),
237+
ExternalDataIdentifier edi = new ExternalDataIdentifier(new KeyValue(fieldDataID), userRestService.getUserFromIdentity(securityIdentity, UserRestService.UserRequirement.REQUIRE_USER),
238238
null);
239-
fieldDataDB.deleteFieldData(edi);
239+
fieldDataService.deleteFieldData(edi);
240240
} catch (DataAccessException e) {
241241
throw new DataAccessWebException(e.getMessage(), e);
242242
}

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