standardize the use of service name handles, e.g. file-setup instead of file_setup

app/services/__init__.py

@@ -2,10 +2,7 @@ from flask import Blueprint
 
 
 SERVICES = {
-    'corpus_analysis': {
-        'name': 'Corpus analysis'
-    },
-    'file_setup': {
+    'file-setup': {
         'name': 'File setup',
         'versions': {
             'latest': '1.0.0b',

app/services/forms.py

@@ -77,7 +77,14 @@ class AddFileSetupJobForm(AddJobForm):
                                       '| .tif')
 
     def __init__(self, *args, **kwargs):
-        version = kwargs.pop('version', SERVICES['file_setup']['versions']['latest'])
+        version = kwargs.pop('version', SERVICES['file-setup']['versions']['latest'])
         super().__init__(*args, **kwargs)
-        self.version.choices = [(x, x) for x in SERVICES['file_setup']['versions'] if x != 'latest']  # noqa
+        self.version.choices = [(x, x) for x in SERVICES['file-setup']['versions'] if x != 'latest']  # noqa
         self.version.default = version
+
+
+AddJobForms = {
+    'file-setup': AddFileSetupJobForm,
+    'ocr': AddOCRJobForm,
+    'nlp': AddNLPJobForm
+}

app/services/views.py

@@ -4,41 +4,36 @@ from flask_login import current_user, login_required
 from werkzeug.utils import secure_filename
 from . import services
 from . import SERVICES
-from .forms import AddFileSetupJobForm, AddNLPJobForm, AddOCRJobForm
 from .. import db, socketio
+from .forms import AddJobForms
 from ..models import Job, JobInput
 import json
 import logging
 import os
 
 
+@services.route('/corpus-analysis')
+@login_required
+def corpus_analysis():
+    return render_template('services/corpus_analysis.html.j2')
+
+
 @services.route('/<service>', methods=['GET', 'POST'])
 @login_required
 def service(service):
-    if service not in SERVICES:
+    # Check if the requested service exist
+    if service not in SERVICES or service not in AddJobForms:
         abort(404)
-    if service == 'corpus_analysis':
-        return render_template('services/{}.html.j2'.format(service),
-                               title=SERVICES[service]['name'])
-    elif service == 'file_setup':
-        form = AddFileSetupJobForm(prefix='add-file-setup-job-form')
-    elif service == 'nlp':
-        version = request.args.get('version')
-        if version is None or version not in SERVICES[service]['versions']:
-            form = AddNLPJobForm(prefix='add-nlp-job-form')
-        else:
-            form = AddNLPJobForm(prefix='add-nlp-job-form', version=version)
-            form.version.data = version
-    elif service == 'ocr':
-        version = request.args.get('version')
-        if version is None or version not in SERVICES[service]['versions']:
-            form = AddOCRJobForm(prefix='add-ocr-job-form')
-        else:
-            form = AddOCRJobForm(prefix='add-ocr-job-form', version=version)
-            form.version.data = version
+    version = request.args.get('version',
+                               SERVICES[service]['versions']['latest'])
+    if version not in SERVICES[service]['versions']:
+        abort(404)
+    form = AddJobForms[service](prefix='add-job-form', version=version)
+    form.version.data = version
+    title = SERVICES[service]['name']
+    versions = SERVICES[service]['versions']
     if form.is_submitted():
         if not form.validate():
-            logging.error(form.errors)
             return make_response(form.errors, 400)
         service_args = []
         if service == 'nlp':
@@ -80,6 +75,5 @@ def service(service):
             socketio.emit(event, jsonpatch, room=room)
             return make_response(
                 {'redirect_url': url_for('jobs.job', job_id=job.id)}, 201)
-    return render_template('services/{}.html.j2'.format(service),
-                           form=form, title=SERVICES[service]['name'],
-                           versions=SERVICES[service]['versions'])
+    return render_template('services/{}.html.j2'.format(service.replace('-', '_')),
+                           form=form, title=title, versions=versions)

app/static/css/materialize_fixes.css

-/* Fix material icon vertical alignment when nested in various elements */
-h1 .nopaque-icons, h2 .nopaque-icons, h3 .nopaque-icons, h4 .nopaque-icons,
-.tab .nopaque-icons, .tab .material-icons {
-  line-height: inherit;
-}
-
 .parallax-container .parallax {
   z-index: 0;
 }

app/static/css/nopaque.css

@@ -101,6 +101,11 @@ indicator will show up how the column is sorted right now.; */
   font-size: 2.5rem;
 }
 
+/* Fix material icon vertical alignment when nested in various elements */
+h1 .nopaque-icons, h2 .nopaque-icons, h3 .nopaque-icons, h4 .nopaque-icons,
+.tab .nopaque-icons, .tab .material-icons {
+  line-height: inherit;
+}
 .nopaque-icons.service-icon[data-service="corpus-analysis"]:empty:before {content: "H";}
 .nopaque-icons.service-icon[data-service="file-setup"]:empty:before {content: "E";}
 .nopaque-icons.service-icon[data-service="nlp"]:empty:before {content: "G";}

app/tasks/job_utils.bak.py

+from datetime import datetime
+from werkzeug.utils import secure_filename
+from .. import db, mail
+from ..email import create_message
+from ..models import Job, JobResult
+import docker
+import logging
+import json
+import os
+
+
+DOCKER_REGISTRY = 'gitlab.ub.uni-bielefeld.de:4567'
+
+
+class CheckJobsMixin:
+    def check_jobs(self):
+        jobs = Job.query.all()
+        canceling_jobs = list(filter(lambda job: job.status == 'canceling', jobs))  # noqa
+        queued_jobs = list(filter(lambda job: job.status == 'queued', jobs))
+        running_jobs = list(filter(lambda job: job.status == 'running', jobs))
+        submitted_jobs = list(filter(lambda job: job.status == 'submitted', jobs))  # noqa
+        for job in submitted_jobs:
+            self.create_job_service(job)
+        for job in queued_jobs + running_jobs:
+            self.checkout_job_service(job)
+        for job in canceling_jobs:
+            self.remove_job_service(job)
+
+    def create_job_service(self, job):
+        if job.service == 'file-setup':
+            mem_mb = 2048
+            n_cores = 2
+            executable = 'file-setup'
+            image = '{}/sfb1288inf/file-setup:{}'.format(DOCKER_REGISTRY, job.service_version)  # noqa
+        elif job.service == 'ocr':
+            mem_mb = 4096
+            n_cores = 4
+            executable = 'ocr'
+            image = '{}/sfb1288inf/ocr:{}'.format(DOCKER_REGISTRY, job.service_version)  # noqa
+        elif job.service == 'nlp':
+            mem_mb = 2048
+            n_cores = 2
+            executable = 'nlp'
+            image = '{}/sfb1288inf/nlp:{}'.format(DOCKER_REGISTRY, job.service_version)  # noqa
+        # Command
+        command = '{} -i /input -o /output'.format(executable)
+        command += ' --log-dir /input'
+        command += ' --mem-mb {}'.format(mem_mb)
+        command += ' --n-cores {}'.format(n_cores)
+        command += ' --zip [{}]_{}'.format(job.service, secure_filename(job.title))
+        command += ' ' + ' '.join(json.loads(job.service_args))
+        # Constraints
+        constraints = ['node.role==worker']
+        # Labels
+        labels = {'origin': 'nopaque', 'type': 'job', 'job_id': str(job.id)}
+        # Mounts
+        ## Input mount
+        input_mount_source = job.path
+        input_mount_target = os.path.abspath('/input')
+        if job.service == 'file-setup':
+            input_mount_target = os.path.join(input_mount_target, secure_filename(job.title))  # noqa
+        input_mount = '{}:{}:rw'.format(input_mount_source, input_mount_target)
+        ## Output mount
+        output_mount_source = os.path.join(job.path, 'output')
+        output_mount_target = os.path.abspath('/output')
+        output_mount = '{}:{}:rw'.format(output_mount_source, output_mount_target)  # noqa
+        os.makedirs(output_mount_src)
+        mounts = [input_mount, output_mount]
+        # Name
+        name = 'job_{}'.format(job.id)
+        # Ressources
+        ressources = docker.types.Resources(
+            cpu_reservation=n_cores * (10 ** 9),
+            mem_reservation=mem_mb * (10 ** 6)
+        )
+        # Restart policy
+        restart_policy = docker.types.RestartPolicy()
+        try:
+            self.docker.services.create(
+                image,
+                command=command,
+                constraints=constraints,
+                labels=labels,
+                mounts=mounts,
+                name=name,
+                ressources=ressources,
+                restart_policy=restart_policy
+            )
+        except docker.errors.APIError as e:
+            logging.error(
+                'Create "{}" service raised '.format(service_kwargs['name'])
+                + '"docker.errors.APIError" The server returned an error. '
+                + 'Details: {}'.format(e)
+            )
+            return
+        else:
+            job.status = 'queued'
+            patch_operation = {'op': 'replace', 'path': '/jobs/{}/status'.format(job.id), 'value': job.status}  # noqa
+            self.buffer_user_patch_operation(job, patch_operation)
+        finally:
+            self.send_job_notification(job)
+
+    def checkout_job_service(self, job):
+        service_name = 'job_{}'.format(job.id)
+        try:
+            service = self.docker.services.get(service_name)
+        except docker.errors.NotFound:
+            logging.error('Get "{}" service raised '.format(service_name)
+                          + '"docker.errors.NotFound" The service does not exist. '
+                          + '(job.status: {} -> failed)'.format(job.status))
+            job.status = 'failed'
+            patch_operation = {'op': 'replace', 'path': '/jobs/{}/status'.format(job.id), 'value': job.status}  # noqa
+            self.buffer_user_patch_operation(job, patch_operation)
+        except docker.errors.APIError as e:
+            logging.error(
+                'Get "{}" service raised '.format(service_name)
+                + '"docker.errors.APIError" The server returned an error. '
+                + 'Details: {}'.format(e)
+            )
+            return
+        except docker.errors.InvalidVersion:
+            logging.error(
+                'Get "{}" service raised '.format(service_name)
+                + '"docker.errors.InvalidVersion" One of the arguments is '
+                + 'not supported with the current API version.'
+            )
+            return
+        else:
+            service_tasks = service.tasks()
+            if not service_tasks:
+                return
+            task_state = service_tasks[0].get('Status').get('State')
+            if job.status == 'queued' and task_state != 'pending':
+                job.status = 'running'
+                patch_operation = {'op': 'replace', 'path': '/jobs/{}/status'.format(job.id), 'value': job.status}  # noqa
+                self.buffer_user_patch_operation(job, patch_operation)
+            elif job.status == 'running' and task_state in ['complete', 'failed']:
+                try:
+                    service.remove()
+                except docker.errors.APIError as e:
+                    logging.error(
+                        'Remove "{}" service raised '.format(service_name)
+                        + '"docker.errors.APIError" The server returned an error. '  # noqa
+                        + 'Details: {}'.format(e)
+                    )
+                    return
+                else:
+                    if task_state == 'complete':
+                        results_dir = os.path.join(job.path, 'output')
+                        result_files = filter(lambda x: x.endswith('.zip'),
+                                              os.listdir(results_dir))
+                        for result_file in result_files:
+                            job_result = JobResult(filename=result_file, job=job)  # noqa
+                            db.session.add(job_result)
+                            db.session.flush()
+                            db.session.refresh(job_result)
+                            patch_operation = {'op': 'add', 'path': '/jobs/{}/results/{}'.format(job.id, job_result.id), 'value': job_result.to_dict()}  # noqa
+                            self.buffer_user_patch_operation(job, patch_operation)  # noqa
+                    job.end_date = datetime.utcnow()
+                    patch_operation = {'op': 'replace', 'path': '/jobs/{}/end_date'.format(job.id), 'value': job.end_date.timestamp()}  # noqa
+                    self.buffer_user_patch_operation(job, patch_operation)
+                    job.status = task_state
+                    patch_operation = {'op': 'replace', 'path': '/jobs/{}/status'.format(job.id), 'value': job.status}  # noqa
+                    self.buffer_user_patch_operation(job, patch_operation)
+        finally:
+            self.send_job_notification(job)
+
+    def remove_job_service(self, job):
+        service_name = 'job_{}'.format(job.id)
+        try:
+            service = self.docker.services.get(service_name)
+        except docker.errors.NotFound:
+            job.status = 'canceled'
+            patch_operation = {'op': 'replace', 'path': '/jobs/{}/status'.format(job.id), 'value': job.status}  # noqa
+            self.buffer_user_patch_operation(job, patch_operation)
+        except docker.errors.APIError as e:
+            logging.error(
+                'Get "{}" service raised '.format(service_name)
+                + '"docker.errors.APIError" The server returned an error. '
+                + 'Details: {}'.format(e)
+            )
+            return
+        except docker.errors.InvalidVersion:
+            logging.error(
+                'Get "{}" service raised '.format(service_name)
+                + '"docker.errors.InvalidVersion" One of the arguments is '
+                + 'not supported with the current API version.'
+            )
+            return
+        else:
+            try:
+                service.update(mounts=None)
+            except docker.errors.APIError as e:
+                logging.error(
+                    'Update "{}" service raised '.format(service_name)
+                    + '"docker.errors.APIError" The server returned an error. '
+                    + 'Details: {}'.format(e)
+                )
+                return
+            try:
+                service.remove()
+            except docker.errors.APIError as e:
+                logging.error(
+                    'Remove "{}" service raised '.format(service_name)
+                    + '"docker.errors.APIError" The server returned an error. '
+                    + 'Details: {}'.format(e)
+                )
+
+    def send_job_notification(self, job):
+        if job.creator.setting_job_status_mail_notifications == 'none':
+            return
+        if (job.creator.setting_job_status_mail_notifications == 'end'
+                and job.status not in ['complete', 'failed']):
+            return
+        msg = create_message(job.creator.email,
+                             'Status update for your Job "{}"'.format(job.title),  # noqa
+                             'tasks/email/notification', job=job)
+        mail.send(msg)

app/tasks/job_utils.py

@@ -9,24 +9,8 @@ import json
 import os
 
 
-# TODO: Integrate the service_settings into app/services/__init__.py
-service_settings = {
-    'file-setup': {
-        'default_args': ' --mem-mb 2048 --n-cores 2',
-        'ressources': docker.types.Resources(cpu_reservation=2 * (10 ** 9),
-                                             mem_reservation=2048 * (10 ** 6))
-    },
-    'nlp': {
-        'default_args': ' --mem-mb 2048 --n-cores 2',
-        'ressources': docker.types.Resources(cpu_reservation=2 * (10 ** 9),
-                                             mem_reservation=2048 * (10 ** 6))
-    },
-    'ocr': {
-        'default_args': ' --mem-mb 4096 --n-cores 4',
-        'ressources': docker.types.Resources(cpu_reservation=4 * (10 ** 9),
-                                             mem_reservation=4096 * (10 ** 6))
-    }
-}
+DOCKER_REGISTRY = 'gitlab.ub.uni-bielefeld.de:4567'
+DOCKER_IMAGE_PREFIX = '{}/sfb1288inf/'.format(DOCKER_REGISTRY)
 
 
 class CheckJobsMixin:
@@ -44,36 +28,66 @@ class CheckJobsMixin:
             self.remove_job_service(job)
 
     def create_job_service(self, job):
-        cmd = job.service
-        cmd += ' -i /input'
-        cmd += ' -o /output'
-        cmd += ' --log-dir /input'
-        cmd += ' --zip [{}]_{}'.format(job.service, secure_filename(job.title))
-        cmd += service_settings[job.service]['default_args']
-        cmd += ' ' + ' '.join(json.loads(job.service_args))
-        # Setup input mount
-        input_mount_src = job.path
-        input_mount_dest = os.path.abspath('/input')
+        # Service specific settings
         if job.service == 'file-setup':
-            input_mount_dest = os.path.join(input_mount_dest, secure_filename(job.title))  # noqa
-        input_mount = '{}:{}:rw'.format(input_mount_src, input_mount_dest)
-        # Setup output mount
-        output_mount_src = os.path.join(job.path, 'output')
-        output_mount_dest = os.path.abspath('/output')
-        os.makedirs(output_mount_src)
-        output_mount = '{}:{}:rw'.format(output_mount_src, output_mount_dest)
-        service_kwargs = {'command': cmd,
-                          'constraints': ['node.role==worker'],
-                          'labels': {'origin': 'nopaque',
-                                     'type': 'job',
-                                     'job_id': str(job.id)},
-                          'mounts': [input_mount, output_mount],
-                          'name': 'job_{}'.format(job.id),
-                          'resources': service_settings[job.service]['ressources'],  # noqa
-                          'restart_policy': docker.types.RestartPolicy()}
-        service_image = 'gitlab.ub.uni-bielefeld.de:4567/sfb1288inf/{}:{}'.format(job.service, job.service_version)  # noqa
+            mem_mb = 2048
+            n_cores = 2
+            executable = 'file-setup'
+            image = DOCKER_IMAGE_PREFIX + 'file-setup:' + job.service_version
+        elif job.service == 'ocr':
+            mem_mb = 4096
+            n_cores = 4
+            executable = 'ocr'
+            image = DOCKER_IMAGE_PREFIX + 'ocr:' + job.service_version
+        elif job.service == 'nlp':
+            mem_mb = 2048
+            n_cores = 2
+            executable = 'nlp'
+            image = DOCKER_IMAGE_PREFIX + 'nlp:' + job.service_version
+        # Command
+        command = '{} -i /input -o /output'.format(executable)
+        command += ' --log-dir /input'
+        command += ' --mem-mb {}'.format(mem_mb)
+        command += ' --n-cores {}'.format(n_cores)
+        command += ' --zip [' + job.service + ']_' + secure_filename(job.title)
+        command += ' ' + ' '.join(json.loads(job.service_args))
+        # Constraints
+        constraints = ['node.role==worker']
+        # Labels
+        labels = {'origin': 'nopaque', 'type': 'job', 'job_id': str(job.id)}
+        # Mounts
+        ## Input mount
+        input_mount_source = job.path
+        input_mount_target = '/input'
+        if job.service == 'file-setup':
+            input_mount_target += '/' + secure_filename(job.title)
+        input_mount = input_mount_source + ':' + input_mount_target + ':rw'
+        ## Output mount
+        output_mount_source = os.path.join(job.path, 'output')
+        output_mount_target = '/output'
+        output_mount = output_mount_source + ':' + output_mount_target + ':rw'
+        os.makedirs(output_mount_source)
+        mounts = [input_mount, output_mount]
+        # Name
+        name = 'job_{}'.format(job.id)
+        # Resources
+        resources = docker.types.Resources(
+            cpu_reservation=n_cores * (10 ** 9),
+            mem_reservation=mem_mb * (10 ** 6)
+        )
+        # Restart policy
+        restart_policy = docker.types.RestartPolicy()
         try:
-            self.docker.services.create(service_image, **service_kwargs)
+            self.docker.services.create(
+                image,
+                command=command,
+                constraints=constraints,
+                labels=labels,
+                mounts=mounts,
+                name=name,
+                resources=resources,
+                restart_policy=restart_policy
+            )
         except docker.errors.APIError as e:
             logging.error(
                 'Create "{}" service raised '.format(service_kwargs['name'])

app/templates/_sidenav.html.j2

@@ -14,7 +14,7 @@
   <li><a href="{{ url_for('main.dashboard', _anchor='jobs') }}" style="padding-left: 47px;"><i class="nopaque-icons">J</i>My Jobs</a></li>
   <li><div class="divider"></div></li>
   <li><a class="subheader">Processes & Services</a></li>
-  <li class="service-color service-color-border border-darken" data-service="file-setup" style="border-left: 10px solid; margin-top: 5px;"><a href="{{ url_for('services.service', service='file_setup') }}"><i class="nopaque-icons service-icon" data-service="file-setup"></i>File setup</a></li>
+  <li class="service-color service-color-border border-darken" data-service="file-setup" style="border-left: 10px solid; margin-top: 5px;"><a href="{{ url_for('services.service', service='file-setup') }}"><i class="nopaque-icons service-icon" data-service="file-setup"></i>File setup</a></li>
   <li class="service-color service-color-border border-darken" data-service="ocr" style="border-left: 10px solid; margin-top: 5px;"><a href="{{ url_for('services.service', service='ocr') }}"><i class="nopaque-icons service-icon" data-service="ocr"></i>OCR</a></li>
   <li class="service-color service-color-border border-darken" data-service="nlp" style="border-left: 10px solid; margin-top: 5px;"><a href="{{ url_for('services.service', service='nlp') }}"><i class="nopaque-icons service-icon" data-service="nlp"></i>NLP</a></li>
   <li class="service-color service-color-border border-darken" data-service="corpus-analysis" style="border-left: 10px solid; margin-top: 5px;"><a href="{{ url_for('services.service', service='corpus_analysis') }}"><i class="nopaque-icons service-icon" data-service="corpus-analysis"></i>Corpus analysis</a></li>

app/templates/jobs/job.html.j2

@@ -9,7 +9,7 @@
     <div class="col s12" data-job-id="{{ job.id }}" data-user-id="{{ job.creator.id }}" id="job-display">
       <div class="row">
         <div class="col s8 m9 l10">
-          <h1 id="title">[<span class="job-service"></span>] <span class="job-title"></span></h1>
+          <h1 id="title"><i style="font-size: inherit;" class="nopaque-icons service-icon" data-service="{{ job.service }}"></i> <span class="job-title"></span></h1>
         </div>
         <div class="col s4 m3 l2 right-align">
           <p>&nbsp;</p>

app/templates/services/_breadcrumbs.html.j2

@@ -4,8 +4,8 @@
 <li class="tab disabled"><i class="material-icons">navigate_next</i></li>
 {% if request.path == url_for('.service', service='corpus_analysis') %}
 <li class="tab"><a class="active" href="{{ url_for('.service', service='corpus_analysis') }}" target="_self">{{ title }}</a></li>
-{% elif request.path == url_for('.service', service='file_setup') %}
-<li class="tab"><a class="active" href="{{ url_for('.service', service='file_setup') }}" target="_self">{{ title }}</a></li>
+{% elif request.path == url_for('.service', service='file-setup') %}
+<li class="tab"><a class="active" href="{{ url_for('.service', service='file-setup') }}" target="_self">{{ title }}</a></li>
 {% elif request.path == url_for('.service', service='nlp') %}
 <li class="tab"><a class="active" href="{{ url_for('.service', service='nlp') }}" target="_self">{{ title }}</a></li>
 {% elif request.path == url_for('.service', service='ocr') %}