diff --git a/catalog/migrations/0003_release_efotrait_count.py b/catalog/migrations/0003_release_efotrait_count.py new file mode 100644 index 00000000..c0e275f4 --- /dev/null +++ b/catalog/migrations/0003_release_efotrait_count.py @@ -0,0 +1,18 @@ +# Generated by Django 4.2.10 on 2024-03-25 15:57 + +from django.db import migrations, models + + +class Migration(migrations.Migration): + + dependencies = [ + ('catalog', '0002_alter_metric_name'), + ] + + operations = [ + migrations.AddField( + model_name='release', + name='efotrait_count', + field=models.IntegerField(default=0, verbose_name='Number of new EFO traits released'), + ), + ] diff --git a/catalog/models.py b/catalog/models.py index d712796d..32bc47f7 100644 --- a/catalog/models.py +++ b/catalog/models.py @@ -1138,6 +1138,7 @@ class Release(models.Model): score_count = models.IntegerField('Number of new PGS scores released', default=0) performance_count = models.IntegerField('Number of new PGS Performance metrics released', default=0) publication_count = models.IntegerField('Number of new PGS Publication released', default=0) + efotrait_count = models.IntegerField('Number of new EFO traits released', default=0) notes = models.TextField(verbose_name='Release notes', max_length=600, blank=True) updated_score_count = models.IntegerField('Number of PGS scores updated', default=0) updated_performance_count = models.IntegerField('Number of PGS Performance metrics updated', default=0) @@ -1160,3 +1161,9 @@ def released_publication_ids(self): def released_performance_ids(self): performances = Performance.objects.values_list('id', flat=True).filter(date_released__exact=self.date).order_by('id') return list(performances) + + @property + def released_new_trait_ids(self): + previous_traits = Score.objects.values_list('trait_efo__id', flat=True).filter(date_released__lt=self.date).distinct() + new_traits = Score.objects.values_list('trait_efo__id', flat=True).filter(date_released__exact=self.date).distinct() + return list(new_traits.difference(previous_traits)) diff --git a/catalog/static/catalog/pgs_bar_charts.js b/catalog/static/catalog/pgs_bar_charts.js index 9ab4378a..a07c0bdd 100644 --- a/catalog/static/catalog/pgs_bar_charts.js +++ b/catalog/static/catalog/pgs_bar_charts.js @@ -1,15 +1,17 @@ -var rest_url = 'https://www.pgscatalog.org/rest/release/' +var rest_url = '/rest/release/' bg_colours = { 'score': '#007C82', 'publication': '#BE4A81', 'performance': 'DodgerBlue', + 'trait': '#c03b23', 'new_entry': '#FFC200' }; bg_hover_colours = { 'score': '#00adb5', 'publication': '#e83e8c', 'performance': '#51a9ff', + 'trait': '#f67d51', 'new_entry': '#FFD700' }; @@ -41,6 +43,15 @@ $('.get_pgs_ids').click(function() { html_pub += ''; $(list_pub_id).html(html_pub); $('#list_'+id).show(); + + list_trait_id = '#list_'+id.replace(type,'trait'); + html_trait = "'; + $(list_trait_id).html(html_trait); + $('#list_'+id).show(); }) .fail(function (xhRequest, ErrorText, thrownError) { console.log(xhRequest); diff --git a/catalog/templates/catalog/releases.html b/catalog/templates/catalog/releases.html index 5cc3858b..df34d598 100644 --- a/catalog/templates/catalog/releases.html +++ b/catalog/templates/catalog/releases.html @@ -20,6 +20,7 @@

Score(s) Publication(s) Performance(s) + Trait(s) Notes @@ -32,7 +33,7 @@

0 %} {{ latest_release.score_count }} -
+
{% else %} - {% endif %} @@ -41,7 +42,7 @@

0 %} {{ latest_release.publication_count }} -
+
{% else %} - {% endif %} @@ -53,6 +54,15 @@

+ + {% if latest_release.efotrait_count > 0 %} + {{ latest_release.efotrait_count }} + +
+ {% else %} + - + {% endif %} + {{ latest_release.notes }} @@ -70,6 +80,7 @@

{{ release.score_count }} -
+
{% else %} - {% endif %} @@ -97,7 +108,7 @@

{{ release.publication_count }} -
+
{% else %} - {% endif %} @@ -109,6 +120,15 @@

{{ release.efotrait_count }} + +
+ {% else %} + - + {% endif %} + {{ release.notes }} {% endfor %} @@ -130,6 +150,7 @@

-

Scores, Publications and Performance Metrics per release

+

Scores, Publications, Performance Metrics and Traits per release

@@ -159,6 +180,9 @@

+
+ +

Distribution of publications per year

diff --git a/catalog/views.py b/catalog/views.py index 8b04d792..12c67a00 100644 --- a/catalog/views.py +++ b/catalog/views.py @@ -689,6 +689,7 @@ def releases(request): total_score = 0 total_perf = 0 total_publi = 0 + total_trait = 0 max_score = 0 max_publi = 0 max_perf = 0 @@ -756,6 +757,7 @@ def releases(request): score = release.score_count perf = release.performance_count publi = release.publication_count + trait = release.efotrait_count date = release.date release_item = { @@ -763,13 +765,16 @@ def releases(request): 'score_count': score, 'performance_count': perf, 'publication_count': publi, + 'trait_count': trait, 'total_score_count': total_score, 'total_performance_count': total_perf, - 'total_publication_count': total_publi + 'total_publication_count': total_publi, + 'total_trait_count': total_trait } total_score += score total_perf += perf total_publi += publi + total_trait += trait release_data.append(release_item) diff --git a/release/scripts/CreateRelease.py b/release/scripts/CreateRelease.py index 9b38be81..2f14eb04 100644 --- a/release/scripts/CreateRelease.py +++ b/release/scripts/CreateRelease.py @@ -11,6 +11,7 @@ class CreateRelease: new_scores = {} new_performances = {} + new_traits = set() def __init__(self, release_tomorrow=None): self.release_tomorrow = release_tomorrow @@ -30,6 +31,7 @@ def update_data_to_release(self): by adding a date in the 'date_released' columns """ self.get_release_date() + previous_traits = set(Score.objects.values_list('trait_efo__id', flat=True).exclude(date_released__isnull=True).distinct()) #### Add release date for each publications and dependent models #### for publication in self.new_publications: publication.date_released = self.new_release_date @@ -42,6 +44,9 @@ def update_data_to_release(self): # Update date_release score.date_released = self.new_release_date score.save() + # Get new traits + score_traits = {efotrait.id for efotrait in score.trait_efo.all()} + self.new_traits.update(score_traits.difference(previous_traits)) # Performances performances_list = Performance.objects.filter(date_released__isnull=True, publication=publication) @@ -55,12 +60,13 @@ def update_data_to_release(self): def create_new_release(self): """ Create new release instance and save it in the database """ #### Create new release instance #### - release_notes = 'This release contains {} new Score(s), {} new Publication(s) and {} new Performance metric(s)'.format(len(self.new_scores.keys()), len(self.new_publications), len(self.new_performances.keys())) + release_notes = 'This release contains {} new Score(s), {} new Publication(s), {} new Performance metric(s) and {} new Trait(s)'.format(len(self.new_scores.keys()), len(self.new_publications), len(self.new_performances.keys()), len(self.new_traits)) release = Release.objects.create( date=self.new_release_date, performance_count=len(self.new_performances.keys()), publication_count=len(self.new_publications), score_count=len(self.new_scores.keys()), + efotrait_count=len(self.new_traits), notes=release_notes ) return release @@ -123,6 +129,7 @@ def run(): print(', '.join(release.new_scores.keys())) print("Number of new Publications: "+str(new_release.publication_count)) print("Number of new Performances: "+str(new_release.performance_count)) + print("Number of new Traits: " + str(new_release.efotrait_count)) # Scores scores_direct = Score.objects.filter(date_released__isnull=True) diff --git a/release/scripts/run_release_script.py b/release/scripts/run_release_script.py index 266c281f..338bb393 100644 --- a/release/scripts/run_release_script.py +++ b/release/scripts/run_release_script.py @@ -181,6 +181,7 @@ def call_create_release(): output_report(', '.join(release.new_scores.keys())) output_report("Number of new Publications: "+str(new_release.publication_count)) output_report("Number of new Performances: "+str(new_release.performance_count)) + output_report("Number of new Traits: " + str(new_release.efotrait_count)) if new_release.score_count == 0 or new_release.publication_count == 0 or new_release.performance_count == 0: error_report("at least one of the main components (Score, Publication or Performance Metrics) hasn't a new entry this release") diff --git a/rest_api/serializers.py b/rest_api/serializers.py index efbef993..9d011131 100644 --- a/rest_api/serializers.py +++ b/rest_api/serializers.py @@ -196,8 +196,8 @@ class ReleaseSerializer(serializers.ModelSerializer): class Meta: model = Release - meta_fields = ('date', 'score_count', 'performance_count', 'publication_count', 'notes', - 'released_score_ids', 'released_publication_ids', 'released_performance_ids') + meta_fields = ('date', 'score_count', 'performance_count', 'publication_count', 'efotrait_count', 'notes', + 'released_score_ids', 'released_publication_ids', 'released_performance_ids', 'released_new_trait_ids') fields = meta_fields read_only_fields = meta_fields