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Merge pull request 'new-is-app-with-new-msro' (#13) from new-is-app-with-new-msro into new-is-app 

Reviewed-on: #13
This commit is contained in:
Michele Artini 2023-03-21 12:15:25 +01:00
parent 3faf80e84d 806f8e9227
commit 8c3ae35dc4
108 changed files with 4025 additions and 271 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

6
apps/dnet-is-application/pom.xml
View File

@ -20,6 +20,12 @@
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>eu.dnetlib.dhp</groupId>
<artifactId>dnet-wf-service</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>eu.dnetlib.dhp</groupId>
<artifactId>dnet-data-services</artifactId>

8
apps/dnet-is-application/src/main/java/eu/dnetlib/MainDBConfig.java
View File

@ -20,7 +20,11 @@ import org.springframework.transaction.annotation.EnableTransactionManagement;
@Configuration
@EnableTransactionManagement
@EnableJpaRepositories(entityManagerFactoryRef = "mainEntityManagerFactory", transactionManagerRef = "mainTransactionManager", basePackages = {
"eu.dnetlib.is", "eu.dnetlib.data.mdstore", "eu.dnetlib.msro"
"eu.dnetlib.is",
"eu.dnetlib.common",
"eu.dnetlib.manager.history",
"eu.dnetlib.manager.wf",
"eu.dnetlib.data.mdstore"
})
public class MainDBConfig {
@ -38,7 +42,7 @@ public class MainDBConfig {
@Qualifier("mainDataSource") final DataSource ds) {
return builder
.dataSource(ds)
.packages("eu.dnetlib.is.model", "eu.dnetlib.msro.model", "eu.dnetlib.data.mdstore.model")
.packages("eu.dnetlib.is.model", "eu.dnetlib.manager.history.model", "eu.dnetlib.common.model", "eu.dnetlib.manager.wf.model", "eu.dnetlib.data.mdstore.model")
.persistenceUnit("is")
.build();
}

1
apps/dnet-is-application/src/main/java/eu/dnetlib/data/mdstore/ZeppelinAjaxController.java
View File

@ -21,7 +21,6 @@ public class ZeppelinAjaxController extends AbstractDnetController {
@GetMapping("/templates")
public List<String> getTemplates() throws MDStoreManagerException {
try {
// if (zeppelinClient.get)
return zeppelinClient.listTemplates();
} catch (final Throwable e) {
throw new MDStoreManagerException("Zeppelin is unreachable", e);

4
apps/dnet-is-application/src/main/java/eu/dnetlib/dsm/DsmAjaxController.java
View File

@ -40,9 +40,9 @@ public class DsmAjaxController extends AbstractDnetController {
private ProtocolService protocolService;
@GetMapping("/browsableFields")
public List<KeyValue> browsableFields() {
public List<KeyValue<String>> browsableFields() {
return Arrays.stream(DsmBrowsableFields.values())
.map(f -> new KeyValue(f.name(), f.desc))
.map(f -> new KeyValue<>(f.name(), f.desc))
.collect(Collectors.toList());
}

41
apps/dnet-is-application/src/main/java/eu/dnetlib/is/email/EmailTemplateController.java Normal file
View File

@ -0,0 +1,41 @@
package eu.dnetlib.is.email;
import java.util.List;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.web.bind.annotation.DeleteMapping;
import org.springframework.web.bind.annotation.GetMapping;
import org.springframework.web.bind.annotation.PathVariable;
import org.springframework.web.bind.annotation.PostMapping;
import org.springframework.web.bind.annotation.RequestBody;
import org.springframework.web.bind.annotation.RequestMapping;
import org.springframework.web.bind.annotation.RestController;
import eu.dnetlib.common.controller.AbstractDnetController;
import eu.dnetlib.common.model.EmailTemplate;
import eu.dnetlib.notifications.mail.EmailService;
@RestController
@RequestMapping("/ajax/templates/email")
public class EmailTemplateController extends AbstractDnetController {
@Autowired
protected EmailService emailService;
@GetMapping("/")
public List<EmailTemplate> listEmailTemplates() {
return emailService.listEmailTemplates();
}
@PostMapping("/")
public List<EmailTemplate> saveEmailTemplate(@RequestBody final EmailTemplate email) {
emailService.saveEmailTemplate(email);
return emailService.listEmailTemplates();
}
@DeleteMapping("/{id}")
public List<EmailTemplate> deleteEmailTemplate(@PathVariable final String id) {
emailService.deleteEmailTemplate(id);
return emailService.listEmailTemplates();
}
}

4
apps/dnet-is-application/src/main/java/eu/dnetlib/is/importer/OldProfilesImporter.java
View File

@ -1,6 +1,6 @@
package eu.dnetlib.is.importer;
import java.util.Date;
import java.time.LocalDateTime;
import javax.transaction.Transactional;
@ -47,7 +47,7 @@ public class OldProfilesImporter {
final Document doc = DocumentHelper.parseText(xml);
final String id = StringUtils.substringBefore(doc.valueOf("//RESOURCE_IDENTIFIER/@value"), "_");
final Date now = new Date();
final LocalDateTime now = LocalDateTime.now();
final SimpleResource res = new SimpleResource();
res.setId(id);

14
apps/dnet-is-application/src/main/java/eu/dnetlib/is/importer/WfHistoryImporter.java
View File

@ -1,11 +1,13 @@
package eu.dnetlib.is.importer;
import java.io.File;
import java.util.Date;
import java.time.Instant;
import java.time.LocalDateTime;
import java.util.Iterator;
import java.util.LinkedHashMap;
import java.util.Map;
import java.util.Map.Entry;
import java.util.TimeZone;
import org.apache.commons.lang3.BooleanUtils;
import org.apache.commons.lang3.math.NumberUtils;
@ -17,8 +19,8 @@ import org.springframework.stereotype.Service;
import com.fasterxml.jackson.databind.JsonNode;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.msro.history.repository.WfProcessExecutionRepository;
import eu.dnetlib.msro.model.history.WfProcessExecution;
import eu.dnetlib.manager.history.model.WfProcessExecution;
import eu.dnetlib.manager.history.repository.WfProcessExecutionRepository;
@Service
public class WfHistoryImporter {
@ -53,8 +55,10 @@ public class WfHistoryImporter {
wf.setDsApi(node.get("dataprovider:interface").asText());
}
wf.setStartDate(new Date(NumberUtils.toLong(node.get("system:startDate").asText())));
wf.setEndDate(new Date(NumberUtils.toLong(node.get("system:endDate").asText())));
wf.setStartDate(LocalDateTime
.ofInstant(Instant.ofEpochMilli(NumberUtils.toLong(node.get("system:startDate").asText())), TimeZone.getDefault().toZoneId()));
wf.setEndDate(LocalDateTime.ofInstant(Instant.ofEpochMilli(NumberUtils.toLong(node.get("system:endDate").asText())), TimeZone.getDefault().toZoneId()));
if (BooleanUtils.toBoolean(node.get("system:isCompletedSuccessfully").asText())) {
wf.setStatus("success");

36
apps/dnet-is-application/src/main/java/eu/dnetlib/is/info/InfoAjaxController.java
View File

@ -56,30 +56,30 @@ public class InfoAjaxController extends AbstractDnetController {
return res;
}
private InfoSection<KeyValue> jvm() {
final InfoSection<KeyValue> jvm = new InfoSection<>("JVM");
jvm.getData().add(new KeyValue("JVM Name", mxbean.getVmName()));
jvm.getData().add(new KeyValue("JVM Vendor", mxbean.getVmVendor()));
jvm.getData().add(new KeyValue("JVM Version", mxbean.getVmVersion()));
jvm.getData().add(new KeyValue("JVM Spec Name", mxbean.getSpecName()));
jvm.getData().add(new KeyValue("JVM Spec Vendor", mxbean.getSpecVendor()));
jvm.getData().add(new KeyValue("JVM Spec Version", mxbean.getSpecVersion()));
jvm.getData().add(new KeyValue("Running JVM Name", mxbean.getName()));
jvm.getData().add(new KeyValue("Management Spec Version", mxbean.getManagementSpecVersion()));
private InfoSection<KeyValue<String>> jvm() {
final InfoSection<KeyValue<String>> jvm = new InfoSection<>("JVM");
jvm.getData().add(new KeyValue<>("JVM Name", mxbean.getVmName()));
jvm.getData().add(new KeyValue<>("JVM Vendor", mxbean.getVmVendor()));
jvm.getData().add(new KeyValue<>("JVM Version", mxbean.getVmVersion()));
jvm.getData().add(new KeyValue<>("JVM Spec Name", mxbean.getSpecName()));
jvm.getData().add(new KeyValue<>("JVM Spec Vendor", mxbean.getSpecVendor()));
jvm.getData().add(new KeyValue<>("JVM Spec Version", mxbean.getSpecVersion()));
jvm.getData().add(new KeyValue<>("Running JVM Name", mxbean.getName()));
jvm.getData().add(new KeyValue<>("Management Spec Version", mxbean.getManagementSpecVersion()));
return jvm;
}
private InfoSection<KeyValue> args() {
final InfoSection<KeyValue> libs = new InfoSection<>("Arguments");
libs.getData().add(new KeyValue("Input arguments", StringUtils.join(mxbean.getInputArguments(), " ")));
private InfoSection<KeyValue<String>> args() {
final InfoSection<KeyValue<String>> libs = new InfoSection<>("Arguments");
libs.getData().add(new KeyValue<>("Input arguments", StringUtils.join(mxbean.getInputArguments(), " ")));
return libs;
}
private List<InfoSection<KeyValue>> props() {
final List<InfoSection<KeyValue>> res = new ArrayList<>();
private List<InfoSection<KeyValue<?>>> props() {
final List<InfoSection<KeyValue<?>>> res = new ArrayList<>();
configurableEnvironment.getPropertySources().forEach(ps -> {
final InfoSection<KeyValue> section = new InfoSection<>("Properties: " + ps.getName());
final InfoSection<KeyValue<?>> section = new InfoSection<>("Properties: " + ps.getName());
addAllProperties(section, ps);
res.add(section);
});
@ -87,13 +87,13 @@ public class InfoAjaxController extends AbstractDnetController {
return res;
}
private void addAllProperties(final InfoSection<KeyValue> res, final PropertySource<?> ps) {
private void addAllProperties(final InfoSection<KeyValue<?>> res, final PropertySource<?> ps) {
if (ps instanceof CompositePropertySource) {
final CompositePropertySource cps = (CompositePropertySource) ps;
cps.getPropertySources().forEach(x -> addAllProperties(res, x));
} else if (ps instanceof EnumerablePropertySource<?>) {
final EnumerablePropertySource<?> eps = (EnumerablePropertySource<?>) ps;
Arrays.asList(eps.getPropertyNames()).forEach(k -> res.getData().add(new KeyValue(k, eps.getProperty(k))));
Arrays.asList(eps.getPropertyNames()).forEach(k -> res.getData().add(new KeyValue<>(k, eps.getProperty(k))));
} else {}
}

8
apps/dnet-is-application/src/main/java/eu/dnetlib/is/info/KeyValue.java
View File

@ -1,11 +1,11 @@
package eu.dnetlib.is.info;
public class KeyValue {
public class KeyValue<T> {
private final String k;
private final Object v;
private final T v;
public KeyValue(final String k, final Object v) {
public KeyValue(final String k, final T v) {
this.k = k;
this.v = v;
}
@ -14,7 +14,7 @@ public class KeyValue {
return k;
}
public Object getV() {
public T getV() {
return v;
}

3
apps/dnet-is-application/src/main/java/eu/dnetlib/is/resource/ResourceAjaxController.java
View File

@ -25,11 +25,12 @@ public class ResourceAjaxController extends AbstractResourceController {
@PostMapping("/")
public SimpleResource newResource(@RequestParam final String name,
@RequestParam final String type,
@RequestParam(required = false, defaultValue = "") final String subtype,
@RequestParam(required = false, defaultValue = "") final String description,
@RequestParam final String content)
throws InformationServiceException {
return service.saveNewResource(name, type, description, content);
return service.saveNewResource(name, type, subtype, description, content);
}
@DeleteMapping("/{resId}")

36
apps/dnet-is-application/src/main/java/eu/dnetlib/manager/wf/WfHistoryAjaxController.java Normal file
View File

@ -0,0 +1,36 @@
package eu.dnetlib.manager.wf;
import java.util.List;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.web.bind.annotation.GetMapping;
import org.springframework.web.bind.annotation.PathVariable;
import org.springframework.web.bind.annotation.RequestMapping;
import org.springframework.web.bind.annotation.RequestParam;
import org.springframework.web.bind.annotation.RestController;
import eu.dnetlib.common.controller.AbstractDnetController;
import eu.dnetlib.manager.history.WorkflowLogger;
import eu.dnetlib.manager.history.model.WfProcessExecution;
@RestController
@RequestMapping("/ajax/wf_history")
public class WfHistoryAjaxController extends AbstractDnetController {
@Autowired
private WorkflowLogger logger;
@GetMapping("/")
public List<WfProcessExecution> history(
@RequestParam(required = true) final int total,
@RequestParam(required = false) final Long from,
@RequestParam(required = false) final Long to) {
return logger.history(total, from, to);
}
@GetMapping("/{processId}")
public WfProcessExecution getProcessExecution(@PathVariable final String processId) {
return logger.getProcessExecution(processId);
}
}

41
apps/dnet-is-application/src/main/java/eu/dnetlib/manager/wf/WfInstancesController.java Normal file
View File

@ -0,0 +1,41 @@
package eu.dnetlib.manager.wf;
import java.util.List;
import java.util.stream.Collectors;
import org.springframework.web.bind.annotation.GetMapping;
import org.springframework.web.bind.annotation.PathVariable;
import org.springframework.web.bind.annotation.RequestMapping;
import org.springframework.web.bind.annotation.RequestParam;
import org.springframework.web.bind.annotation.RestController;
import eu.dnetlib.common.controller.AbstractDnetController;
import eu.dnetlib.is.info.KeyValue;
import eu.dnetlib.manager.wf.model.WorkflowInstance;
@RestController
@RequestMapping("/ajax/wf_instances")
public class WfInstancesController extends AbstractDnetController {
private WorkflowManagerService wfManagerService;
@GetMapping("/instance/{id}")
public WorkflowInstance getWfInstance(@PathVariable final String id) throws Exception {
return wfManagerService.findWorkflowInstance(id);
}
@GetMapping("/search")
public List<KeyValue<String>> listWfInstances(@RequestParam final String section) throws Exception {
return wfManagerService.streamWfInstancesBySection(section)
.map(x -> new KeyValue<>(x.getId(), x.getName()))
.collect(Collectors.toList());
}
@GetMapping("/sections")
public List<KeyValue<Long>> listWfFamilies() throws Exception {
return wfManagerService.streamSections()
.map(x -> new KeyValue<>(x.getValue(), x.getCount()))
.collect(Collectors.toList());
}
}

49
apps/dnet-is-application/src/main/java/eu/dnetlib/msro/history/WfHistoryAjaxController.java
View File

@ -1,49 +0,0 @@
package eu.dnetlib.msro.history;
import java.util.Date;
import java.util.List;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.data.domain.PageRequest;
import org.springframework.data.domain.Sort;
import org.springframework.web.bind.annotation.GetMapping;
import org.springframework.web.bind.annotation.PathVariable;
import org.springframework.web.bind.annotation.RequestMapping;
import org.springframework.web.bind.annotation.RequestParam;
import org.springframework.web.bind.annotation.RestController;
import eu.dnetlib.msro.history.repository.WfProcessExecutionRepository;
import eu.dnetlib.msro.model.history.WfProcessExecution;
@RestController
@RequestMapping("/ajax/wfs")
public class WfHistoryAjaxController {
@Autowired
private WfProcessExecutionRepository wfProcessExecutionRepository;
@Deprecated
public static final int MAX_NUMBER_OF_RECENT_WFS = 100;
@GetMapping("/")
public List<WfProcessExecution> history(
@RequestParam(required = true) final int total,
@RequestParam(required = false) final Long from,
@RequestParam(required = false) final Long to) {
if (from == null && to == null) {
return wfProcessExecutionRepository.findAll(PageRequest.of(0, total, Sort.by("endDate").descending())).toList();
} else if (from == null) {
return wfProcessExecutionRepository.findByEndDateBetweenOrderByEndDateDesc(new Date(0), new Date(to));
} else if (to == null) {
return wfProcessExecutionRepository.findByEndDateBetweenOrderByEndDateDesc(new Date(from), new Date());
} else {
return wfProcessExecutionRepository.findByEndDateBetweenOrderByEndDateDesc(new Date(from), new Date(to));
}
}
@GetMapping("/{processId}")
public WfProcessExecution getProcess(@PathVariable final String processId) {
return wfProcessExecutionRepository.findById(processId).get();
}
}

11
apps/dnet-is-application/src/main/resources/application.properties
View File

@ -3,6 +3,8 @@ server.port=8280
server.public_url =
server.public_desc = API Base URL
dnet.configuration.infrastructure = LOCAL DEV
spring.profiles.active=dev
maven.pom.path = /META-INF/maven/eu.dnetlib.dhp/dnet-is-application/effective-pom.xml
@ -57,5 +59,12 @@ dhp.mdstore-manager.hadoop.zeppelin.login =
dhp.mdstore-manager.hadoop.zeppelin.password =
dhp.mdstore-manager.hadoop.zeppelin.name-prefix = mdstoreManager
# Email Configuration
dnet.configuration.mail.sender.email =
dnet.configuration.mail.sender.name =
dnet.configuration.mail.cc =
dnet.configuration.mail.smtp.host =
dnet.configuration.mail.smtp.port = 25
dnet.configuration.mail.smtp.user =
dnet.configuration.mail.smtp.password =

4
frontends/dnet-is-application/src/app/app-routing.module.ts
View File

@ -9,6 +9,8 @@ import { ContextViewerComponent, ContextsComponent } from './contexts/contexts.c
import { DsmSearchComponent, DsmResultsComponent, DsmApiComponent } from './dsm/dsm.component';
import { MdstoreInspectorComponent, MdstoresComponent } from './mdstores/mdstores.component';
import { CleanerTesterComponent } from './cleaner-tester/cleaner-tester.component';
import { EmailsComponent } from './emails/emails.component';
import { WfInstancesComponent } from './wf-instances/wf-instances.component';
const routes: Routes = [
{ path: "", redirectTo: 'info', pathMatch: 'full' },
@ -17,6 +19,8 @@ const routes: Routes = [
{ path: "adv_resources/context", component: ContextsComponent },
{ path: "adv_resources/vocabulary", component: VocabulariesComponent },
{ path: "adv_resources/protocol", component: ProtocolsComponent },
{ path: "adv_resources/email", component: EmailsComponent },
{ path: "wfs", component: WfInstancesComponent },
{ path: "wf_history", component: WfHistoryComponent },
{ path: "ctx_viewer", component: ContextViewerComponent },
{ path: "voc_editor", component: VocabularyEditorComponent },

11
frontends/dnet-is-application/src/app/app.module.ts
View File

@ -36,6 +36,9 @@ import { MatProgressSpinnerModule } from '@angular/material/progress-spinner';
import { SpinnerHttpInterceptor } from './common/spinner.service';
import { MdstoresComponent, MdstoreInspectorComponent, MDStoreVersionsDialog, AddMDStoreDialog } from './mdstores/mdstores.component';
import { CleanerTesterComponent } from './cleaner-tester/cleaner-tester.component';
import { EmailDialog, EmailsComponent } from './emails/emails.component';
import { WfInstancesComponent } from './wf-instances/wf-instances.component';
import { MatTabsModule } from '@angular/material/tabs';
@NgModule({
declarations: [
@ -66,7 +69,10 @@ import { CleanerTesterComponent } from './cleaner-tester/cleaner-tester.componen
MdstoreInspectorComponent,
MDStoreVersionsDialog,
AddMDStoreDialog,
CleanerTesterComponent
CleanerTesterComponent,
EmailsComponent,
EmailDialog,
WfInstancesComponent
],
imports: [
BrowserModule,
@ -95,7 +101,8 @@ import { CleanerTesterComponent } from './cleaner-tester/cleaner-tester.componen
ReactiveFormsModule,
MatSnackBarModule,
MatPaginatorModule,
MatProgressSpinnerModule
MatProgressSpinnerModule,
MatTabsModule
],
providers: [{
provide: HTTP_INTERCEPTORS,

27
frontends/dnet-is-application/src/app/common/is.model.ts
View File

@ -54,6 +54,7 @@ export interface SimpleResource {
id: string,
name: string,
type: string,
subtype?: string,
description?: string,
creationDate?: string,
modificationDate?: string
@ -198,3 +199,29 @@ export interface MDStoreRecord {
dateOfTransformation: string,
provenance: any
}
export interface EmailTemplate {
id: string,
description: string,
subject: string,
message: string
}
export interface WfInstance {
id: string,
details: Map<string, string>,
priority: number,
dsId?: string,
dsName?: string,
apiId?: string,
enabled: boolean,
configured: boolean,
schedulingEnabled: boolean,
cronExpression?: string,
cronMinInterval?: number,
workflow: string,
destroyWf?: string,
systemParams: Map<string, string>,
userParams: Map<string, string>
}

48
frontends/dnet-is-application/src/app/common/is.service.ts
View File

@ -1,6 +1,6 @@
import { Injectable } from '@angular/core';
import { HttpClient, HttpHeaders, HttpParams } from '@angular/common/http';
import { Page, DsmConf, ResourceType, Protocol, WfHistoryEntry, SimpleResource, Context, ContextNode, Vocabulary, VocabularyTerm, KeyValue, BrowseTerm, Datasource, MDStore, MDStoreVersion, MDStoreRecord } from './is.model';
import { Page, DsmConf, ResourceType, Protocol, WfHistoryEntry, SimpleResource, Context, ContextNode, Vocabulary, VocabularyTerm, KeyValue, BrowseTerm, Datasource, MDStore, MDStoreVersion, MDStoreRecord, EmailTemplate } from './is.model';
import { FormGroup } from '@angular/forms';
import { MatSnackBar } from '@angular/material/snack-bar';
@ -72,11 +72,12 @@ export class ISService {
});
}
addSimpleResource(name: string, type: string, description: string, content: string, onSuccess: Function, relatedForm?: FormGroup): void {
addSimpleResource(name: string, type: string, subtype: string, description: string, content: string, onSuccess: Function, relatedForm?: FormGroup): void {
const headers = new HttpHeaders().set('Content-Type', 'application/x-www-form-urlencoded')
let body = new HttpParams()
.set('name', name)
.set('type', type)
.set('subtype', subtype)
.set('description', description)
.set('content', content);
this.client.post<void>('/ajax/resources/', body, { headers: headers }).subscribe({
@ -98,7 +99,7 @@ export class ISService {
if (from && from > 0) { params = params.append('from', from); }
if (to && to > 0) { params = params.append('to', to); }
this.client.get<WfHistoryEntry[]>('/ajax/wfs/', { params: params }).subscribe({
this.client.get<WfHistoryEntry[]>('/ajax/wf_history/', { params: params }).subscribe({
next: data => onSuccess(data),
error: error => this.showError(error)
});
@ -328,6 +329,47 @@ export class ISService {
});
}
loadEmailTemplates(onSuccess: Function): void {
this.client.get<void>('./ajax/templates/email/').subscribe({
next: data => onSuccess(data),
error: error => this.showError(error)
});
}
saveEmailTemplate(email: EmailTemplate, onSuccess: Function, relatedForm?: FormGroup): void {
this.client.post<void>('./ajax/templates/email/', email).subscribe({
next: data => onSuccess(data),
error: error => this.showError(error, relatedForm)
});
}
deleteEmailTemplate(id: string, onSuccess: Function): void {
this.client.delete<void>('./ajax/templates/email/' + encodeURIComponent(id)).subscribe({
next: data => onSuccess(data),
error: error => this.showError(error)
});
}
loadWfIntancesSections(onSuccess: Function): void {
this.client.get<void>('./ajax/wf_instances/sections').subscribe({
next: data => onSuccess(data),
error: error => this.showError(error)
});
}
loadWfIntances(section: string, onSuccess: Function): void {
this.client.get<void>('./ajax/wf_instances/search?section=' + encodeURIComponent(section)).subscribe({
next: data => onSuccess(data),
error: error => this.showError(error)
});
}
loadWfIntance(id: string, onSuccess: Function): void {
this.client.get<void>('./ajax/wf_instances/instance/' + encodeURIComponent(id)).subscribe({
next: data => onSuccess(data),
error: error => this.showError(error)
});
}
private showError(error: any, form?: FormGroup) {

41
frontends/dnet-is-application/src/app/emails/email-dialog.html Normal file
View File

@ -0,0 +1,41 @@
<form [formGroup]="emailForm" (ngSubmit)="onSubmit()">
<h1 mat-dialog-title *ngIf="emailForm.get('id')?.value">Edit Email Template</h1>
<h1 mat-dialog-title *ngIf="!emailForm.get('id')?.value">New Email Template</h1>
<div mat-dialog-content>
<mat-form-field appearance="fill" floatLabel="always" style="width: 100%;" *ngIf="emailForm.get('id')?.value">
<mat-label>ID</mat-label>
<input matInput formControlName="id" readonly="readonly" />
</mat-form-field>
<mat-form-field appearance="fill" floatLabel="always" style="width: 100%;">
<mat-label>Description</mat-label>
<input matInput formControlName="description" />
<mat-error *ngIf="emailForm.get('description')?.invalid">This field is <strong>required</strong></mat-error>
</mat-form-field>
<mat-form-field appearance="fill" floatLabel="always" style="width: 100%;">
<mat-label>Email: subject</mat-label>
<input matInput formControlName="subject" />
<mat-error *ngIf="emailForm.get('subject')?.invalid">This field is <strong>required</strong></mat-error>
</mat-form-field>
<mat-form-field appearance="fill" floatLabel="always" style="width: 100%;">
<mat-label>Email: message</mat-label>
<textarea matInput formControlName="message" required rows="16" style="font-size: 0.8em;"></textarea>
<mat-error *ngIf="emailForm.get('message')?.invalid">This field is <strong>required</strong></mat-error>
</mat-form-field>
</div>
<div mat-dialog-actions>
<button mat-stroked-button color="primary" type="submit" [disabled]="!emailForm.valid">Submit</button>
<button mat-stroked-button color="primary" mat-dialog-close>Close</button>
<mat-error *ngIf="emailForm.errors?.['serverError']">
{{ emailForm.errors?.['serverError'] }}
</mat-error>
</div>
</form>

0
frontends/dnet-is-application/src/app/emails/emails.component.css Normal file
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42
frontends/dnet-is-application/src/app/emails/emails.component.html Normal file
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@ -0,0 +1,42 @@
<h2>Email Templates</h2>
<button mat-stroked-button color="primary" (click)="openAddEmailTemplateDialog()">
<mat-icon fontIcon="add"></mat-icon>
create a new template
</button>
<mat-form-field appearance="fill" floatLabel="always" style="width: 100%; margin-top: 10px;">
<mat-label>Filter</mat-label>
<input matInput (keyup)="applyFilter($event)" placeholder="Filter..." #input />
</mat-form-field>
<table mat-table [dataSource]="emailsDatasource" matSort class="mat-elevation-z8">
<ng-container matColumnDef="id">
<th mat-header-cell *matHeaderCellDef style="width: 25%;" mat-sort-header sortActionDescription="Sort by ID"> Id
</th>
<td mat-cell *matCellDef="let element">
<a (click)="openEditEmailTemplateDialog(element)">{{element.id}}</a>
</td>
</ng-container>
<ng-container matColumnDef="description">
<th mat-header-cell *matHeaderCellDef mat-sort-header sortActionDescription="Sort by Description"> Description </th>
<td mat-cell *matCellDef="let element"> {{element.description}} </td>
</ng-container>
<ng-container matColumnDef="buttons">
<th mat-header-cell *matHeaderCellDef style="text-align: right;" style="width: 20%"></th>
<td mat-cell *matCellDef="let element" class="table-buttons">
<button mat-stroked-button color="warn" (click)="deleteEmailTemplate(element)">delete</button>
</td>
</ng-container>
<tr mat-header-row *matHeaderRowDef="colums"></tr>
<tr mat-row *matRowDef="let row; columns: colums;"></tr>
<!-- Row shown when there is no matching data. -->
<tr class="mat-row" *matNoDataRow>
<td class="mat-cell" colspan="4" style="padding: 0 16px;">No data matching the filter "{{input.value}}"</td>
</tr>
</table>

98
frontends/dnet-is-application/src/app/emails/emails.component.ts Normal file
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@ -0,0 +1,98 @@
import { AfterViewInit, Component, Inject, OnInit, ViewChild } from '@angular/core';
import { FormControl, FormGroup, Validators } from '@angular/forms';
import { MatDialog, MatDialogRef, MAT_DIALOG_DATA } from '@angular/material/dialog';
import { MatSort } from '@angular/material/sort';
import { MatTableDataSource } from '@angular/material/table';
import { ActivatedRoute } from '@angular/router';
import { EmailTemplate } from '../common/is.model';
import { ISService } from '../common/is.service';
@Component({
selector: 'app-emails',
templateUrl: './emails.component.html',
styleUrls: ['./emails.component.css']
})
export class EmailsComponent implements OnInit, AfterViewInit {
emailsDatasource: MatTableDataSource<EmailTemplate> = new MatTableDataSource<EmailTemplate>([]);
colums: string[] = ['id', 'description', 'buttons'];
@ViewChild(MatSort) sort: MatSort | undefined
searchText: string = '';
constructor(public service: ISService, public route: ActivatedRoute, public dialog: MatDialog) { }
ngOnInit() { this.reload() }
ngAfterViewInit() { if (this.sort) this.emailsDatasource.sort = this.sort; }
reload() { this.service.loadEmailTemplates((data: EmailTemplate[]) => this.emailsDatasource.data = data); }
applyFilter(event: Event) {
const filterValue = (event.target as HTMLInputElement).value.trim().toLowerCase();
this.emailsDatasource.filter = filterValue;
}
openAddEmailTemplateDialog(): void {
const dialogRef = this.dialog.open(EmailDialog, {
data: {
id: '',
description: '',
subject: '',
message: ''
},
width: '80%'
});
dialogRef.afterClosed().subscribe(result => {
if (result) this.reload();
});
}
openEditEmailTemplateDialog(email: EmailTemplate): void {
const dialogRef = this.dialog.open(EmailDialog, {
data: email,
width: '80%'
});
dialogRef.afterClosed().subscribe(result => {
if (result) this.reload();
});
}
deleteEmailTemplate(email: EmailTemplate) {
if (confirm('Are you sure?')) {
this.service.deleteEmailTemplate(email.id, (data: void) => this.reload());
}
}
}
@Component({
selector: 'email-dialog',
templateUrl: './email-dialog.html',
styleUrls: ['./emails.component.css']
})
export class EmailDialog {
emailForm = new FormGroup({
id: new FormControl(''),
description: new FormControl('', [Validators.required]),
subject: new FormControl('', [Validators.required]),
message: new FormControl('', [Validators.required])
});
constructor(public dialogRef: MatDialogRef<EmailDialog>, @Inject(MAT_DIALOG_DATA) public data: any, public service: ISService) {
this.emailForm.get('id')?.setValue(data.id);
this.emailForm.get('description')?.setValue(data.description);
this.emailForm.get('subject')?.setValue(data.subject);
this.emailForm.get('message')?.setValue(data.message);
}
onSubmit(): void {
const email = Object.assign({}, this.data, this.emailForm.value);
this.service.saveEmailTemplate(email, (data: void) => this.dialogRef.close(1), this.emailForm);
}
onNoClick(): void {
this.dialogRef.close();
}
}

9
frontends/dnet-is-application/src/app/main-menu-panels/main-menu-panels.component.html
View File

@ -51,6 +51,15 @@
</div>
</mat-expansion-panel>
<mat-expansion-panel>
<mat-expansion-panel-header>
<mat-panel-title>Workflows</mat-panel-title>
</mat-expansion-panel-header>
<div>
<a class="menu-item" routerLink="wfs">Workflows</a>
</div>
</mat-expansion-panel>
<mat-expansion-panel>
<mat-expansion-panel-header>
<mat-panel-title>Tools</mat-panel-title>

7
frontends/dnet-is-application/src/app/resources/metadata-dialog.html
View File

@ -13,9 +13,14 @@
<input matInput readonly value="{{data.type}}" />
</mat-form-field>
<mat-form-field appearance="fill" floatLabel="always" style="width: 100%;">
<mat-label>SubType (optional)</mat-label>
<input matInput formControlName="subtype" />
</mat-form-field>
<mat-form-field appearance="fill" floatLabel="always" style="width: 100%;">
<mat-label>Name</mat-label>
<input matInput formControlName="name" required />
<input matInput formControlName="name" />
<mat-error *ngIf="metadataForm.get('name')?.invalid">This field is <strong>required</strong></mat-error>
</mat-form-field>

9
frontends/dnet-is-application/src/app/resources/new-dialog.html
View File

@ -5,10 +5,15 @@
<mat-form-field appearance="fill" floatLabel="always" style="width: 100%;">
<mat-label>Name</mat-label>
<input matInput formControlName="name" required />
<input matInput formControlName="name" />
<mat-error *ngIf="newResourceForm.get('name')?.invalid">This field is <strong>required</strong></mat-error>
</mat-form-field>
<mat-form-field appearance="fill" floatLabel="always" style="width: 100%;">
<mat-label>SubType (optional)</mat-label>
<input matInput formControlName="subtype" />
</mat-form-field>
<mat-form-field appearance="fill" floatLabel="always" style="width: 100%;">
<mat-label>Description</mat-label>
<textarea matInput formControlName="description" rows="2"></textarea>
@ -16,7 +21,7 @@
<mat-form-field appearance="fill" floatLabel="always" style="width: 100%;">
<mat-label>Content ({{data.contentType}})</mat-label>
<textarea matInput formControlName="content" required rows="10" style="font-size: 0.8em;"></textarea>
<textarea matInput formControlName="content" rows="10" style="font-size: 0.8em;"></textarea>
<mat-error *ngIf="newResourceForm.get('content')?.invalid">This field is <strong>required</strong></mat-error>
</mat-form-field>

12
frontends/dnet-is-application/src/app/resources/resources.component.html
View File

@ -12,14 +12,18 @@
<mat-card *ngFor="let r of resources | searchFilter: searchText" style="margin-top: 10px;">
<mat-card-header>
<mat-card-title title="{{r.id}}">{{r.name}} <span class="badge-label badge-info"
style="font-size: 0.7em;">{{type.contentType}}</span></mat-card-title>
<mat-card-title title="{{r.id}}">
{{r.name}}
<span class="badge-label badge-warning" style="font-size: 0.7em;" *ngIf="r.subtype">{{r.subtype}}</span>
<span class="badge-label badge-info" style="font-size: 0.7em;">{{type.contentType}}</span>
</mat-card-title>
</mat-card-header>
<mat-card-content>
<p>{{r.description}}</p>
<p class="muted small">
<b>Id:</b> {{r.id}}<br /> <b>Creation date:</b> {{r.creationDate}}<br /> <b>Modification date:</b>
{{r.modificationDate}}
<b>Id:</b> {{r.id}}<br />
<b>Creation date:</b> {{r.creationDate}}<br />
<b>Modification date:</b> {{r.modificationDate}}
</p>
</mat-card-content>
<mat-card-actions>

16
frontends/dnet-is-application/src/app/resources/resources.component.ts
View File

@ -3,7 +3,7 @@ import { ISService } from '../common/is.service';
import { ActivatedRoute } from '@angular/router';
import { MatDialog, MAT_DIALOG_DATA, MatDialogRef } from '@angular/material/dialog';
import { ResourceType, SimpleResource } from '../common/is.model';
import { FormControl, FormGroup } from '@angular/forms';
import { FormControl, FormGroup, Validators } from '@angular/forms';
@Component({
selector: 'app-resources',
@ -115,12 +115,16 @@ export class ResContentDialog {
})
export class ResMetadataDialog {
metadataForm = new FormGroup({
name: new FormControl(''),
name: new FormControl('', [Validators.required]),
subtype: new FormControl(''),
description: new FormControl('')
});
constructor(public dialogRef: MatDialogRef<ResMetadataDialog>, @Inject(MAT_DIALOG_DATA) public data: any, public service: ISService) {
this.metadataForm.get('name')?.setValue(data.name);
if (data.subtype) {
this.metadataForm.get('subtype')?.setValue(data.subtype);
}
if (data.description) {
this.metadataForm.get('description')?.setValue(data.description);
}
@ -143,9 +147,10 @@ export class ResMetadataDialog {
})
export class ResCreateNewDialog {
newResourceForm = new FormGroup({
name: new FormControl(''),
name: new FormControl('', [Validators.required]),
subtype: new FormControl(''),
description: new FormControl(''),
content: new FormControl('')
content: new FormControl('', [Validators.required])
});
constructor(public dialogRef: MatDialogRef<ResCreateNewDialog>, @Inject(MAT_DIALOG_DATA) public data: any, public service: ISService) { }
@ -153,10 +158,11 @@ export class ResCreateNewDialog {
onSubmit(): void {
let name: string = this.newResourceForm.get('name')?.value!;
let type: string = this.data.id!;
let subtype: string = this.newResourceForm.get('subtype')?.value!;
let description: string = this.newResourceForm.get('description')?.value!;
let content: string = this.newResourceForm.get('content')?.value!;
this.service.addSimpleResource(name, type, description, content, (data: void) => this.dialogRef.close(1), this.newResourceForm);
this.service.addSimpleResource(name, type, subtype, description, content, (data: void) => this.dialogRef.close(1), this.newResourceForm);
}
onNoClick(): void {
this.dialogRef.close();

2
frontends/dnet-is-application/src/app/vocabularies/vocabularies.component.ts
View File

@ -137,8 +137,6 @@ export class VocabularyEditorComponent implements OnInit, AfterViewInit {
}
}
}
@Component({

0
frontends/dnet-is-application/src/app/wf-instances/wf-instance.dialog.html Normal file
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0
frontends/dnet-is-application/src/app/wf-instances/wf-instances.component.css Normal file
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7
frontends/dnet-is-application/src/app/wf-instances/wf-instances.component.html Normal file
View File

@ -0,0 +1,7 @@
<h2>Workflow Instances</h2>
<mat-tab-group animationDuration="0ms">
<mat-tab label="First">Content 1</mat-tab>
<mat-tab label="Second">Content 2</mat-tab>
<mat-tab label="Third">Content 3</mat-tab>
</mat-tab-group>

10
frontends/dnet-is-application/src/app/wf-instances/wf-instances.component.ts Normal file
View File

@ -0,0 +1,10 @@
import { Component } from '@angular/core';
@Component({
selector: 'app-wf-instances',
templateUrl: './wf-instances.component.html',
styleUrls: ['./wf-instances.component.css']
})
export class WfInstancesComponent {
}

11
libs/dnet-data-services/src/main/java/eu/dnetlib/data/mdstore/MDStoreService.java
View File

@ -1,7 +1,8 @@
package eu.dnetlib.data.mdstore;
import java.time.LocalDateTime;
import java.time.ZoneOffset;
import java.util.Comparator;
import java.util.Date;
import java.util.LinkedHashMap;
import java.util.List;
import java.util.Map;
@ -112,9 +113,9 @@ public class MDStoreService {
private MDStoreVersion newMDStoreVersion(final MDStore md, final boolean writing) {
final MDStoreVersion v = new MDStoreVersion();
final Date now = new Date();
final LocalDateTime now = LocalDateTime.now();
final String versionId = md.getId() + "-" + now.getTime();
final String versionId = md.getId() + "-" + now.toEpochSecond(ZoneOffset.UTC);
v.setId(versionId);
v.setMdstore(md.getId());
v.setLastUpdate(null);
@ -189,7 +190,7 @@ public class MDStoreService {
mdstoreCurrentVersionRepository.save(MDStoreCurrentVersion.newInstance(v));
v.setWriting(false);
v.setSize(size);
v.setLastUpdate(new Date());
v.setLastUpdate(LocalDateTime.now());
mdstoreVersionRepository.save(v);
return v;
@ -258,7 +259,7 @@ public class MDStoreService {
md.setLayout(layout);
md.setType(type);
md.setInterpretation(interpretation);
md.setCreationDate(new Date());
md.setCreationDate(LocalDateTime.now());
md.setDatasourceName(dsName);
md.setDatasourceId(dsId);
md.setApiId(apiId);

6
libs/dnet-data-services/src/main/java/eu/dnetlib/data/mdstore/backends/MockBackend.java
View File

@ -1,8 +1,8 @@
package eu.dnetlib.data.mdstore.backends;
import java.time.Instant;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Date;
import java.util.LinkedHashSet;
import java.util.List;
import java.util.Set;
@ -49,8 +49,8 @@ public class MockBackend implements MDStoreBackend {
rec.setOriginalId("mck-" + i);
rec.setId("mock________::mck-" + i);
rec.setBody("<RECORD>" + i + "</RECORD>");
rec.setDateOfCollection(new Date().getTime());
rec.setDateOfTransformation(new Date().getTime());
rec.setDateOfCollection(Instant.now().toEpochMilli());
rec.setDateOfTransformation(Instant.now().toEpochMilli());
rec.setEncoding("XML");
rec.setProvenance(MOCK_PROVENANCE);
list.add(rec);

61
libs/dnet-is-common/src/main/java/eu/dnetlib/common/model/EmailTemplate.java Normal file
View File

@ -0,0 +1,61 @@
package eu.dnetlib.common.model;
import java.io.Serializable;
import javax.persistence.Column;
import javax.persistence.Entity;
import javax.persistence.Id;
import javax.persistence.Table;
@Entity
@Table(name = "emails")
public class EmailTemplate implements Serializable {
private static final long serialVersionUID = -8424437958140000626L;
@Id
@Column(name = "id")
private String id;
@Column(name = "description")
private String description;
@Column(name = "subject")
private String subject;
@Column(name = "message")
private String message;
public String getId() {
return id;
}
public void setId(final String id) {
this.id = id;
}
public String getDescription() {
return description;
}
public void setDescription(final String description) {
this.description = description;
}
public String getSubject() {
return subject;
}
public void setSubject(final String subject) {
this.subject = subject;
}
public String getMessage() {
return message;
}
public void setMessage(final String message) {
this.message = message;
}
}

11
libs/dnet-is-common/src/main/java/eu/dnetlib/data/mdstore/model/MDStore.java
View File

@ -1,7 +1,7 @@
package eu.dnetlib.data.mdstore.model;
import java.io.Serializable;
import java.util.Date;
import java.time.LocalDateTime;
import java.util.LinkedHashMap;
import java.util.Map;
import java.util.Objects;
@ -12,8 +12,6 @@ import javax.persistence.EnumType;
import javax.persistence.Enumerated;
import javax.persistence.Id;
import javax.persistence.Table;
import javax.persistence.Temporal;
import javax.persistence.TemporalType;
import org.hibernate.annotations.Type;
@ -55,8 +53,7 @@ public class MDStore implements Serializable {
private Map<String, Object> params = new LinkedHashMap<>();
@Column(name = "creation_date")
@Temporal(TemporalType.TIMESTAMP)
private Date creationDate;
private LocalDateTime creationDate;
@Override
public int hashCode() {
@ -143,11 +140,11 @@ public class MDStore implements Serializable {
this.params = params;
}
public Date getCreationDate() {
public LocalDateTime getCreationDate() {
return creationDate;
}
public void setCreationDate(final Date creationDate) {
public void setCreationDate(final LocalDateTime creationDate) {
this.creationDate = creationDate;
}

11
libs/dnet-is-common/src/main/java/eu/dnetlib/data/mdstore/model/MDStoreVersion.java
View File

@ -1,7 +1,7 @@
package eu.dnetlib.data.mdstore.model;
import java.io.Serializable;
import java.util.Date;
import java.time.LocalDateTime;
import java.util.LinkedHashMap;
import java.util.Map;
import java.util.Objects;
@ -10,8 +10,6 @@ import javax.persistence.Column;
import javax.persistence.Entity;
import javax.persistence.Id;
import javax.persistence.Table;
import javax.persistence.Temporal;
import javax.persistence.TemporalType;
import org.hibernate.annotations.Type;
@ -36,8 +34,7 @@ public class MDStoreVersion implements Serializable {
private int readCount = 0;
@Column(name = "lastupdate")
@Temporal(TemporalType.TIMESTAMP)
private Date lastUpdate;
private LocalDateTime lastUpdate;
@Column(name = "size")
private long size = 0;
@ -78,11 +75,11 @@ public class MDStoreVersion implements Serializable {
this.readCount = readCount;
}
public Date getLastUpdate() {
public LocalDateTime getLastUpdate() {
return lastUpdate;
}
public void setLastUpdate(final Date lastUpdate) {
public void setLastUpdate(final LocalDateTime lastUpdate) {
this.lastUpdate = lastUpdate;
}

18
libs/dnet-is-common/src/main/java/eu/dnetlib/data/mdstore/model/MDStoreWithInfo.java
View File

@ -1,7 +1,7 @@
package eu.dnetlib.data.mdstore.model;
import java.io.Serializable;
import java.util.Date;
import java.time.LocalDateTime;
import java.util.LinkedHashMap;
import java.util.Map;
import java.util.Objects;
@ -12,8 +12,6 @@ import javax.persistence.EnumType;
import javax.persistence.Enumerated;
import javax.persistence.Id;
import javax.persistence.Table;
import javax.persistence.Temporal;
import javax.persistence.TemporalType;
import org.hibernate.annotations.Type;
@ -54,12 +52,10 @@ public class MDStoreWithInfo implements Serializable {
private String currentVersion;
@Column(name = "creation_date")
@Temporal(TemporalType.TIMESTAMP)
private Date creationDate;
private LocalDateTime creationDate;
@Column(name = "lastupdate")
@Temporal(TemporalType.TIMESTAMP)
private Date lastUpdate;
private LocalDateTime lastUpdate;
@Column(name = "size")
private long size = 0;
@ -143,19 +139,19 @@ public class MDStoreWithInfo implements Serializable {
this.currentVersion = currentVersion;
}
public Date getCreationDate() {
public LocalDateTime getCreationDate() {
return creationDate;
}
public void setCreationDate(final Date creationDate) {
public void setCreationDate(final LocalDateTime creationDate) {
this.creationDate = creationDate;
}
public Date getLastUpdate() {
public LocalDateTime getLastUpdate() {
return lastUpdate;
}
public void setLastUpdate(final Date lastUpdate) {
public void setLastUpdate(final LocalDateTime lastUpdate) {
this.lastUpdate = lastUpdate;
}

19
libs/dnet-is-common/src/main/java/eu/dnetlib/dsm/model/Datasource.java
View File

@ -2,6 +2,7 @@ package eu.dnetlib.dsm.model;
import java.io.Serializable;
import java.sql.Date;
import java.time.LocalDateTime;
import java.util.HashSet;
import java.util.Set;
@ -89,7 +90,7 @@ public class Datasource implements Serializable {
private String registeredby;
private Date registrationdate;
private LocalDateTime registrationdate;
private String subjects;
@ -99,10 +100,10 @@ public class Datasource implements Serializable {
private Boolean consentTermsOfUse;
@Column(name = "consenttermsofusedate")
private Date consentTermsOfUseDate;
private LocalDateTime consentTermsOfUseDate;
@Column(name = "lastconsenttermsofusedate")
private Date lastConsentTermsOfUseDate;
private LocalDateTime lastConsentTermsOfUseDate;
@Column(name = "fulltextdownload")
private Boolean fullTextDownload;
@ -401,11 +402,11 @@ public class Datasource implements Serializable {
this.registeredby = registeredby;
}
public Date getRegistrationdate() {
public LocalDateTime getRegistrationdate() {
return registrationdate;
}
public void setRegistrationdate(final Date registrationdate) {
public void setRegistrationdate(final LocalDateTime registrationdate) {
this.registrationdate = registrationdate;
}
@ -433,19 +434,19 @@ public class Datasource implements Serializable {
this.consentTermsOfUse = consentTermsOfUse;
}
public Date getConsentTermsOfUseDate() {
public LocalDateTime getConsentTermsOfUseDate() {
return consentTermsOfUseDate;
}
public void setConsentTermsOfUseDate(final Date consentTermsOfUseDate) {
public void setConsentTermsOfUseDate(final LocalDateTime consentTermsOfUseDate) {
this.consentTermsOfUseDate = consentTermsOfUseDate;
}
public Date getLastConsentTermsOfUseDate() {
public LocalDateTime getLastConsentTermsOfUseDate() {
return lastConsentTermsOfUseDate;
}
public void setLastConsentTermsOfUseDate(final Date lastConsentTermsOfUseDate) {
public void setLastConsentTermsOfUseDate(final LocalDateTime lastConsentTermsOfUseDate) {
this.lastConsentTermsOfUseDate = lastConsentTermsOfUseDate;
}

8
libs/dnet-is-common/src/main/java/eu/dnetlib/dsm/model/Organization.java
View File

@ -1,7 +1,7 @@
package eu.dnetlib.dsm.model;
import java.io.Serializable;
import java.sql.Date;
import java.time.LocalDateTime;
import java.util.Set;
import javax.persistence.CascadeType;
@ -34,7 +34,7 @@ public class Organization implements Serializable {
private String country;
private String collectedfrom;
private Date dateofcollection;
private LocalDateTime dateofcollection;
private String provenanceaction;
@ManyToMany(cascade = {
@ -98,11 +98,11 @@ public class Organization implements Serializable {
this.collectedfrom = collectedfrom;
}
public Date getDateofcollection() {
public LocalDateTime getDateofcollection() {
return dateofcollection;
}
public void setDateofcollection(final Date dateofcollection) {
public void setDateofcollection(final LocalDateTime dateofcollection) {
this.dateofcollection = dateofcollection;
}

14
libs/dnet-is-common/src/main/java/eu/dnetlib/errors/WorkflowManagerException.java Normal file
View File

@ -0,0 +1,14 @@
package eu.dnetlib.errors;
public class WorkflowManagerException extends Exception {
private static final long serialVersionUID = -9067581185191425823L;
public WorkflowManagerException(final String message, final Throwable cause) {
super(message, cause);
}
public WorkflowManagerException(final String message) {
super(message);
}
}

29
libs/dnet-is-common/src/main/java/eu/dnetlib/is/model/resource/SimpleResource.java
View File

@ -1,14 +1,12 @@
package eu.dnetlib.is.model.resource;
import java.io.Serializable;
import java.util.Date;
import java.time.LocalDateTime;
import javax.persistence.Column;
import javax.persistence.Entity;
import javax.persistence.Id;
import javax.persistence.Table;
import javax.persistence.Temporal;
import javax.persistence.TemporalType;
@Entity
@Table(name = "resources")
@ -26,16 +24,17 @@ public class SimpleResource implements Serializable {
@Column(name = "type")
private String type;
@Column(name = "subtype")
private String subtype;
@Column(name = "description")
private String description;
@Temporal(TemporalType.TIMESTAMP)
@Column(name = "creation_date")
private Date creationDate;
private LocalDateTime creationDate;
@Temporal(TemporalType.TIMESTAMP)
@Column(name = "modification_date")
private Date modificationDate;
private LocalDateTime modificationDate;
public String getId() {
return id;
@ -61,6 +60,14 @@ public class SimpleResource implements Serializable {
this.type = type;
}
public String getSubtype() {
return subtype;
}
public void setSubtype(final String subtype) {
this.subtype = subtype;
}
public String getDescription() {
return description;
}
@ -69,19 +76,19 @@ public class SimpleResource implements Serializable {
this.description = description;
}
public Date getCreationDate() {
public LocalDateTime getCreationDate() {
return creationDate;
}
public void setCreationDate(final Date creationDate) {
public void setCreationDate(final LocalDateTime creationDate) {
this.creationDate = creationDate;
}
public Date getModificationDate() {
public LocalDateTime getModificationDate() {
return modificationDate;
}
public void setModificationDate(final Date modificationDate) {
public void setModificationDate(final LocalDateTime modificationDate) {
this.modificationDate = modificationDate;
}

31
libs/dnet-is-common/src/main/java/eu/dnetlib/msro/model/history/WfProcessExecution.java → libs/dnet-is-common/src/main/java/eu/dnetlib/manager/history/model/WfProcessExecution.java
View File

@ -1,15 +1,13 @@
package eu.dnetlib.msro.model.history;
package eu.dnetlib.manager.history.model;
import java.io.Serializable;
import java.util.Date;
import java.time.LocalDateTime;
import java.util.Map;
import javax.persistence.Column;
import javax.persistence.Entity;
import javax.persistence.Id;
import javax.persistence.Table;
import javax.persistence.Temporal;
import javax.persistence.TemporalType;
import org.hibernate.annotations.Type;
import org.hibernate.annotations.TypeDef;
@ -32,6 +30,9 @@ public class WfProcessExecution implements Serializable {
@Column(name = "process_id")
private String processId;
@Column(name = "wf_instance_id")
private String wfInstanceId;
@Column(name = "name")
private String name;
@ -41,13 +42,11 @@ public class WfProcessExecution implements Serializable {
@Column(name = "status")
private String status;
@Temporal(TemporalType.TIMESTAMP)
@Column(name = "start_date")
private Date startDate;
private LocalDateTime startDate;
@Temporal(TemporalType.TIMESTAMP)
@Column(name = "end_date")
private Date endDate;
private LocalDateTime endDate;
@Column(name = "ds_id")
private String dsId;
@ -70,6 +69,14 @@ public class WfProcessExecution implements Serializable {
this.processId = processId;
}
public String getWfInstanceId() {
return wfInstanceId;
}
public void setWfInstanceId(final String wfInstanceId) {
this.wfInstanceId = wfInstanceId;
}
public String getName() {
return name;
}
@ -94,19 +101,19 @@ public class WfProcessExecution implements Serializable {
this.status = status;
}
public Date getStartDate() {
public LocalDateTime getStartDate() {
return startDate;
}
public void setStartDate(final Date startDate) {
public void setStartDate(final LocalDateTime startDate) {
this.startDate = startDate;
}
public Date getEndDate() {
public LocalDateTime getEndDate() {
return endDate;
}
public void setEndDate(final Date endDate) {
public void setEndDate(final LocalDateTime endDate) {
this.endDate = endDate;
}

5
libs/dnet-is-common/src/main/java/eu/dnetlib/manager/wf/model/NotificationCondition.java Normal file
View File

@ -0,0 +1,5 @@
package eu.dnetlib.manager.wf.model;
public enum NotificationCondition {
ALWAYS, NEVER, ONLY_SUCCESS, ONLY_FAILED
}

269
libs/dnet-is-common/src/main/java/eu/dnetlib/manager/wf/model/WorkflowGraph.java Normal file
View File

@ -0,0 +1,269 @@
package eu.dnetlib.manager.wf.model;
import java.io.Serializable;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import java.util.regex.Matcher;
import java.util.regex.Pattern;
import java.util.stream.Collectors;
import org.apache.commons.lang3.StringUtils;
import org.springframework.core.env.Environment;
public class WorkflowGraph implements Serializable {
private static final long serialVersionUID = 5919290887480115842L;
public List<WfParam> parameters;
public List<Node> graph;
public List<Node> getGraph() {
return graph;
}
public void setGraph(final List<Node> graph) {
this.graph = graph;
}
public List<WfParam> getParameters() {
return parameters;
}
public void setParameters(final List<WfParam> parameters) {
this.parameters = parameters;
}
class WfParam implements Serializable {
private static final long serialVersionUID = 5885589803738655166L;
private String name;
private String description;
private String type;
private String defaultValue;
private boolean required;
public String getName() {
return name;
}
public void setName(final String name) {
this.name = name;
}
public String getDescription() {
return description;
}
public void setDescription(final String description) {
this.description = description;
}
public String getType() {
return type;
}
public void setType(final String type) {
this.type = type;
}
public String getDefaultValue() {
return defaultValue;
}
public void setDefaultValue(final String defaultValue) {
this.defaultValue = defaultValue;
}
public boolean isRequired() {
return required;
}
public void setRequired(final boolean required) {
this.required = required;
}
}
public class Node implements Serializable {
private static final long serialVersionUID = -3695762832959801906L;
private static final String regExRef = "\\$\\{(\\w*)\\}";
private String name;
private String type;
private boolean isStart = false;
private boolean isJoin = false;
private List<Arc> arcs;
private List<NodeParam> input;
public String getName() {
return name;
}
public void setName(final String name) {
this.name = name;
}
public String getType() {
return type;
}
public void setType(final String type) {
this.type = type;
}
public boolean isStart() {
return isStart;
}
public void setStart(final boolean isStart) {
this.isStart = isStart;
}
public boolean isJoin() {
return isJoin;
}
public void setJoin(final boolean isJoin) {
this.isJoin = isJoin;
}
public List<Arc> getArcs() {
return arcs;
}
public void setArcs(final List<Arc> arcs) {
this.arcs = arcs;
}
public List<NodeParam> getInput() {
return input;
}
public void setInput(final List<NodeParam> input) {
this.input = input;
}
public Map<String, String> findEnvParams() {
return input.stream()
.filter(p -> StringUtils.isNotBlank(p.getEnv()))
.collect(Collectors.toMap(NodeParam::getName, NodeParam::getEnv));
}
public Map<String, Object> calculateInitialParams(final Map<String, String> globalParams, final Environment environment) {
final Map<String, Object> map = new HashMap<>();
input.stream()
.filter(p -> StringUtils.isBlank(p.getEnv()))
.forEach(p -> map.put(p.getName(), calculateSimpleValue(p, globalParams, environment)));
return map;
}
private Object calculateSimpleValue(final NodeParam p, final Map<String, String> globalParams, final Environment environment) {
String value = p.getValue();
final String ref = p.getRef();
final String prop = p.getProperty();
if (StringUtils.isNotBlank(ref) && StringUtils.isNotBlank(globalParams.get(ref))) {
return globalParams.get(ref);
} else if (StringUtils.isNotBlank(value)) {
final Matcher matcher = Pattern.compile(regExRef, Pattern.MULTILINE).matcher(value);
while (matcher.find()) {
final String rName = matcher.group(1);
final String rValue = globalParams.get(rName);
if (StringUtils.isBlank(rValue)) { return null; }
value = value.replaceAll(Pattern.quote(matcher.group(0)), rValue);
System.out.println("NEW VALUE " + value);
}
return value;
} else if (StringUtils.isNotBlank(prop)) {
return environment.getProperty(prop);
} else {
return null;
}
}
}
public class Arc implements Serializable {
private static final long serialVersionUID = 7866138976929522262L;
private String to;
private String condition;
public String getTo() {
return to;
}
public void setTo(final String to) {
this.to = to;
}
public String getCondition() {
return condition;
}
public void setCondition(final String condition) {
this.condition = condition;
}
}
class NodeParam implements Serializable {
private static final long serialVersionUID = 7815785723401725707L;
private String name;
private String value;
private String ref;
private String property;
private String env;
public String getName() {
return name;
}
public void setName(final String name) {
this.name = name;
}
public String getValue() {
return value;
}
public void setValue(final String value) {
this.value = value;
}
public String getRef() {
return ref;
}
public void setRef(final String ref) {
this.ref = ref;
}
public String getProperty() {
return property;
}
public void setProperty(final String property) {
this.property = property;
}
public String getEnv() {
return env;
}
public void setEnv(final String env) {
this.env = env;
}
}
}

232
libs/dnet-is-common/src/main/java/eu/dnetlib/manager/wf/model/WorkflowInstance.java Normal file
View File

@ -0,0 +1,232 @@
package eu.dnetlib.manager.wf.model;
import java.io.Serializable;
import java.util.LinkedHashMap;
import java.util.Map;
import javax.persistence.Column;
import javax.persistence.Entity;
import javax.persistence.Id;
import javax.persistence.Table;
import javax.persistence.Transient;
import org.hibernate.annotations.Type;
import org.hibernate.annotations.TypeDef;
import org.hibernate.annotations.TypeDefs;
import com.vladmihalcea.hibernate.type.json.JsonBinaryType;
import com.vladmihalcea.hibernate.type.json.JsonStringType;
@Entity
@Table(name = "workflow_instances")
@TypeDefs({
@TypeDef(name = "json", typeClass = JsonStringType.class),
@TypeDef(name = "jsonb", typeClass = JsonBinaryType.class)
})
public class WorkflowInstance implements Serializable {
private static final long serialVersionUID = 7503841966138333044L;
@Id
@Column(name = "id")
private String id;
@Column(name = "name")
private String name;
@Column(name = "section")
private String section;
@Type(type = "jsonb")
@Column(name = "details", columnDefinition = "jsonb")
private Map<String, String> details = new LinkedHashMap<>();
@Column(name = "priority")
private Integer priority;
@Column(name = "dsid")
private String dsId;
@Column(name = "dsname")
private String dsName;
@Column(name = "apiid")
private String apiId;
@Column(name = "enabled")
private boolean enabled;
@Column(name = "configured")
private boolean configured;
@Column(name = "scheduling_enabled")
private boolean schedulingEnabled;
@Column(name = "scheduling_cron")
private String cronExpression;
@Column(name = "scheduling_min_interval")
private int cronMinInterval;
@Column(name = "workflow")
private String workflow;
@Column(name = "destroy_wf")
private String destroyWf;
@Type(type = "jsonb")
@Column(name = "system_params", columnDefinition = "jsonb")
private Map<String, String> systemParams = new LinkedHashMap<>();
@Type(type = "jsonb")
@Column(name = "user_params", columnDefinition = "jsonb")
private Map<String, String> userParams = new LinkedHashMap<>();
@Transient
private String parentId;
public String getId() {
return id;
}
public void setId(final String id) {
this.id = id;
}
public String getName() {
return name;
}
public void setName(final String name) {
this.name = name;
}
public String getSection() {
return section;
}
public void setSection(final String section) {
this.section = section;
}
public Map<String, String> getDetails() {
return details;
}
public void setDetails(final Map<String, String> details) {
this.details = details;
}
public Integer getPriority() {
return priority;
}
public void setPriority(final Integer priority) {
this.priority = priority;
}
public String getDsId() {
return dsId;
}
public void setDsId(final String dsId) {
this.dsId = dsId;
}
public String getDsName() {
return dsName;
}
public void setDsName(final String dsName) {
this.dsName = dsName;
}
public String getApiId() {
return apiId;
}
public void setApiId(final String apiId) {
this.apiId = apiId;
}
public boolean isEnabled() {
return enabled;
}
public void setEnabled(final boolean enabled) {
this.enabled = enabled;
}
public boolean isConfigured() {
return configured;
}
public void setConfigured(final boolean configured) {
this.configured = configured;
}
public boolean isSchedulingEnabled() {
return schedulingEnabled;
}
public void setSchedulingEnabled(final boolean schedulingEnabled) {
this.schedulingEnabled = schedulingEnabled;
}
public String getCronExpression() {
return cronExpression;
}
public void setCronExpression(final String cronExpression) {
this.cronExpression = cronExpression;
}
public int getCronMinInterval() {
return cronMinInterval;
}
public void setCronMinInterval(final int cronMinInterval) {
this.cronMinInterval = cronMinInterval;
}
public String getWorkflow() {
return workflow;
}
public void setWorkflow(final String workflow) {
this.workflow = workflow;
}
public String getDestroyWf() {
return destroyWf;
}
public void setDestroyWf(final String destroyWf) {
this.destroyWf = destroyWf;
}
public Map<String, String> getSystemParams() {
return systemParams;
}
public void setSystemParams(final Map<String, String> systemParams) {
this.systemParams = systemParams;
}
public Map<String, String> getUserParams() {
return userParams;
}
public void setUserParams(final Map<String, String> userParams) {
this.userParams = userParams;
}
public String getParentId() {
return parentId;
}
public void setParentId(final String parentId) {
this.parentId = parentId;
}
}

5
libs/dnet-is-common/src/main/java/eu/dnetlib/manager/wf/model/WorkflowParamDesc.java Normal file
View File

@ -0,0 +1,5 @@
package eu.dnetlib.manager.wf.model;
public class WorkflowParamDesc {
}

68
libs/dnet-is-common/src/main/java/eu/dnetlib/manager/wf/model/WorkflowSubscription.java Normal file
View File

@ -0,0 +1,68 @@
package eu.dnetlib.manager.wf.model;
import java.io.Serializable;
import javax.persistence.Column;
import javax.persistence.Entity;
import javax.persistence.EnumType;
import javax.persistence.Enumerated;
import javax.persistence.Id;
import javax.persistence.IdClass;
import javax.persistence.Table;
@Entity
@Table(name = "workflow_subscriptions")
@IdClass(WorkflowSubscriptionPK.class)
public class WorkflowSubscription implements Serializable {
private static final long serialVersionUID = -3662770213782581404L;
@Id
@Column(name = "wf_instance_id")
private String wfInstanceId;
@Id
@Column(name = "condition")
@Enumerated(EnumType.STRING)
private NotificationCondition condition;
@Id
@Column(name = "email")
private String email;
@Column(name = "message_id")
private String messageId;
public String getWfInstanceId() {
return wfInstanceId;
}
public void setWfInstanceId(final String wfInstanceId) {
this.wfInstanceId = wfInstanceId;
}
public NotificationCondition getCondition() {
return condition;
}
public void setCondition(final NotificationCondition condition) {
this.condition = condition;
}
public String getEmail() {
return email;
}
public void setEmail(final String email) {
this.email = email;
}
public String getMessageId() {
return messageId;
}
public void setMessageId(final String messageId) {
this.messageId = messageId;
}
}

39
libs/dnet-is-common/src/main/java/eu/dnetlib/manager/wf/model/WorkflowSubscriptionPK.java Normal file
View File

@ -0,0 +1,39 @@
package eu.dnetlib.manager.wf.model;
import java.io.Serializable;
public class WorkflowSubscriptionPK implements Serializable {
private static final long serialVersionUID = -7569690774071644848L;
private String wfInstanceId;
private NotificationCondition condition;
private String email;
public String getWfInstanceId() {
return wfInstanceId;
}
public void setWfInstanceId(final String wfInstanceId) {
this.wfInstanceId = wfInstanceId;
}
public NotificationCondition getCondition() {
return condition;
}
public void setCondition(final NotificationCondition condition) {
this.condition = condition;
}
public String getEmail() {
return email;
}
public void setEmail(final String email) {
this.email = email;
}
}

13
libs/dnet-is-common/src/main/java/eu/dnetlib/utils/CountedValue.java Normal file
View File

@ -0,0 +1,13 @@
package eu.dnetlib.utils;
public interface CountedValue {
public String getValue();
public void setValue();
public long getCount();
public void setCount(final long count);
}

20
libs/dnet-is-common/src/main/java/eu/dnetlib/utils/DateUtils.java
View File

@ -1,9 +1,11 @@
package eu.dnetlib.utils;
import java.io.StringWriter;
import java.text.SimpleDateFormat;
import java.util.Date;
import java.time.Instant;
import java.time.LocalDateTime;
import java.time.format.DateTimeFormatter;
import java.util.Locale;
import java.util.TimeZone;
public class DateUtils {
@ -12,7 +14,7 @@ public class DateUtils {
private static final long HOUR = MINUTE * 60;
private static final long DAY = HOUR * 24;
private static final long YEAR = DAY * 365;
private static final SimpleDateFormat ISO8601FORMAT = new SimpleDateFormat("yyyy-MM-dd'T'HH:mm:ssZ", Locale.US);
private static final DateTimeFormatter ISO8601FORMAT = DateTimeFormatter.ofPattern("yyyy-MM-dd'T'HH:mm:ssZ", Locale.getDefault());
public static String elapsedTime(long t) {
final StringWriter a = new StringWriter();
@ -78,7 +80,13 @@ public class DateUtils {
}
public static String calculate_ISO8601(final long l) {
String result = ISO8601FORMAT.format(new Date(l));
final LocalDateTime time =
LocalDateTime.ofInstant(Instant.ofEpochMilli(l), TimeZone
.getDefault()
.toZoneId());
String result = time.format(ISO8601FORMAT);
// convert YYYYMMDDTHH:mm:ss+HH00 into YYYYMMDDTHH:mm:ss+HH:00
// - note the added colon for the Timezone
result = result.substring(0, result.length() - 2) + ":" + result.substring(result.length() - 2);
@ -89,4 +97,8 @@ public class DateUtils {
return Long.toString(Math.floorDiv(d, n));
}
public static long now() {
return Instant.now().toEpochMilli();
}
}

10
libs/dnet-is-common/src/main/java/eu/dnetlib/utils/Stoppable.java Normal file
View File

@ -0,0 +1,10 @@
package eu.dnetlib.utils;
public interface Stoppable {
void stop();
void resume();
public StoppableDetails getStopDetails();
}

33
libs/dnet-is-common/src/main/java/eu/dnetlib/utils/StoppableDetails.java Normal file
View File

@ -0,0 +1,33 @@
package eu.dnetlib.utils;
public class StoppableDetails {
public enum StopStatus {
STOPPED,
STOPPING,
RUNNING
};
private final String title;
private final String description;
private final StopStatus status;
public StoppableDetails(final String title, final String description, final StopStatus status) {
this.title = title;
this.description = description;
this.status = status;
}
public String getTitle() {
return title;
}
public String getDescription() {
return description;
}
public StopStatus getStatus() {
return status;
}
}

50
libs/dnet-is-common/src/main/resources/sql/schema.sql
View File

@ -106,6 +106,7 @@ CREATE INDEX ON context_cat_concepts_lvl_2 (parent);
CREATE TABLE wf_history (
process_id text PRIMARY KEY,
wf_instance_id text NOT NULL,
name text NOT NULL,
family text NOT NULL,
status text NOT NULL,
@ -130,7 +131,8 @@ INSERT INTO resource_types(id, name, content_type) VALUES
('transformation_rule_legacy', 'Transformation Rules (legacy)', 'text/plain'),
('cleaning_rule', 'Cleaning Rules', 'application/xml'),
('hadoop_job_configuration', 'Hadoop Job Configurations', 'application/xml')
('dedup_configuration', 'Dedup Configurations', 'application/json');
('dedup_configuration', 'Dedup Configurations', 'application/json')
('workflow', 'Workflows', 'application/json');
CREATE TABLE resources (
id text PRIMARY KEY,
@ -138,6 +140,7 @@ CREATE TABLE resources (
description text,
content text NOT NULL DEFAULT '',
type text NOT NULL REFERENCES resource_types(id),
subtype text,
creation_date timestamp NOT NULL DEFAULT now(),
modification_date timestamp NOT NULL DEFAULT now()
);
@ -177,6 +180,14 @@ CREATE VIEW resource_types_view AS (
count(*) AS count,
false AS simple
FROM protocols
) UNION ALL (
SELECT
'email' AS id,
'Email templates' AS name,
'text/plain' AS content_type,
count(*) AS count,
false AS simple
FROM emails
);
CREATE TABLE mdstores (
@ -241,3 +252,40 @@ GROUP BY md.id,
v1.lastupdate,
v1.size;
-- Email Templates
CREATE TABLE emails (
id text PRIMARY KEY,
description text NOT NULL,
subject text NOT NULL,
message text NOT NULL
);
-- Workflows
CREATE TABLE workflow_instances (
id text PRIMARY KEY,
name text NOT NULL,
section text,
details jsonb NOT NULL DEFAULT '{}',
priority int,
dsid text,
dsname text,
apiid text,
enabled boolean NOT NULL DEFAULT false,
configured boolean NOT NULL DEFAULT false,
scheduling_enabled boolean NOT NULL DEFAULT false,
scheduling_cron text,
scheduling_min_interval int,
workflow text REFERENCES resource(id),
destroy_wf text REFERENCES resource(id),
system_params jsonb NOT NULL DEFAULT '{}',
user_params jsonb NOT NULL DEFAULT '{}'
);
CREATE TABLE workflow_subscriptions (
wf_instance_id text NOT NULL REFERENCES workflow_instances(id),
condition text NOT NULL,
email text NOT NULL,
message_id text NOT NULL REFERENCES emails(id),
PRIMARY KEY (wf_instance_id, condition, email)
);

5
libs/dnet-is-services/pom.xml
View File

@ -25,6 +25,11 @@
<artifactId>jaxen</artifactId>
</dependency>
<dependency>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter-thymeleaf</artifactId>
</dependency>
<!-- Tests -->
<dependency>
<groupId>org.junit.jupiter</groupId>

9
libs/dnet-is-services/src/main/java/eu/dnetlib/common/repository/EmailTemplateRepository.java Normal file
View File

@ -0,0 +1,9 @@
package eu.dnetlib.common.repository;
import org.springframework.data.jpa.repository.JpaRepository;
import eu.dnetlib.common.model.EmailTemplate;
public interface EmailTemplateRepository extends JpaRepository<EmailTemplate, String> {
}

4
libs/dnet-is-services/src/main/java/eu/dnetlib/dsm/DsmService.java
View File

@ -9,7 +9,7 @@ import static eu.dnetlib.dsm.utils.DsmMappingUtils.createId;
import java.io.IOException;
import java.nio.charset.Charset;
import java.nio.charset.StandardCharsets;
import java.sql.Date;
import java.time.LocalDate;
import java.util.HashSet;
import java.util.List;
import java.util.Objects;
@ -368,7 +368,7 @@ public class DsmService {
private void ensureRegistrationDate(final String dsId) {
if (!dsRepository.hasRegistrationdate(dsId)) {
log.info("setting registration date for datasource: " + dsId);
dsRepository.setRegistrationDate(dsId, new Date(System.currentTimeMillis()));
dsRepository.setRegistrationDate(dsId, LocalDate.now());
}
}

20
libs/dnet-is-services/src/main/java/eu/dnetlib/dsm/domain/ApiDetails.java
View File

@ -1,6 +1,6 @@
package eu.dnetlib.dsm.domain;
import java.sql.Date;
import java.time.LocalDateTime;
import java.util.Set;
import com.fasterxml.jackson.annotation.JsonAutoDetect;
@ -27,15 +27,15 @@ public class ApiDetails extends ApiIgnoredProperties {
private Integer lastCollectionTotal;
private Date lastCollectionDate;
private LocalDateTime lastCollectionDate;
private Integer lastAggregationTotal;
private Date lastAggregationDate;
private LocalDateTime lastAggregationDate;
private Integer lastDownloadTotal;
private Date lastDownloadDate;
private LocalDateTime lastDownloadDate;
private String baseurl;
@ -71,7 +71,7 @@ public class ApiDetails extends ApiIgnoredProperties {
return lastCollectionTotal;
}
public Date getLastCollectionDate() {
public LocalDateTime getLastCollectionDate() {
return lastCollectionDate;
}
@ -79,7 +79,7 @@ public class ApiDetails extends ApiIgnoredProperties {
return lastAggregationTotal;
}
public Date getLastAggregationDate() {
public LocalDateTime getLastAggregationDate() {
return lastAggregationDate;
}
@ -87,7 +87,7 @@ public class ApiDetails extends ApiIgnoredProperties {
return lastDownloadTotal;
}
public Date getLastDownloadDate() {
public LocalDateTime getLastDownloadDate() {
return lastDownloadDate;
}
@ -125,7 +125,7 @@ public class ApiDetails extends ApiIgnoredProperties {
return this;
}
public ApiDetails setLastCollectionDate(final Date lastCollectionDate) {
public ApiDetails setLastCollectionDate(final LocalDateTime lastCollectionDate) {
this.lastCollectionDate = lastCollectionDate;
return this;
}
@ -135,7 +135,7 @@ public class ApiDetails extends ApiIgnoredProperties {
return this;
}
public ApiDetails setLastAggregationDate(final Date lastAggregationDate) {
public ApiDetails setLastAggregationDate(final LocalDateTime lastAggregationDate) {
this.lastAggregationDate = lastAggregationDate;
return this;
}
@ -145,7 +145,7 @@ public class ApiDetails extends ApiIgnoredProperties {
return this;
}
public ApiDetails setLastDownloadDate(final Date lastDownloadDate) {
public ApiDetails setLastDownloadDate(final LocalDateTime lastDownloadDate) {
this.lastDownloadDate = lastDownloadDate;
return this;
}

32
libs/dnet-is-services/src/main/java/eu/dnetlib/dsm/domain/DatasourceDetails.java
View File

@ -1,6 +1,6 @@
package eu.dnetlib.dsm.domain;
import java.sql.Date;
import java.time.LocalDate;
import java.util.Set;
import javax.persistence.Transient;
@ -48,12 +48,12 @@ public class DatasourceDetails extends DatasourceIgnoredProperties {
private String languages;
private Date dateofvalidation;
private LocalDate dateofvalidation;
@NotBlank
private String eoscDatasourceType;
private Date dateofcollection;
private LocalDate dateofcollection;
private String platform;
@ -82,9 +82,9 @@ public class DatasourceDetails extends DatasourceIgnoredProperties {
private Boolean fullTextDownload;
private Date consentTermsOfUseDate;
private LocalDate consentTermsOfUseDate;
private Date lastConsentTermsOfUseDate;
private LocalDate lastConsentTermsOfUseDate;
private Set<OrganizationDetails> organizations;
@ -95,7 +95,7 @@ public class DatasourceDetails extends DatasourceIgnoredProperties {
@Deprecated
private String typology;
private Date registrationdate;
private LocalDate registrationdate;
public String getId() {
return id;
@ -145,7 +145,7 @@ public class DatasourceDetails extends DatasourceIgnoredProperties {
return namespaceprefix;
}
public Date getDateofvalidation() {
public LocalDate getDateofvalidation() {
return dateofvalidation;
}
@ -153,7 +153,7 @@ public class DatasourceDetails extends DatasourceIgnoredProperties {
return eoscDatasourceType;
}
public Date getDateofcollection() {
public LocalDate getDateofcollection() {
return dateofcollection;
}
@ -277,7 +277,7 @@ public class DatasourceDetails extends DatasourceIgnoredProperties {
return this;
}
public DatasourceDetails setDateofvalidation(final Date dateofvalidation) {
public DatasourceDetails setDateofvalidation(final LocalDate dateofvalidation) {
this.dateofvalidation = dateofvalidation;
return this;
}
@ -287,7 +287,7 @@ public class DatasourceDetails extends DatasourceIgnoredProperties {
return this;
}
public DatasourceDetails setDateofcollection(final Date dateofcollection) {
public DatasourceDetails setDateofcollection(final LocalDate dateofcollection) {
this.dateofcollection = dateofcollection;
return this;
}
@ -367,11 +367,11 @@ public class DatasourceDetails extends DatasourceIgnoredProperties {
return this;
}
public Date getConsentTermsOfUseDate() {
public LocalDate getConsentTermsOfUseDate() {
return consentTermsOfUseDate;
}
public DatasourceDetails setConsentTermsOfUseDate(final Date consentTermsOfUseDate) {
public DatasourceDetails setConsentTermsOfUseDate(final LocalDate consentTermsOfUseDate) {
this.consentTermsOfUseDate = consentTermsOfUseDate;
return this;
}
@ -396,20 +396,20 @@ public class DatasourceDetails extends DatasourceIgnoredProperties {
return this;
}
public Date getLastConsentTermsOfUseDate() {
public LocalDate getLastConsentTermsOfUseDate() {
return lastConsentTermsOfUseDate;
}
public DatasourceDetails setLastConsentTermsOfUseDate(final Date lastConsentTermsOfUseDate) {
public DatasourceDetails setLastConsentTermsOfUseDate(final LocalDate lastConsentTermsOfUseDate) {
this.lastConsentTermsOfUseDate = lastConsentTermsOfUseDate;
return this;
}
public Date getRegistrationdate() {
public LocalDate getRegistrationdate() {
return registrationdate;
}
public DatasourceDetails setRegistrationdate(final Date registrationdate) {
public DatasourceDetails setRegistrationdate(final LocalDate registrationdate) {
this.registrationdate = registrationdate;
return this;
}

14
libs/dnet-is-services/src/main/java/eu/dnetlib/dsm/domain/DatasourceDetailsUpdate.java
View File

@ -1,6 +1,6 @@
package eu.dnetlib.dsm.domain;
import java.sql.Date;
import java.time.LocalDate;
import java.util.Set;
import javax.validation.constraints.Email;
@ -57,9 +57,9 @@ public class DatasourceDetailsUpdate {
private Boolean consentTermsOfUse;
private Date consentTermsOfUseDate;
private LocalDate consentTermsOfUseDate;
private Date lastConsentTermsOfUseDate;
private LocalDate lastConsentTermsOfUseDate;
private Boolean fullTextDownload;
@ -207,11 +207,11 @@ public class DatasourceDetailsUpdate {
return this;
}
public Date getConsentTermsOfUseDate() {
public LocalDate getConsentTermsOfUseDate() {
return consentTermsOfUseDate;
}
public DatasourceDetailsUpdate setConsentTermsOfUseDate(final Date consentTermsOfUseDate) {
public DatasourceDetailsUpdate setConsentTermsOfUseDate(final LocalDate consentTermsOfUseDate) {
this.consentTermsOfUseDate = consentTermsOfUseDate;
return this;
}
@ -225,11 +225,11 @@ public class DatasourceDetailsUpdate {
return this;
}
public Date getLastConsentTermsOfUseDate() {
public LocalDate getLastConsentTermsOfUseDate() {
return lastConsentTermsOfUseDate;
}
public DatasourceDetailsUpdate setLastConsentTermsOfUseDate(final Date lastConsentTermsOfUseDate) {
public DatasourceDetailsUpdate setLastConsentTermsOfUseDate(final LocalDate lastConsentTermsOfUseDate) {
this.lastConsentTermsOfUseDate = lastConsentTermsOfUseDate;
return this;
}

14
libs/dnet-is-services/src/main/java/eu/dnetlib/dsm/domain/DatasourceIgnoredProperties.java
View File

@ -1,6 +1,6 @@
package eu.dnetlib.dsm.domain;
import java.sql.Date;
import java.time.LocalDate;
import com.fasterxml.jackson.annotation.JsonIgnore;
@ -13,10 +13,10 @@ public abstract class DatasourceIgnoredProperties {
protected String provenanceaction;
@JsonIgnore
protected Date releasestartdate;
protected LocalDate releasestartdate;
@JsonIgnore
protected Date releaseenddate;
protected LocalDate releaseenddate;
@JsonIgnore
protected String missionstatementurl;
@ -76,19 +76,19 @@ public abstract class DatasourceIgnoredProperties {
this.provenanceaction = provenanceaction;
}
public Date getReleasestartdate() {
public LocalDate getReleasestartdate() {
return releasestartdate;
}
public void setReleasestartdate(final Date releasestartdate) {
public void setReleasestartdate(final LocalDate releasestartdate) {
this.releasestartdate = releasestartdate;
}
public Date getReleaseenddate() {
public LocalDate getReleaseenddate() {
return releaseenddate;
}
public void setReleaseenddate(final Date releaseenddate) {
public void setReleaseenddate(final LocalDate releaseenddate) {
this.releaseenddate = releaseenddate;
}

20
libs/dnet-is-services/src/main/java/eu/dnetlib/dsm/domain/DatasourceSnippetExtended.java
View File

@ -1,6 +1,6 @@
package eu.dnetlib.dsm.domain;
import java.util.Date;
import java.time.LocalDateTime;
import java.util.Set;
import javax.validation.constraints.Email;
@ -28,7 +28,7 @@ public class DatasourceSnippetExtended {
@Email
private String registeredby;
private Date registrationdate;
private LocalDateTime registrationdate;
private String eoscDatasourceType;
@ -38,9 +38,9 @@ public class DatasourceSnippetExtended {
private Boolean consentTermsOfUse;
private Date consentTermsOfUseDate;
private LocalDateTime consentTermsOfUseDate;
private Date lastConsentTermsOfUseDate;
private LocalDateTime lastConsentTermsOfUseDate;
private Boolean fullTextDownload;
@ -89,11 +89,11 @@ public class DatasourceSnippetExtended {
this.registeredby = registeredby;
}
public Date getRegistrationdate() {
public LocalDateTime getRegistrationdate() {
return registrationdate;
}
public void setRegistrationdate(final Date registrationdate) {
public void setRegistrationdate(final LocalDateTime registrationdate) {
this.registrationdate = registrationdate;
}
@ -118,11 +118,11 @@ public class DatasourceSnippetExtended {
return this;
}
public Date getConsentTermsOfUseDate() {
public LocalDateTime getConsentTermsOfUseDate() {
return consentTermsOfUseDate;
}
public DatasourceSnippetExtended setConsentTermsOfUseDate(final Date consentTermsOfUseDate) {
public DatasourceSnippetExtended setConsentTermsOfUseDate(final LocalDateTime consentTermsOfUseDate) {
this.consentTermsOfUseDate = consentTermsOfUseDate;
return this;
}
@ -170,11 +170,11 @@ public class DatasourceSnippetExtended {
return this;
}
public Date getLastConsentTermsOfUseDate() {
public LocalDateTime getLastConsentTermsOfUseDate() {
return lastConsentTermsOfUseDate;
}
public DatasourceSnippetExtended setLastConsentTermsOfUseDate(final Date lastConsentTermsOfUseDate) {
public DatasourceSnippetExtended setLastConsentTermsOfUseDate(final LocalDateTime lastConsentTermsOfUseDate) {
this.lastConsentTermsOfUseDate = lastConsentTermsOfUseDate;
return this;
}

8
libs/dnet-is-services/src/main/java/eu/dnetlib/dsm/domain/OrganizationIgnoredProperties.java
View File

@ -1,6 +1,6 @@
package eu.dnetlib.dsm.domain;
import java.util.Date;
import java.time.LocalDateTime;
import java.util.Set;
import com.fasterxml.jackson.annotation.JsonIgnore;
@ -14,7 +14,7 @@ public class OrganizationIgnoredProperties {
protected String collectedfrom;
@JsonIgnore
protected Date dateofcollection;
protected LocalDateTime dateofcollection;
@JsonIgnore
protected String provenanceaction;
@ -38,11 +38,11 @@ public class OrganizationIgnoredProperties {
this.collectedfrom = collectedfrom;
}
public Date getDateofcollection() {
public LocalDateTime getDateofcollection() {
return dateofcollection;
}
public void setDateofcollection(final Date dateofcollection) {
public void setDateofcollection(final LocalDateTime dateofcollection) {
this.dateofcollection = dateofcollection;
}

4
libs/dnet-is-services/src/main/java/eu/dnetlib/dsm/repository/DatasourceRepository.java
View File

@ -1,6 +1,6 @@
package eu.dnetlib.dsm.repository;
import java.sql.Date;
import java.time.LocalDate;
import java.util.Optional;
import javax.transaction.Transactional;
@ -64,7 +64,7 @@ public interface DatasourceRepository extends JpaRepository<Datasource, String>,
@Modifying
@Transactional
@Query("update #{#entityName} d set d.registrationdate = ?2 where d.id = ?1")
void setRegistrationDate(String id, Date registrationdate);
void setRegistrationDate(String id, LocalDate registrationdate);
@Modifying
@Transactional

4
libs/dnet-is-services/src/main/java/eu/dnetlib/dsm/utils/DsmMappingUtils.java
View File

@ -1,6 +1,6 @@
package eu.dnetlib.dsm.utils;
import java.sql.Date;
import java.time.LocalDateTime;
import java.util.HashSet;
import java.util.Set;
import java.util.stream.Collectors;
@ -98,7 +98,7 @@ public class DsmMappingUtils {
final String prefix = StringUtils.isNotBlank(dbe.getNamespaceprefix()) ? dbe.getNamespaceprefix() : dbe.getId();
o.setId(prefix + ID_SEPARATOR + o.getLegalname());
if (o.getDateofcollection() == null) {
o.setDateofcollection(new Date(System.currentTimeMillis()));
o.setDateofcollection(LocalDateTime.now());
}
o.setCollectedfrom(dbe.getCollectedfrom());
});

6
libs/dnet-is-services/src/main/java/eu/dnetlib/is/resource/SimpleResourceService.java
View File

@ -1,6 +1,6 @@
package eu.dnetlib.is.resource;
import java.util.Date;
import java.time.LocalDateTime;
import java.util.List;
import java.util.UUID;
import java.util.stream.Collectors;
@ -60,17 +60,19 @@ public class SimpleResourceService {
@Transactional
public SimpleResource saveNewResource(final String name,
final String type,
final String subtype,
final String description,
final String content) throws InformationServiceException {
resourceValidator.validate(type, content);
final Date now = new Date();
final LocalDateTime now = LocalDateTime.now();
final SimpleResource res = new SimpleResource();
res.setId(UUID.randomUUID().toString());
res.setName(name);
res.setType(type);
res.setSubtype(subtype);
res.setDescription(description);
res.setCreationDate(now);
res.setModificationDate(now);

51
libs/dnet-is-services/src/main/java/eu/dnetlib/manager/history/WorkflowLogger.java Normal file
View File

@ -0,0 +1,51 @@
package eu.dnetlib.manager.history;
import java.time.Instant;
import java.time.LocalDateTime;
import java.util.List;
import java.util.Optional;
import java.util.TimeZone;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.data.domain.PageRequest;
import org.springframework.data.domain.Sort;
import org.springframework.stereotype.Service;
import eu.dnetlib.manager.history.model.WfProcessExecution;
import eu.dnetlib.manager.history.repository.WfProcessExecutionRepository;
@Service
public class WorkflowLogger {
@Autowired
private WfProcessExecutionRepository wfProcessExecutionRepository;
public List<WfProcessExecution> history(final int total, final Long from, final Long to) {
if (from == null && to == null) {
return wfProcessExecutionRepository.findAll(PageRequest.of(0, total, Sort.by("endDate").descending())).toList();
} else {
final LocalDateTime fromTime = from != null ? LocalDateTime.ofInstant(Instant.ofEpochMilli(from), TimeZone
.getDefault()
.toZoneId()) : LocalDateTime.MIN;
final LocalDateTime toTime = to != null ? LocalDateTime.ofInstant(Instant.ofEpochMilli(to), TimeZone
.getDefault()
.toZoneId()) : LocalDateTime.MAX;
return wfProcessExecutionRepository.findByEndDateBetweenOrderByEndDateDesc(fromTime, toTime);
}
}
public WfProcessExecution getProcessExecution(final String processId) {
return wfProcessExecutionRepository.findById(processId).get();
}
public void saveProcessExecution(final WfProcessExecution pe) {
wfProcessExecutionRepository.save(pe);
}
public Optional<WfProcessExecution> getLastExecutionForInstance(final String id) {
return wfProcessExecutionRepository.findOneByWfInstanceIdOrderByEndDateAsc(id);
}
}

16
libs/dnet-is-services/src/main/java/eu/dnetlib/manager/history/repository/WfProcessExecutionRepository.java Normal file
View File

@ -0,0 +1,16 @@
package eu.dnetlib.manager.history.repository;
import java.time.LocalDateTime;
import java.util.List;
import java.util.Optional;
import org.springframework.data.jpa.repository.JpaRepository;
import eu.dnetlib.manager.history.model.WfProcessExecution;
public interface WfProcessExecutionRepository extends JpaRepository<WfProcessExecution, String> {
List<WfProcessExecution> findByEndDateBetweenOrderByEndDateDesc(LocalDateTime start, LocalDateTime end);
Optional<WfProcessExecution> findOneByWfInstanceIdOrderByEndDateAsc(String id);
}

21
libs/dnet-is-services/src/main/java/eu/dnetlib/manager/wf/repository/WorkflowInstanceRepository.java Normal file
View File

@ -0,0 +1,21 @@
package eu.dnetlib.manager.wf.repository;
import java.util.stream.Stream;
import org.springframework.data.jpa.repository.JpaRepository;
import org.springframework.data.jpa.repository.Query;
import eu.dnetlib.manager.wf.model.WorkflowInstance;
import eu.dnetlib.utils.CountedValue;
public interface WorkflowInstanceRepository extends JpaRepository<WorkflowInstance, String> {
@Query(value = "select section as value, count(*) as count "
+ "from workflow_instances "
+ "group by section "
+ "order by count desc;", nativeQuery = true)
Stream<CountedValue> streamSections();
Stream<WorkflowInstance> findBySection(String section);
}

13
libs/dnet-is-services/src/main/java/eu/dnetlib/manager/wf/repository/WorkflowSubscriptionRepository.java Normal file
View File

@ -0,0 +1,13 @@
package eu.dnetlib.manager.wf.repository;
import java.util.List;
import org.springframework.data.jpa.repository.JpaRepository;
import eu.dnetlib.manager.wf.model.WorkflowSubscription;
import eu.dnetlib.manager.wf.model.WorkflowSubscriptionPK;
public interface WorkflowSubscriptionRepository extends JpaRepository<WorkflowSubscription, WorkflowSubscriptionPK> {
List<WorkflowSubscription> findByWfInstanceId(String wfInstanceId);
}

13
libs/dnet-is-services/src/main/java/eu/dnetlib/msro/history/repository/WfProcessExecutionRepository.java
View File

@ -1,13 +0,0 @@
package eu.dnetlib.msro.history.repository;
import java.util.Date;
import java.util.List;
import org.springframework.data.jpa.repository.JpaRepository;
import eu.dnetlib.msro.model.history.WfProcessExecution;
public interface WfProcessExecutionRepository extends JpaRepository<WfProcessExecution, String> {
List<WfProcessExecution> findByEndDateBetweenOrderByEndDateDesc(Date start, Date end);
}

170
libs/dnet-is-services/src/main/java/eu/dnetlib/notifications/mail/EmailService.java Normal file
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@ -0,0 +1,170 @@
package eu.dnetlib.notifications.mail;
import java.util.Date;
import java.util.List;
import java.util.Map;
import java.util.Map.Entry;
import java.util.Properties;
import java.util.UUID;
import java.util.concurrent.BlockingQueue;
import java.util.concurrent.LinkedBlockingQueue;
import javax.annotation.PostConstruct;
import javax.mail.Authenticator;
import javax.mail.Message;
import javax.mail.MessagingException;
import javax.mail.PasswordAuthentication;
import javax.mail.Session;
import javax.mail.Transport;
import javax.mail.internet.InternetAddress;
import javax.mail.internet.MimeMessage;
import org.apache.commons.lang3.StringUtils;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.beans.factory.annotation.Value;
import org.springframework.stereotype.Service;
import com.google.common.base.Splitter;
import eu.dnetlib.common.model.EmailTemplate;
import eu.dnetlib.common.repository.EmailTemplateRepository;
@Service
public class EmailService {
private static final Log log = LogFactory.getLog(EmailService.class);
private final BlockingQueue<Message> queue = new LinkedBlockingQueue<>();
@Value("${dnet.configuration.mail.sender.email}")
private String from;
@Value("${dnet.configuration.mail.sender.name}")
private String fromName;
@Value("${dnet.configuration.mail.cc}")
private String cc;
@Value("${dnet.configuration.mail.smtp.host}")
private String smtpHost;
@Value("${dnet.configuration.mail.smtp.port}")
private final int smtpPort = 587;
@Value("${dnet.configuration.mail.smtp.user}")
private String smtpUser;
@Value("${dnet.configuration.mail.smtp.password}")
private String smtpPassword;
@Value("${server.public_url}")
private String baseUrl;
@Value("${dnet.configuration.infrastructure}")
private String infrastructure;
@Autowired
private EmailTemplateRepository emailTemplateRepository;
@PostConstruct
private void init() {
new Thread(() -> {
while (true) {
try {
final Message message = this.queue.take();
if (message != null) {
try {
log.info("Sending mail...");
Transport.send(message);
log.info("...sent");
} catch (final MessagingException e) {
log.error("Error sending email", e);
this.queue.add(message);
}
}
} catch (final InterruptedException e1) {
throw new RuntimeException(e1);
}
}
}).start();
}
public List<EmailTemplate> listEmailTemplates() {
return emailTemplateRepository.findAll();
}
public void saveEmailTemplate(final EmailTemplate email) {
if (StringUtils.isBlank(email.getId()) || email.getId().length() < 10) {
email.setId("email-" + UUID.randomUUID());
log.info("Saving new email with id: " + email.getId());
}
emailTemplateRepository.save(email);
}
public void deleteEmailTemplate(final String id) {
emailTemplateRepository.deleteById(id);
}
public void sendMail(final String to, final String subject, final String message) {
try {
final Session session = Session.getInstance(obtainProperties(), obtainAuthenticator());
final MimeMessage mimeMessage = new MimeMessage(session);
mimeMessage.setFrom(new InternetAddress(this.from, this.fromName));
mimeMessage.setSubject(subject);
mimeMessage.setContent(message, "text/html; charset=utf-8");
mimeMessage.setSentDate(new Date());
mimeMessage.addRecipient(Message.RecipientType.TO, new InternetAddress(to));
if (this.cc != null && !this.cc.isEmpty()) {
for (final String aCC : Splitter.on(",").omitEmptyStrings().trimResults().split(cc)) {
mimeMessage.addRecipient(Message.RecipientType.CC, new InternetAddress(aCC));
}
}
this.queue.add(mimeMessage);
log.info("Mail to " + to + " in queue");
} catch (final Exception e) {
log.error("Error sending mail", e);
}
}
public void sendStoredMail(final String to, final String emailId, final Map<String, Object> params) {
// TODO use a real template library
emailTemplateRepository.findById(emailId).ifPresent(tmpl -> {
String msg = tmpl.getMessage();
String subject = tmpl.getSubject();
for (final Entry<String, Object> e : params.entrySet()) {
msg = msg.replaceAll("{" + e.getKey() + "}", e.getValue().toString());
subject = subject.replaceAll("{" + e.getKey() + "}", e.getValue().toString());
}
sendMail(to, subject, msg);
});
}
private Properties obtainProperties() {
final Properties props = new Properties();
props.put("mail.transport.protocol", "smtp");
props.put("mail.smtp.host", this.smtpHost);
props.put("mail.smtp.port", this.smtpPort);
props.put("mail.smtp.auth", Boolean.toString(this.smtpUser != null && !this.smtpUser.isEmpty()));
return props;
}
private Authenticator obtainAuthenticator() {
if (this.smtpUser == null || this.smtpUser.isEmpty()) { return null; }
final String user = this.smtpUser;
final String passwd = this.smtpPassword;
return new Authenticator() {
private final PasswordAuthentication authentication = new PasswordAuthentication(user, passwd);
@Override
protected PasswordAuthentication getPasswordAuthentication() {
return this.authentication;
}
};
}
}

48
libs/dnet-wf-service/pom.xml Normal file
View File

@ -0,0 +1,48 @@
<?xml version="1.0"?>
<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
<parent>
<groupId>eu.dnetlib.dhp</groupId>
<artifactId>libs</artifactId>
<version>3.3.3-SNAPSHOT</version>
<relativePath>../</relativePath>
</parent>
<modelVersion>4.0.0</modelVersion>
<artifactId>dnet-wf-service</artifactId>
<packaging>jar</packaging>
<dependencies>
<dependency>
<groupId>eu.dnetlib.dhp</groupId>
<artifactId>dnet-is-services</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>eu.dnetlib.dhp</groupId>
<artifactId>dnet-data-services</artifactId>
<version>${project.version}</version>
</dependency>
<!-- Tests -->
<dependency>
<groupId>org.junit.jupiter</groupId>
<artifactId>junit-jupiter</artifactId>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.mockito</groupId>
<artifactId>mockito-core</artifactId>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.mockito</groupId>
<artifactId>mockito-junit-jupiter</artifactId>
<scope>test</scope>
</dependency>
</dependencies>
</project>

26
libs/dnet-wf-service/src/main/java/eu/dnetlib/manager/wf/NodeInfo.java Normal file
View File

@ -0,0 +1,26 @@
package eu.dnetlib.manager.wf;
import java.util.LinkedHashMap;
import java.util.Map;
public class NodeInfo {
private String name;
private Map<String, String> params = new LinkedHashMap<>();
public String getName() {
return name;
}
public void setName(final String name) {
this.name = name;
}
public Map<String, String> getParams() {
return params;
}
public void setParams(final Map<String, String> params) {
this.params = params;
}
}

20
libs/dnet-wf-service/src/main/java/eu/dnetlib/manager/wf/WfManager.java Normal file
View File

@ -0,0 +1,20 @@
package eu.dnetlib.manager.wf;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.context.ApplicationContext;
import org.springframework.stereotype.Service;
@Service
public class WfManager {
@Autowired
private ApplicationContext applicationContext;
/*
* public Object obtainBaseNode(final String name) { return applicationContext.getBean(name); }
*
* public NodeInfo obtainInfo(final BaseNode<?, ?> node) { final NodeInfo info = new NodeInfo(); final WfNode annotation =
* node.getClass().getAnnotation(WfNode.class); info.setName(annotation.name()); for (final WfParam p : annotation.inputParams()) {
* info.getParams().put(p.name(), p.type()); } return info; }
*/
}

198
libs/dnet-wf-service/src/main/java/eu/dnetlib/manager/wf/WorkflowManagerService.java Normal file
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@ -0,0 +1,198 @@
package eu.dnetlib.manager.wf;
import java.util.HashMap;
import java.util.Objects;
import java.util.UUID;
import java.util.concurrent.Executors;
import java.util.concurrent.TimeUnit;
import java.util.stream.Stream;
import javax.annotation.PostConstruct;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.stereotype.Service;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dsm.DsmService;
import eu.dnetlib.errors.DsmException;
import eu.dnetlib.errors.WorkflowManagerException;
import eu.dnetlib.is.model.resource.SimpleResource;
import eu.dnetlib.is.resource.repository.SimpleResourceRepository;
import eu.dnetlib.manager.wf.model.WorkflowGraph;
import eu.dnetlib.manager.wf.model.WorkflowInstance;
import eu.dnetlib.manager.wf.repository.WorkflowInstanceRepository;
import eu.dnetlib.manager.wf.workflows.procs.ProcessEngine;
import eu.dnetlib.manager.wf.workflows.procs.ProcessFactory;
import eu.dnetlib.manager.wf.workflows.procs.ProcessRegistry;
import eu.dnetlib.manager.wf.workflows.procs.WorkflowProcess;
import eu.dnetlib.manager.wf.workflows.util.ExecutionCallback;
import eu.dnetlib.manager.wf.workflows.util.WorkflowsConstants;
import eu.dnetlib.utils.CountedValue;
import eu.dnetlib.utils.Stoppable;
import eu.dnetlib.utils.StoppableDetails;
@Service
public class WorkflowManagerService implements Stoppable {
private static final Log log = LogFactory.getLog(WorkflowManagerService.class);
@Autowired
private ProcessRegistry processRegistry;
@Autowired
private ProcessFactory processFactory;
@Autowired
private ProcessEngine processEngine;
@Autowired
private DsmService dsmService;
@Autowired
private SimpleResourceRepository simpleResourceRepository;
@Autowired
private WorkflowInstanceRepository workflowInstanceRepository;
private boolean paused = false;
@PostConstruct
public void init() {
Executors.newSingleThreadScheduledExecutor().scheduleAtFixedRate(() -> {
if (isPaused() || processRegistry.countRunningWfs() >= WorkflowsConstants.MAX_RUNNING_PROCS_SIZE) { return; }
final WorkflowProcess process = processRegistry.nextProcessToStart();
if (process != null) {
processEngine.startProcess(process);
} else {
log.debug("WorkflowProcess queue is empty");
}
}, 10, 10, TimeUnit.SECONDS);
}
public WorkflowInstance findWorkflowInstance(final String id) throws WorkflowManagerException {
return workflowInstanceRepository.findById(id).orElseThrow(() -> new WorkflowManagerException("WF instance not found: " + id));
}
public String startRepoHiWorkflow(final String wfId,
final String dsId,
final String apiId,
final ExecutionCallback<WorkflowProcess> callback)
throws WorkflowManagerException {
if (isPaused()) {
log.warn("Wf " + wfId + " not launched, because WorkflowExecutor is preparing for shutdown");
throw new WorkflowManagerException("WorkflowExecutor is preparing for shutdown");
}
try {
final String dsName = dsmService.getDs(dsId).getOfficialname();
final WorkflowInstance instance = new WorkflowInstance();
instance.setId("REPO_HI_" + UUID.randomUUID());
instance.setDetails(new HashMap<>());
instance.setPriority(100);
instance.setDsId(dsId);
instance.setDsName(dsName);
instance.setApiId(apiId);
instance.setEnabled(true);
instance.setConfigured(true);
instance.setSchedulingEnabled(false);
instance.setCronExpression("");
instance.setCronMinInterval(0);
instance.setWorkflow(wfId);
instance.setDestroyWf(null);
instance.setSystemParams(new HashMap<>());
instance.setUserParams(new HashMap<>());
return startWorkflowInstance(instance, callback);
} catch (final DsmException e) {
throw new WorkflowManagerException("Invalid datasource: " + dsId, e);
}
}
public String startWorkflowInstance(final String wfInstanceId,
final String parent,
final ExecutionCallback<WorkflowProcess> callback) throws Exception {
if (isPaused()) {
log.warn("Wf instance " + wfInstanceId + " not launched, because WorkflowExecutor is preparing for shutdown");
throw new WorkflowManagerException("WorkflowExecutor is preparing for shutdown");
}
final WorkflowInstance instance = findWorkflowInstance(wfInstanceId);
return startWorkflowInstance(instance, callback);
}
public String startWorkflowInstance(final WorkflowInstance wfInstance,
final ExecutionCallback<WorkflowProcess> callback)
throws WorkflowManagerException {
if (!wfInstance.isEnabled() || !wfInstance.isConfigured()) {
log.warn("Wf instance " + wfInstance.getId() + " is not ready to start");
throw new WorkflowManagerException("Wf instance " + wfInstance.getId() + " is not ready to start");
}
final SimpleResource wfMetadata = simpleResourceRepository
.findById(wfInstance.getWorkflow())
.filter(r -> r.getType().equals("workflows"))
.orElseThrow(() -> new WorkflowManagerException("WF not found: " + wfInstance.getWorkflow()));
final WorkflowGraph wfGraph = simpleResourceRepository.findContentById(wfMetadata.getId())
.map(s -> {
try {
return new ObjectMapper().readValue(s, WorkflowGraph.class);
} catch (final Exception e) {
return (WorkflowGraph) null;
}
})
.filter(Objects::nonNull)
.orElseThrow(() -> new WorkflowManagerException("Invalid wf: " + wfMetadata.getId()));
final WorkflowProcess process =
processFactory.newProcess(wfMetadata, wfGraph, wfInstance, callback);
return processRegistry.registerProcess(process, wfInstance);
}
@Override
public void stop() {
paused = true;
}
@Override
public void resume() {
paused = false;
}
@Override
public StoppableDetails getStopDetails() {
final int count = processRegistry.countRunningWfs();
final StoppableDetails.StopStatus status =
isPaused() ? count == 0 ? StoppableDetails.StopStatus.STOPPED : StoppableDetails.StopStatus.STOPPING : StoppableDetails.StopStatus.RUNNING;
return new StoppableDetails("D-NET workflow manager", "Running workflows: " + count, status);
}
public ProcessRegistry getProcessRegistry() {
return processRegistry;
}
public boolean isPaused() {
return paused;
}
public void setPaused(final boolean paused) {
this.paused = paused;
}
public Stream<CountedValue> streamSections() {
return workflowInstanceRepository.streamSections();
}
public Stream<WorkflowInstance> streamWfInstancesBySection(final String section) {
return workflowInstanceRepository.findBySection(section);
}
}

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libs/dnet-wf-service/src/main/java/eu/dnetlib/manager/wf/annotations/StreamMimeType.java Normal file
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package eu.dnetlib.manager.wf.annotations;
public enum StreamMimeType {
XML,
JSON,
TEXT,
UNDEFINED
}

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libs/dnet-wf-service/src/main/java/eu/dnetlib/manager/wf/annotations/WfNode.java Normal file
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package eu.dnetlib.manager.wf.annotations;
public @interface WfNode {
String name();
WfNodeOperation operation();
Class<?> inputStreamType() default void.class;
StreamMimeType inputStreamMimeType() default StreamMimeType.UNDEFINED;
Class<?> outputStreamType() default void.class;
StreamMimeType outputStreamMimeType() default StreamMimeType.UNDEFINED;
WfParam[] inputParams() default {};
WfParam[] outputParams() default {};
}

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libs/dnet-wf-service/src/main/java/eu/dnetlib/manager/wf/annotations/WfNodeOperation.java Normal file
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package eu.dnetlib.manager.wf.annotations;
public enum WfNodeOperation {
CREATE,
DROP,
READ,
WRITE,
PRODUCER,
TRANSFORM,
SETENV
}

8
libs/dnet-wf-service/src/main/java/eu/dnetlib/manager/wf/annotations/WfParam.java Normal file
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package eu.dnetlib.manager.wf.annotations;
public @interface WfParam {
String name();
String type();
}

138
libs/dnet-wf-service/src/main/java/eu/dnetlib/manager/wf/cron/ScheduledWorkflowLauncher.java Normal file
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package eu.dnetlib.manager.wf.cron;
import java.time.LocalDateTime;
import java.time.temporal.ChronoUnit;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.beans.factory.annotation.Value;
import org.springframework.scheduling.annotation.Scheduled;
import org.springframework.scheduling.support.CronExpression;
import org.springframework.stereotype.Service;
import eu.dnetlib.manager.history.WorkflowLogger;
import eu.dnetlib.manager.wf.WorkflowManagerService;
import eu.dnetlib.manager.wf.model.WorkflowInstance;
import eu.dnetlib.manager.wf.repository.WorkflowInstanceRepository;
import eu.dnetlib.manager.wf.workflows.procs.ProcessRegistry;
import eu.dnetlib.manager.wf.workflows.procs.WorkflowProcess;
@Service
public class ScheduledWorkflowLauncher {
private static final Log log = LogFactory.getLog(ScheduledWorkflowLauncher.class);
@Autowired
private WorkflowManagerService wfManagerService;
@Autowired
private ProcessRegistry processRegistry;
@Autowired
private WorkflowInstanceRepository workflowInstanceRepository;
@Autowired
private WorkflowLogger logger;
@Value("${dnet.workflow.scheduler.windowSize:1800000}")
private int windowSize; // 1800000 are 30 minutes
@Scheduled(fixedRateString = "${dnet.workflow.scheduler.fixedRate:900000}") // 900000 are 5 minutes
public void verifySheduledWorkflows() {
log.debug("Verifying scheduled workflows - START");
workflowInstanceRepository.findAll()
.stream()
.filter(WorkflowInstance::isEnabled)
.filter(WorkflowInstance::isConfigured)
.filter(WorkflowInstance::isSchedulingEnabled)
.filter(this::isNotRunning)
.filter(this::isReady)
.forEach(instance -> {
try {
wfManagerService.startWorkflowInstance(instance, null);
} catch (final Exception e) {
log.error("Error launching scheduled wf instance: " + instance.getId(), e);
}
});
log.debug("Verifying scheduled workflows - END");
}
private boolean isReady(final WorkflowInstance instance) {
final LocalDateTime lastExecutionDate = calculateLastExecutionDate(instance.getId());
final LocalDateTime now = LocalDateTime.now();
final String cron = instance.getCronExpression();
if (CronExpression.isValidExpression(cron)) {
final int minInterval = instance.getCronMinInterval(); // in minutes
final boolean res;
if (lastExecutionDate != null) {
final long elapsed = ChronoUnit.MINUTES.between(lastExecutionDate, now);
res = elapsed > minInterval && verifyCron(cron, now);
} else {
res = verifyCron(cron, now);
}
if (log.isDebugEnabled()) {
log.debug("**************************************************************");
log.debug("WORKFLOW INSTANCE ID : " + instance.getId());
log.debug("NOW : " + now);
log.debug("LAST EXECUTION DATE : " + lastExecutionDate);
log.debug("MIN INTERVAL (minutes) : " + minInterval);
log.debug("WINDOW SIZE (ms) : " + windowSize);
log.debug("MUST BE EXECUTED : " + res);
log.debug("**************************************************************");
}
return res;
}
return false;
}
private LocalDateTime calculateLastExecutionDate(final String id) {
return logger.getLastExecutionForInstance(id)
.map(e -> e.getEndDate())
.orElse(LocalDateTime.MIN);
}
private boolean verifyCron(final String cronExpression, final LocalDateTime now) {
try {
final CronExpression cron = CronExpression.parse(cronExpression);
final LocalDateTime date = now.minus(windowSize, ChronoUnit.MINUTES);
final LocalDateTime nextDate = cron.next(date);
if (log.isDebugEnabled()) {
log.debug("NEXT EXECUTION DATE: " + nextDate);
log.debug("FIRED : " + nextDate.isBefore(now));
}
return nextDate.isBefore(now);
} catch (final Exception e) {
log.error("Error calculating next cron event: " + cronExpression, e);
return false;
}
}
private boolean isNotRunning(final WorkflowInstance instance) {
final WorkflowProcess p = processRegistry.findProcsByInstanceId(instance.getId());
if (p != null) {
switch (p.getStatus()) {
case CREATED:
return false;
case EXECUTING:
return false;
default:
break;
}
}
return true;
}
}

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libs/dnet-wf-service/src/main/java/eu/dnetlib/manager/wf/nodes/AbstractJobNode.java Normal file
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package eu.dnetlib.manager.wf.nodes;
import java.util.concurrent.ExecutorService;
import java.util.concurrent.Executors;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import eu.dnetlib.manager.wf.workflows.procs.Token;
import eu.dnetlib.manager.wf.workflows.util.ExecutionCallback;
public abstract class AbstractJobNode extends ProcessNode {
private static final Log log = LogFactory.getLog(AbstractJobNode.class);
private final boolean async;
public AbstractJobNode(final boolean async) {
this.async = async;
}
private final ExecutorService executor = Executors.newCachedThreadPool();
@Override
public final void execute(final Token token, final ExecutionCallback<Token> callback) {
try {
log.debug("START NODE: " + getBeanName());
token.setProgressMessage(getNodeName());
beforeStart(token);
if (isAsync()) {
executor.execute(() -> doExecute(token, callback));
} else {
doExecute(token, callback);
}
log.debug("END NODE (SUCCESS): " + getBeanName());
} catch (final Throwable e) {
log.error("got exception while executing workflow node", e);
log.debug("END NODE (FAILED): " + getBeanName());
beforeFailed(token);
callback.onFail(token);
}
}
private final void doExecute(final Token token, final ExecutionCallback<Token> callback) {
execute(token);
beforeCompleted(token);
callback.onSuccess(token);
}
protected abstract void execute(Token token);
public final boolean isAsync() {
return async;
}
protected void beforeStart(final Token token) {
// For optional overwrites
}
protected void beforeCompleted(final Token token) {
// For optional overwrites
}
protected void beforeFailed(final Token token) {
// For optional overwrites
}
}

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libs/dnet-wf-service/src/main/java/eu/dnetlib/manager/wf/nodes/CollectOAINode.java Normal file
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package eu.dnetlib.manager.wf.nodes;
import java.util.function.Supplier;
import java.util.stream.Stream;
import org.springframework.context.annotation.Scope;
import org.springframework.stereotype.Component;
import eu.dnetlib.manager.wf.annotations.StreamMimeType;
import eu.dnetlib.manager.wf.annotations.WfNode;
import eu.dnetlib.manager.wf.annotations.WfNodeOperation;
import eu.dnetlib.manager.wf.annotations.WfParam;
@Component("oai_collect")
@Scope("prototype")
@WfNode(name = "oai_collect", operation = WfNodeOperation.PRODUCER, inputParams = {
@WfParam(name = "configuration", type = "ApiDescriptor.class"),
}, outputStreamType = String.class, outputStreamMimeType = StreamMimeType.XML)
public class CollectOAINode implements Supplier<Stream<String>> {
private String datasourceID;
@Override
public Stream<String> get() {
// TODO Auto-generated method stub
return null;
}
}

18
libs/dnet-wf-service/src/main/java/eu/dnetlib/manager/wf/nodes/DefaultJobNode.java Normal file
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package eu.dnetlib.manager.wf.nodes;
import eu.dnetlib.manager.wf.workflows.procs.Token;
/**
* Created by michele on 26/11/15.
*/
public final class DefaultJobNode extends AbstractJobNode {
public DefaultJobNode(final String name) {
super(false);
setNodeName(name);
}
@Override
public void execute(final Token token) {}
}

96
libs/dnet-wf-service/src/main/java/eu/dnetlib/manager/wf/nodes/LaunchWorkflowJobNode.java Normal file
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package eu.dnetlib.manager.wf.nodes;
import java.util.HashMap;
import java.util.UUID;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import org.springframework.beans.factory.annotation.Autowired;
import eu.dnetlib.manager.wf.WorkflowManagerService;
import eu.dnetlib.manager.wf.model.WorkflowInstance;
import eu.dnetlib.manager.wf.workflows.procs.ProcessAware;
import eu.dnetlib.manager.wf.workflows.procs.Token;
import eu.dnetlib.manager.wf.workflows.procs.WorkflowProcess;
import eu.dnetlib.manager.wf.workflows.util.ExecutionCallback;
/**
* Created by michele on 18/11/15.
*/
public class LaunchWorkflowJobNode extends ProcessNode implements ProcessAware {
private static final Log log = LogFactory.getLog(LaunchWorkflowJobNode.class);
private String wfId;
@Autowired
private WorkflowManagerService wfManagerService;
private WorkflowProcess process;
@Override
public final void execute(final Token token, final ExecutionCallback<Token> callback) {
try {
final WorkflowInstance instance = new WorkflowInstance();
instance.setId("CHILD_" + UUID.randomUUID());
instance.setParentId(process.getWfInstanceId());
instance.setDetails(new HashMap<>());
instance.setPriority(100);
instance.setDsId(process.getDsId());
instance.setDsName(process.getDsName());
instance.setApiId(process.getDsInterface());
instance.setEnabled(true);
instance.setConfigured(true);
instance.setSchedulingEnabled(false);
instance.setCronExpression("");
instance.setCronMinInterval(0);
instance.setWorkflow(wfId);
instance.setDestroyWf(null);
instance.setSystemParams(process.getGlobalParams());
instance.setUserParams(new HashMap<>());
final String procId = wfManagerService.startWorkflowInstance(instance, new ExecutionCallback<WorkflowProcess>() {
@Override
public void onSuccess(final WorkflowProcess t) {
log.debug("Child workflow has been completed successfully");
token.release();
callback.onSuccess(token);
}
@Override
public void onFail(final WorkflowProcess t) {
log.error("Child workflow is failed");
token.releaseAsFailed("Child workflow is failed");
callback.onFail(token);
}
});
if (log.isDebugEnabled()) {
log.debug("The child workflow [instance: " + instance.getId() + "] is starting with procId: " + procId);
}
token.setProgressMessage("Launched sub workflow, proc: " + procId);
} catch (final Throwable e) {
log.error("got exception while launching child workflow", e);
callback.onFail(token);
}
}
@Override
public void setProcess(final WorkflowProcess process) {
this.process = process;
}
public String getWfId() {
return wfId;
}
public void setWfId(final String wfId) {
this.wfId = wfId;
}
}

8
libs/dnet-wf-service/src/main/java/eu/dnetlib/manager/wf/nodes/NodeStatus.java Normal file
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package eu.dnetlib.manager.wf.nodes;
public enum NodeStatus {
CONFIGURED,
NOT_CONFIGURED,
DISABLED,
SYSTEM
}

38
libs/dnet-wf-service/src/main/java/eu/dnetlib/manager/wf/nodes/ProcessNode.java Normal file
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package eu.dnetlib.manager.wf.nodes;
import org.springframework.beans.factory.BeanNameAware;
import eu.dnetlib.manager.wf.workflows.procs.Token;
import eu.dnetlib.manager.wf.workflows.util.ExecutionCallback;
public abstract class ProcessNode implements BeanNameAware {
private String beanName;
private String nodeName;
public abstract void execute(final Token token, ExecutionCallback<Token> callback);
public String getBeanName() {
return this.beanName;
}
@Override
public void setBeanName(final String beanName) {
this.beanName = beanName;
}
public String getNodeName() {
return this.nodeName;
}
public void setNodeName(final String nodeName) {
this.nodeName = nodeName;
}
@Override
public String toString() {
return String.format("[node beanName=%s, name=%s]", this.beanName, this.nodeName);
}
}

9
libs/dnet-wf-service/src/main/java/eu/dnetlib/manager/wf/nodes/SimpleJobNode.java Normal file
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package eu.dnetlib.manager.wf.nodes;
public abstract class SimpleJobNode extends AbstractJobNode {
public SimpleJobNode() {
super(false);
}
}

18
libs/dnet-wf-service/src/main/java/eu/dnetlib/manager/wf/nodes/SuccessNode.java Normal file
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package eu.dnetlib.manager.wf.nodes;
import eu.dnetlib.manager.wf.workflows.procs.Token;
/**
* Created by michele on 26/11/15.
*/
public class SuccessNode extends AbstractJobNode {
public SuccessNode() {
super(false);
setNodeName("success");
}
@Override
protected void execute(final Token token) {}
}

46
libs/dnet-wf-service/src/main/java/eu/dnetlib/manager/wf/notification/EmailSender.java Normal file
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package eu.dnetlib.manager.wf.notification;
import java.util.HashMap;
import java.util.Map;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.stereotype.Service;
import eu.dnetlib.manager.wf.model.NotificationCondition;
import eu.dnetlib.manager.wf.repository.WorkflowSubscriptionRepository;
import eu.dnetlib.manager.wf.workflows.procs.WorkflowProcess;
import eu.dnetlib.manager.wf.workflows.procs.WorkflowProcess.Status;
import eu.dnetlib.notifications.mail.EmailService;
@Service
public class EmailSender {
private static final Log log = LogFactory.getLog(EmailSender.class);
@Autowired
private WorkflowSubscriptionRepository wfSubscriptionRepository;
@Autowired
private EmailService emailService;
public void sendMails(final WorkflowProcess proc) {
wfSubscriptionRepository.findByWfInstanceId(proc.getWfInstanceId()).forEach(s -> {
if (s.getCondition() == NotificationCondition.ALWAYS ||
s.getCondition() == NotificationCondition.ONLY_FAILED && proc.getStatus() == Status.FAILURE ||
s.getCondition() == NotificationCondition.ONLY_SUCCESS && proc.getStatus() == Status.SUCCESS) {
try {
final Map<String, Object> params = new HashMap<>();
emailService.sendStoredMail(s.getEmail(), s.getMessageId(), params);
} catch (final Exception e) {
log.error("Error sending mail to " + s.getEmail(), e);
}
}
});
}
}

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libs/dnet-wf-service/src/main/java/eu/dnetlib/manager/wf/workflows/graph/Arc.java Normal file
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package eu.dnetlib.manager.wf.workflows.graph;
import com.google.common.base.Function;
import eu.dnetlib.manager.wf.workflows.procs.Env;
public class Arc {
private final String from;
private final String to;
private final Function<Env, Boolean> condFunction;
public Arc(final String from, final String to, final Function<Env, Boolean> condFunction) {
this.from = from;
this.to = to;
this.condFunction = condFunction;
}
public String getFrom() {
return this.from;
}
public String getTo() {
return this.to;
}
public boolean isValid(final Env env) {
if (condFunction != null) {
return condFunction.apply(env);
} else {
return true;
}
}
@Override
public String toString() {
return String.format("[ %s -> %s, %s ]", this.from, this.to, this.condFunction != null ? "with cond" : "without cond");
}
}

84
libs/dnet-wf-service/src/main/java/eu/dnetlib/manager/wf/workflows/graph/Graph.java Normal file
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package eu.dnetlib.manager.wf.workflows.graph;
import java.util.ArrayList;
import java.util.Collection;
import java.util.HashMap;
import java.util.HashSet;
import java.util.List;
import java.util.Map;
import java.util.Set;
import java.util.stream.Collectors;
import org.apache.commons.lang3.StringUtils;
import eu.dnetlib.manager.wf.workflows.procs.Env;
public class Graph {
private final Map<String, GraphNode> nodes = new HashMap<>();
private List<Arc> arcs = new ArrayList<>();
public void addArc(final Arc arc) {
this.arcs.add(arc);
}
public void addNode(final GraphNode node) {
this.nodes.put(node.getName(), node);
}
public Set<String> nodeNames() {
return this.nodes.keySet();
}
public Collection<GraphNode> nodes() {
return this.nodes.values();
}
public GraphNode getNode(final String name) {
return this.nodes.get(name);
}
public List<Arc> getArcs() {
return this.arcs;
}
public void setArcs(final List<Arc> arcs) {
this.arcs = arcs;
}
public Set<GraphNode> startNodes() {
final Set<GraphNode> res = new HashSet<>();
for (final GraphNode n : this.nodes.values()) {
if (n.isStart()) {
res.add(n);
}
}
return res;
}
public Set<GraphNode> nextNodes(final GraphNode current, final Env env) {
return arcs.stream()
.filter(arc -> StringUtils.equals(arc.getFrom(), current.getName()))
.filter(arc -> arc.isValid(env))
.map(arc -> arc.getTo())
.distinct()
.map(to -> nodes.get(to))
.collect(Collectors.toSet());
}
public int getNumberOfIncomingArcs(final GraphNode node) {
int count = 0;
for (final Arc arc : this.arcs) {
if (arc.getTo().equals(node.getName())) {
count++;
}
}
return count;
}
@Override
public String toString() {
return "\n************************\nNodes: " + this.nodes + "\nArcs: " + this.arcs + "\n************************\n";
}
}

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libs/dnet-wf-service/src/main/java/eu/dnetlib/manager/wf/workflows/graph/GraphLoader.java Normal file
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package eu.dnetlib.manager.wf.workflows.graph;
import java.util.HashSet;
import java.util.Map;
import java.util.Set;
import org.apache.commons.lang3.StringUtils;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.context.expression.MapAccessor;
import org.springframework.core.env.Environment;
import org.springframework.expression.ExpressionParser;
import org.springframework.expression.spel.standard.SpelExpressionParser;
import org.springframework.expression.spel.support.StandardEvaluationContext;
import org.springframework.stereotype.Service;
import com.google.common.base.Function;
import com.google.common.collect.Sets;
import eu.dnetlib.errors.WorkflowManagerException;
import eu.dnetlib.manager.wf.model.WorkflowGraph;
import eu.dnetlib.manager.wf.workflows.procs.Env;
import eu.dnetlib.manager.wf.workflows.util.NodeHelper;
@Service
public class GraphLoader {
@Autowired
private NodeHelper nodeHelper;
@Autowired
private Environment environment;
public Graph loadGraph(final WorkflowGraph workflowGraph, final Map<String, String> globalParams)
throws WorkflowManagerException {
final Graph graph = new Graph();
for (final WorkflowGraph.Node node : workflowGraph.getGraph()) {
final String nodeName = node.getName();
final String nodeType = node.getType();
final boolean isStart = node.isStart();
final boolean isJoin = node.isJoin();
final Map<String, Object> params = node.calculateInitialParams(globalParams, environment);
final Map<String, String> envParams = node.findEnvParams();
if (isStart) {
graph.addNode(GraphNode.newStartNode(nodeName, nodeType, params, envParams));
} else if (isJoin) {
graph.addNode(GraphNode.newJoinNode(nodeName, nodeType, params, envParams));
} else {
graph.addNode(GraphNode.newNode(nodeName, nodeType, params, envParams));
}
if (node.getArcs() != null) {
for (final WorkflowGraph.Arc a : node.getArcs()) {
final String to = a.getTo();
final Function<Env, Boolean> condFunction = generateFunction(a.getCondition());
graph.addArc(new Arc(nodeName, to, condFunction));
}
}
graph.addNode(GraphNode.newSuccessNode());
}
checkValidity(graph);
return graph;
}
private Function<Env, Boolean> generateFunction(final String condition) {
return env -> {
final ExpressionParser parser = new SpelExpressionParser();
final StandardEvaluationContext context = new StandardEvaluationContext(env.getAttributes());
context.addPropertyAccessor(new MapAccessor());
return parser.parseExpression(condition).getValue(context, Boolean.class);
};
}
private void checkValidity(final Graph graph) throws WorkflowManagerException {
final Set<String> nodesFromArcs = new HashSet<>();
boolean foundSuccess = false;
boolean foundStart = false;
for (final Arc arc : graph.getArcs()) {
if (StringUtils.isBlank(arc.getFrom()) || StringUtils.isBlank(arc.getFrom())) {
throw new WorkflowManagerException("Invalid arc: missing from e/o to");
}
if (StringUtils.equals(arc.getTo(), GraphNode.SUCCESS_NODE)) {
foundSuccess = true;
}
nodesFromArcs.add(arc.getFrom());
nodesFromArcs.add(arc.getTo());
}
if (!foundSuccess) { throw new WorkflowManagerException("Arc to success not found"); }
final Set<String> diff = Sets.symmetricDifference(graph.nodeNames(), nodesFromArcs);
if (!diff.isEmpty()) { throw new WorkflowManagerException("Missing or invalid nodes in arcs: " + diff); }
for (final GraphNode n : graph.nodes()) {
if (StringUtils.isBlank(n.getName())) { throw new WorkflowManagerException("Invalid node: missing name"); }
if (n.isStart()) {
foundStart = true;
}
if (!this.nodeHelper.isValidType(n.getType())) { throw new WorkflowManagerException("Invalid node type: " + n.getType()); }
}
if (!foundStart) { throw new WorkflowManagerException("Start node not found"); }
}
}

129
libs/dnet-wf-service/src/main/java/eu/dnetlib/manager/wf/workflows/graph/GraphNode.java Normal file
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package eu.dnetlib.manager.wf.workflows.graph;
import java.io.StringWriter;
import java.util.HashMap;
import java.util.Map;
import org.apache.commons.lang3.StringUtils;
import eu.dnetlib.manager.wf.workflows.procs.Env;
public class GraphNode {
public static final String SUCCESS_NODE = "success";
private final String name;
private final String type;
private final boolean isStart;
private final boolean isJoin;
private final boolean isSucessNode;
private final Map<String, Object> params;
private final Map<String, String> envParams;
private GraphNode(final String name,
final String type,
final boolean isStart,
final boolean isJoin,
final boolean isSuccessNode,
final Map<String, Object> params,
final Map<String, String> envParams) {
this.name = name;
this.type = type;
this.isStart = isStart;
this.isJoin = isJoin;
this.isSucessNode = isSuccessNode;
this.params = params;
this.envParams = envParams;
}
public static GraphNode newNode(final String name,
final String type,
final Map<String, Object> params,
final Map<String, String> envParams) {
return new GraphNode(name, type, false, false, false, params, envParams);
}
public static GraphNode newStartNode(final String name,
final String type,
final Map<String, Object> params,
final Map<String, String> envParams) {
return new GraphNode(name, type, true, false, false, params, envParams);
}
public static GraphNode newJoinNode(final String name,
final String type,
final Map<String, Object> params,
final Map<String, String> envParams) {
return new GraphNode(name, type, false, true, false, params, envParams);
}
public static GraphNode newSuccessNode() {
return new GraphNode(SUCCESS_NODE, null, false, true, true, new HashMap<>(), new HashMap<>());
}
public String getName() {
return this.name;
}
public String getType() {
return this.type;
}
public boolean isStart() {
return this.isStart;
}
public boolean isJoin() {
return this.isJoin;
}
public boolean isSucessNode() {
return this.isSucessNode;
}
@Override
public String toString() {
final StringWriter sw = new StringWriter();
sw.append("[ name: ");
sw.append(this.name);
if (StringUtils.isNotBlank(this.type)) {
sw.append(", type: ");
sw.append(this.type);
}
if (isStart()) {
sw.append(" - isStart");
}
if (isJoin()) {
sw.append(" - isJoin");
}
sw.append(" ]");
return sw.toString();
}
public Map<String, Object> getParams() {
return this.params;
}
public Map<String, String> getEnvParams() {
return this.envParams;
}
public Map<String, Object> resolveParamsWithNoEnv() {
return resolveParams(null);
}
public Map<String, Object> resolveParams(final Env env) {
final Map<String, Object> map = new HashMap<>();
if (this.params != null) {
this.params.forEach((k, v) -> map.put(k, v));
}
if (this.envParams != null && env != null) {
this.envParams.forEach((k, v) -> map.put(k, env.getAttribute(v)));
}
return map;
}
}

54
libs/dnet-wf-service/src/main/java/eu/dnetlib/manager/wf/workflows/procs/Env.java Normal file
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package eu.dnetlib.manager.wf.workflows.procs;
import java.util.HashMap;
import java.util.Map;
/**
* Created by michele on 23/11/15.
*/
public class Env {
private final Map<String, Object> attrs;
public Env() {
this.attrs = new HashMap<>();
}
public Env(final Map<String, Object> attrs) {
this.attrs = attrs;
}
public Map<String, Object> getAttributes() {
return attrs;
}
public void clear() {
attrs.clear();
}
public void addAttributes(final Map<String, Object> map) {
if (map != null) {
attrs.putAll(map);
}
}
public void setAttribute(final String name, final Object value) {
attrs.put(name, value);
}
public Object getAttribute(final String name) {
return attrs.get(name);
}
public <T> T getAttribute(final String name, Class<T> clazz) {
return clazz.cast(attrs.get(name));
}
public boolean hasAttribute(final String name) {
return attrs.containsKey(name);
}
public Object removeAttribute(final String name) {
return attrs.remove(name);
}
}

10
libs/dnet-wf-service/src/main/java/eu/dnetlib/manager/wf/workflows/procs/ProcessAware.java Normal file
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package eu.dnetlib.manager.wf.workflows.procs;
/**
* Created by michele on 24/11/15.
*/
public interface ProcessAware {
void setProcess(WorkflowProcess process);
}

137
libs/dnet-wf-service/src/main/java/eu/dnetlib/manager/wf/workflows/procs/ProcessEngine.java Normal file
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package eu.dnetlib.manager.wf.workflows.procs;
import java.time.LocalDateTime;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.stereotype.Service;
import com.google.common.base.Throwables;
import eu.dnetlib.manager.history.WorkflowLogger;
import eu.dnetlib.manager.wf.nodes.ProcessNode;
import eu.dnetlib.manager.wf.notification.EmailSender;
import eu.dnetlib.manager.wf.workflows.graph.GraphNode;
import eu.dnetlib.manager.wf.workflows.util.ExecutionCallback;
import eu.dnetlib.manager.wf.workflows.util.NodeHelper;
@Service
public class ProcessEngine {
private static final Log log = LogFactory.getLog(ProcessEngine.class);
@Autowired
private NodeHelper nodeHelper;
@Autowired
private EmailSender emailSender;
@Autowired
private WorkflowLogger wfLogger;
public void startProcess(final WorkflowProcess process) {
log.info(process.getGraph());
log.info("Starting workflow: " + process);
final LocalDateTime now = LocalDateTime.now();
process.setStatus(WorkflowProcess.Status.EXECUTING);
process.setStartDate(now);
process.setLastActivityDate(now);
try {
for (final GraphNode node : process.getGraph().startNodes()) {
final ProcessNode pNode = nodeHelper.newProcessNode(node, process, process.getEnv());
final Token token = new Token();
token.getEnv().addAttributes(process.getEnv().getAttributes());
process.getTokens().add(token);
pNode.execute(token, newNodeCallback(process, node));
}
} catch (final Throwable e) {
log.error("WorkflowProcess node instantiation failed", e);
process.setStatus(WorkflowProcess.Status.FAILURE);
}
}
private ExecutionCallback<Token> newNodeCallback(final WorkflowProcess process, final GraphNode node) {
return new ExecutionCallback<Token>() {
@Override
public void onSuccess(final Token t) {
releaseToken(process, node, t);
}
@Override
public void onFail(final Token t) {
completeProcess(process, t);
}
};
}
public void releaseToken(final WorkflowProcess process, final GraphNode oldGraphNode, final Token oldToken) {
process.setLastActivityDate(LocalDateTime.now());
try {
for (final GraphNode node : process.getGraph().nextNodes(oldGraphNode, oldToken.getEnv())) {
if (node.isJoin() || node.isSucessNode()) {
if (!process.getPausedJoinNodeTokens().containsKey(node.getName())) {
process.getPausedJoinNodeTokens().put(node.getName(), new ArrayList<Token>());
}
final List<Token> list = process.getPausedJoinNodeTokens().get(node.getName());
list.add(oldToken);
if (list.size() == process.getGraph().getNumberOfIncomingArcs(node)) {
final Token token = new Token();
token.getEnv().addAttributes(mergeEnvParams(list.toArray(new Token[list.size()])));
final ProcessNode pNode = nodeHelper.newProcessNode(node, process, token.getEnv());
process.getTokens().add(token);
process.setLastActivityDate(LocalDateTime.now());
if (node.isSucessNode()) {
completeProcess(process, token);
} else {
pNode.execute(token, newNodeCallback(process, node));
}
}
} else {
final Token token = new Token();
token.getEnv().addAttributes(oldToken.getEnv().getAttributes());
final ProcessNode pNode = nodeHelper.newProcessNode(node, process, token.getEnv());
process.getTokens().add(token);
process.setLastActivityDate(LocalDateTime.now());
pNode.execute(token, newNodeCallback(process, node));
}
}
} catch (final Throwable e) {
log.error("WorkflowProcess node instantiation failed", e);
process.setStatus(WorkflowProcess.Status.FAILURE);
process.setError(e.getMessage());
process.setErrorStacktrace(Throwables.getStackTraceAsString(e));
process.setLastActivityDate(LocalDateTime.now());
}
}
private Map<String, Object> mergeEnvParams(final Token... tokens) {
final Map<String, Object> map = new HashMap<>();
Arrays.stream(tokens).forEach(t -> map.putAll(t.getEnv().getAttributes()));
return map;
}
private void completeProcess(final WorkflowProcess process, final Token token) {
token.checkStatus();
process.complete(token);
wfLogger.saveProcessExecution(process.asLog());
emailSender.sendMails(process);
}
}

59
libs/dnet-wf-service/src/main/java/eu/dnetlib/manager/wf/workflows/procs/ProcessFactory.java Normal file
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package eu.dnetlib.manager.wf.workflows.procs;
import java.time.LocalDateTime;
import java.time.format.DateTimeFormatter;
import java.util.HashMap;
import java.util.Map;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.stereotype.Component;
import eu.dnetlib.errors.WorkflowManagerException;
import eu.dnetlib.is.model.resource.SimpleResource;
import eu.dnetlib.manager.wf.model.WorkflowGraph;
import eu.dnetlib.manager.wf.model.WorkflowInstance;
import eu.dnetlib.manager.wf.workflows.graph.Graph;
import eu.dnetlib.manager.wf.workflows.graph.GraphLoader;
import eu.dnetlib.manager.wf.workflows.util.ExecutionCallback;
@Component
public class ProcessFactory {
private static final Log log = LogFactory.getLog(ProcessFactory.class);
private String oldGeneratedId = "";
private final DateTimeFormatter processIdFormatter = DateTimeFormatter.ofPattern("yyyyMMdd_HHmmss_S");
@Autowired
private GraphLoader graphLoader;
public WorkflowProcess newProcess(final SimpleResource wfMetadata,
final WorkflowGraph wfGraph,
final WorkflowInstance wfInstance,
final ExecutionCallback<WorkflowProcess> callback) throws WorkflowManagerException {
final Map<String, String> globalParams = new HashMap<>();
globalParams.putAll(wfInstance.getSystemParams());
globalParams.putAll(wfInstance.getUserParams());
final Graph graph = graphLoader.loadGraph(wfGraph, globalParams);
return new WorkflowProcess(generateProcessId(), wfMetadata, wfInstance, graph, globalParams, callback);
}
private synchronized String generateProcessId() {
String id = "";
do {
id = "wf_" + LocalDateTime.now().format(processIdFormatter);
log.info("Generated processID " + id);
} while (id.equals(oldGeneratedId));
oldGeneratedId = id;
return id;
}
}

124
libs/dnet-wf-service/src/main/java/eu/dnetlib/manager/wf/workflows/procs/ProcessRegistry.java Normal file
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package eu.dnetlib.manager.wf.workflows.procs;
import java.time.LocalDateTime;
import java.util.Collection;
import java.util.HashMap;
import java.util.Map;
import java.util.Optional;
import java.util.concurrent.PriorityBlockingQueue;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import org.springframework.beans.factory.annotation.Value;
import org.springframework.stereotype.Service;
import eu.dnetlib.errors.WorkflowManagerException;
import eu.dnetlib.manager.wf.model.WorkflowInstance;
import eu.dnetlib.manager.wf.workflows.util.WorkflowsConstants;
@Service
public class ProcessRegistry {
private static final Log log = LogFactory.getLog(ProcessRegistry.class);
private final Map<String, WorkflowProcess> procs = new HashMap<>();
private final Map<String, WorkflowProcess> byInstanceId = new HashMap<>();
private final PriorityBlockingQueue<WorkflowProcess> pendingProcs = new PriorityBlockingQueue<>();
@Value("${dnet.wf.registry.size:100}")
private int maxSize;
synchronized public int countRunningWfs() {
int count = 0;
for (final Map.Entry<String, WorkflowProcess> e : this.procs.entrySet()) {
final WorkflowProcess proc = e.getValue();
if (!proc.isTerminated()) {
count++;
}
}
return count;
}
public WorkflowProcess findProcess(final String procId) {
return this.procs.get(procId);
}
public Collection<WorkflowProcess> listProcesses() {
return this.procs.values();
}
public WorkflowProcess findProcsByInstanceId(final String id) {
return this.byInstanceId.get(id);
}
public String registerProcess(final WorkflowProcess process, final WorkflowInstance wfInstance) throws WorkflowManagerException {
if (this.procs.containsValue(process) || this.procs.containsKey(process.getId())) {
log.error("Already registerd process: " + process);
throw new WorkflowManagerException("Already registerd process: " + process);
}
if (this.procs.size() >= this.maxSize) {
removeOldestProcess();
}
this.procs.put(process.getId(), process);
this.byInstanceId.put(wfInstance.getId(), process);
synchronized (this.pendingProcs) {
if (this.pendingProcs.size() > WorkflowsConstants.MAX_PENDING_PROCS_SIZE) {
log.warn("Wf [" + process.getName() + "] not launched, Max number of pending procs reached: " + WorkflowsConstants.MAX_PENDING_PROCS_SIZE);
throw new WorkflowManagerException("Max number of pending procs reached: " + WorkflowsConstants.MAX_PENDING_PROCS_SIZE);
}
this.pendingProcs.put(process);
log.info("WorkflowProcess [" + process + "] in queue, priority=" + process.getPriority());
}
return process.getId();
}
private void removeOldestProcess() {
LocalDateTime oldDate = LocalDateTime.now();
String oldId = null;
for (final Map.Entry<String, WorkflowProcess> e : this.procs.entrySet()) {
final WorkflowProcess proc = e.getValue();
if (proc.isTerminated()) {
final LocalDateTime date = proc.getLastActivityDate();
if (date.isBefore(oldDate)) {
oldDate = date;
oldId = e.getKey();
}
}
}
if (oldId != null) {
unregisterProcess(oldId);
}
}
public void unregisterProcess(final String procId) {
synchronized (this) {
final WorkflowProcess process = this.procs.remove(procId);
if (process != null) {
final Optional<String> instanceId = this.byInstanceId.entrySet()
.stream()
.filter(e -> e.getValue().getId().equals(process.getId()))
.map(e -> e.getKey())
.findFirst();
if (instanceId.isPresent()) {
this.byInstanceId.remove(instanceId, process);
}
}
}
}
public WorkflowProcess nextProcessToStart() {
synchronized (this.pendingProcs) {
return this.pendingProcs.poll();
}
}
}

125
libs/dnet-wf-service/src/main/java/eu/dnetlib/manager/wf/workflows/procs/Token.java Normal file
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package eu.dnetlib.manager.wf.workflows.procs;
import java.time.LocalDateTime;
import java.util.UUID;
import org.apache.commons.lang3.StringUtils;
import com.google.common.base.Throwables;
/**
* Created by michele on 19/11/15.
*/
public class Token {
private final String id;
private final Env env = new Env();
private String progressMessage;
private final LocalDateTime startDate;
private LocalDateTime endDate;
private boolean failed;
private boolean active;
private String error = "";
private String errorStackTrace = "";
public Token() {
this.id = "token-" + UUID.randomUUID();
this.startDate = LocalDateTime.now();
this.failed = false;
this.active = true;
}
public String getId() {
return this.id;
}
public Env getEnv() {
return this.env;
}
public LocalDateTime getStartDate() {
return this.startDate;
}
public LocalDateTime getEndDate() {
return this.endDate;
}
public void setEndDate(final LocalDateTime endDate) {
this.endDate = endDate;
}
public boolean isActive() {
return this.active;
}
public void setActive(final boolean active) {
this.active = active;
}
public boolean isFailed() {
return this.failed;
}
public void setFailed(final boolean failed) {
this.failed = failed;
}
public void release() {
setEndDate(LocalDateTime.now());
setActive(false);
}
public void releaseAsFailed(final Throwable e) {
setEndDate(LocalDateTime.now());
setActive(false);
setFailed(true);
setError(e.getMessage());
setErrorStackTrace(Throwables.getStackTraceAsString(e));
}
public void releaseAsFailed(final String error) {
setEndDate(LocalDateTime.now());
setActive(false);
setFailed(true);
setError(error);
}
public void checkStatus() {
if (isActive()) {
if (StringUtils.isNotBlank(error)) {
releaseAsFailed(error);
} else {
release();
}
}
}
public String getProgressMessage() {
return progressMessage;
}
public void setProgressMessage(final String progressMessage) {
this.progressMessage = progressMessage;
}
public String getError() {
return this.error;
}
public void setError(final String error) {
this.error = error;
}
public String getErrorStackTrace() {
return this.errorStackTrace;
}
public void setErrorStackTrace(final String errorStackTrace) {
this.errorStackTrace = errorStackTrace;
}
}

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