Write run config from ui

gulpfile.js

@@ -135,6 +135,12 @@ function modules() {
   var bootstrapJS = gulp.src('./node_modules/bootstrap/dist/js/*')
     .pipe(gulp.dest(paths.vendor + '/bootstrap/js'));
 
+  // Bootstrap Select
+  var bootstrapSelectJS = gulp.src('./node_modules/bootstrap-select/dist/js/*')
+    .pipe(gulp.dest(paths.vendor + '/bootstrap-select/js'));
+  var bootstrapSelectCSS = gulp.src('./node_modules/bootstrap-select/dist/css/*')
+    .pipe(gulp.dest(paths.vendor + '/bootstrap-select/css'));
+
   // ChartJS
   var chartJS = gulp.src([
       './node_modules/chart.js/dist/*.js',
@@ -180,7 +186,19 @@ function modules() {
   var particlesJs = gulp.src('./node_modules/particles.js/particles.js')
     .pipe(gulp.dest(paths.vendor + '/particles.js'));
 
-  return merge(bootstrapJS, chartJS, dataTables, fontAwesome, jquery, jqueryEasing, d3Celestial, d3CelestialData, d3CelestialImage, particlesJs);
+  // PrismJs
+  var prismJs = gulp.src('./node_modules/prismjs/prism.js')
+    .pipe(gulp.dest(paths.vendor + '/prismjs'));
+  var prismJsPy = gulp.src('./node_modules/prismjs/components/prism-python.min.js')
+    .pipe(gulp.dest(paths.vendor + '/prismjs'));
+  var prismJsLineNum = gulp.src('./node_modules/prismjs/plugins/line-numbers/prism-line-numbers.min.js')
+    .pipe(gulp.dest(paths.vendor + '/prismjs/line-numbers'));
+  var prismJsCss = gulp.src('./node_modules/prismjs/themes/prism.css')
+    .pipe(gulp.dest(paths.vendor + '/prismjs'));
+  var prismJsLineNumCss = gulp.src('./node_modules/prismjs/plugins/line-numbers/prism-line-numbers.css')
+    .pipe(gulp.dest(paths.vendor + '/prismjs/line-numbers'));
+
+  return merge(bootstrapJS, chartJS, dataTables, fontAwesome, jquery, jqueryEasing, d3Celestial, d3CelestialData, d3CelestialImage, particlesJs, prismJs, prismJsPy, prismJsLineNum, prismJsCss, prismJsLineNumCss);
 }
 
 // CSS task

package.json

@@ -34,14 +34,16 @@
   "dependencies": {
     "@fortawesome/fontawesome-free": "5.12.0",
     "bootstrap": "4.4.1",
+    "bootstrap-select": "^1.13.18",
     "chart.js": "2.9.3",
     "chartjs-plugin-error-bars": "^1.2.2",
     "d3-celestial": "^0.7.17",
     "datatables.net-bs4": "1.10.20",
     "jquery": "3.4.1",
     "jquery.easing": "^1.4.1",
     "js9": "git+https://github.com/ericmandel/js9.git#v3.0",
-    "particles.js": "^2.0.0"
+    "particles.js": "^2.0.0",
+    "prismjs": "^1.21.0"
   },
   "devDependencies": {
     "@babel/core": "^7.10.2",

pipeline/config_template.py.j2

@@ -12,34 +12,26 @@ PIPE_RUN_PATH = os.path.dirname(os.path.realpath(__file__))
 # IMAGE_FILES[0] image matches SELAVY_FILES[0] file
 IMAGE_FILES = [
     # insert images file path(s) here
-    {% for el in image_files %}
-    {{ el }},
-    {% endfor %}
-]
+    {% for el in image_files %}'{{ el }}',
+    {% endfor %}]
 
 # Selavy catalogue files
 SELAVY_FILES = [
     # insert Selavy file path(s) here
-    {% for el in selavy_files %}
-    {{ el }},
-    {% endfor %}
-]
+    {% for el in selavy_files %}'{{ el }}',
+    {% endfor %}]
 
 # background map files
 BACKGROUND_FILES = [
     # insert background map file path(s) here
-    {% for el in background_files %}
-    {{ el }},
-    {% endfor %}
-]
+    {% for el in background_files %}'{{ el }}',
+    {% endfor %}]
 
 # Noise or RMS files
 NOISE_FILES = [
     # insert RMS file path(s) here
-    {% for el in noise_files %}
-    {{ el }},
-    {% endfor %}
-]
+    {% for el in noise_files %}'{{ el }}',
+    {% endfor %}]
 
 ###
 # SOURCE FINDER OPTIONS

pipeline/forms.py

@@ -0,0 +1,23 @@
+from django import forms
+from .models import Run
+
+
+class PipelineRunForm(forms.Form):
+    run_name = forms.CharField(
+        max_length=Run._meta.get_field('name').max_length
+    )
+    run_comment = forms.CharField(widget=forms.Textarea(), required=False)
+    monitor = forms.BooleanField(required=False)
+    monitor_min_sigma = forms.FloatField()
+    monitor_edge_buffer_scale = forms.FloatField()
+    association_method = forms.CharField()
+    astrometric_uncertainty_ra = forms.FloatField()
+    association_radius = forms.FloatField()
+    astrometric_uncertainty_dec = forms.FloatField()
+    association_de_ruiter_radius = forms.FloatField()
+    new_source_min_sigma = forms.FloatField()
+    default_survey = forms.CharField()
+    association_beamwidth_limit = forms.FloatField()
+    flux_perc_error = forms.FloatField()
+    selavy_local_rms_zero_fill_value = forms.FloatField()
+    use_condon_errors = forms.BooleanField(required=False)

pipeline/management/commands/initpiperun.py

@@ -7,10 +7,53 @@
 from jinja2 import Template
 
 from pipeline.models import Run
+from pipeline.pipeline.errors import PipelineInitError
+from pipeline.pipeline.utils import get_create_p_run
+
 
 logger = logging.getLogger(__name__)
 
 
+def initialise_run(run_name, run_comment='', user=None, config=None):
+    # check for duplicated run name
+    p_run = Run.objects.filter(name__exact=run_name)
+    if p_run:
+        msg = 'Pipeline run name already used. Change name'
+        raise PipelineInitError(msg)
+
+    # create the pipeline run folder
+    run_path = os.path.join(cfg.PIPELINE_WORKING_DIR, run_name)
+
+    if os.path.exists(run_path):
+        msg = 'pipeline run path already present!'
+        raise PipelineInitError(msg)
+    else:
+        logger.info('creating pipeline run folder')
+        os.mkdir(run_path)
+
+    # copy default config into the pipeline run folder
+    logger.info('copying default config in pipeline run folder')
+    template_f = os.path.join(
+        cfg.BASE_DIR,
+        'pipeline',
+        'config_template.py.j2'
+    )
+    with open(template_f, 'r') as fp:
+        template_str = fp.read()
+
+    tm = Template(template_str)
+    with open(os.path.join(run_path, 'config.py'), 'w') as fp:
+        if config:
+            fp.write(tm.render(**config))
+        else:
+            fp.write(tm.render(**cfg.PIPE_RUN_CONFIG_DEFAULTS))
+
+    # create entry in db
+    p_run = get_create_p_run(run_name, run_path, run_comment, user)
+
+    return p_run
+
+
 class Command(BaseCommand):
     """
     This script initialise the Pipeline Run folder and related config
@@ -40,33 +83,11 @@ def handle(self, *args, **options):
             options['traceback'] = True
 
         name = options['run_folder_path'][0]
-        # check for duplicated run name
-        p_run = Run.objects.filter(name__exact=name)
-        if p_run:
-            raise CommandError('Pipeline run name already used. Change name')
-
-        # create the pipeline run folder
-        ds_path = os.path.join(cfg.PIPELINE_WORKING_DIR, name)
 
-        if os.path.exists(ds_path):
-            raise CommandError('pipeline run path already present!')
-        else:
-            logger.info('creating pipeline run folder')
-            os.mkdir(ds_path)
-
-        # copy default config into the pipeline run folder
-        logger.info('copying default config in pipeline run folder')
-        template_f = os.path.join(
-            cfg.BASE_DIR,
-            'pipeline',
-            'config_template.py.j2'
-        )
-        with open(template_f, 'r') as fp:
-            template_str = fp.read()
-
-        tm = Template(template_str)
-        with open(os.path.join(ds_path, 'config.py'), 'w') as fp:
-            fp.write(tm.render(**cfg.PIPE_RUN_CONFIG_DEFAULTS))
+        try:
+            p_run = initialise_run(name)
+        except Exception as e:
+            raise CommandError(e)
 
         logger.info((
             'pipeline run initialisation successful! Please modify the '

pipeline/migrations/0001_initial.py

@@ -1,5 +1,6 @@
 # Generated by Django 3.0.5 on 2020-08-12 04:41
 
+from django.conf import settings
 import django.core.validators
 from django.db import migrations, models
 import django.db.models.deletion
@@ -10,6 +11,7 @@ class Migration(migrations.Migration):
     initial = True
 
     dependencies = [
+        migrations.swappable_dependency(settings.AUTH_USER_MODEL),
     ]
 
     operations = [
@@ -90,6 +92,7 @@ class Migration(migrations.Migration):
                 ('status', models.CharField(choices=[('INI', 'Initialised'), ('RUN', 'Running'), ('END', 'Completed'), ('ERR', 'Error')], default='INI', help_text='Status of the pipeline run.', max_length=3)),
                 ('n_images', models.IntegerField(default=0, help_text='number of images processed in this run')),
                 ('n_sources', models.IntegerField(default=0, help_text='number of sources extracted in this run')),
+                ('user', models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.SET_NULL, to=settings.AUTH_USER_MODEL)),
             ],
             options={
                 'ordering': ['name'],

pipeline/models.py

@@ -2,6 +2,7 @@
 import math
 from django.db import models
 from django.core.validators import RegexValidator
+from django.contrib.auth.models import User
 
 
 # Create your models here.
@@ -129,6 +130,8 @@ class Run(models.Model):
     A Run is essentially a pipeline run/processing istance over a set of
     images
     """
+    user = models.ForeignKey(User, on_delete=models.SET_NULL, null=True, blank=True)
+
     name = models.CharField(
         max_length=64,
         unique=True,

pipeline/pipeline/errors.py

@@ -5,8 +5,8 @@ class PipelineError(Exception):
 
     def __init__(self, msg=None):
         self.msg = (
-            'Generic Pipeline error: {0}.'.format(msg) if msg else
-            'Generic Pipeline error.'
+            'Pipeline error: {0}.'.format(msg) if msg else
+            'Undefined Pipeline error.'
         )
 
     def __str__(self):
@@ -29,3 +29,10 @@ class PipelineConfigError(PipelineError):
     def __init__(self, msg=None):
         super(PipelineConfigError, self).__init__(msg)
 
+
+class PipelineInitError(PipelineError):
+    """
+    Error for issue in the pipeline initialisation
+    """
+    def __init__(self, msg=None):
+        super(PipelineInitError, self).__init__(msg)