Merge pull request #401 from fyvon/improve/set_release_date

Set specific optional release date

release/scripts/CreateRelease.py

@@ -1,7 +1,8 @@
 import re
 from catalog.models import *
-from datetime import date,timedelta
+from datetime import date, timedelta
 from ftplib import FTP
+from typing import Self
 
 
 class CreateRelease:
@@ -13,36 +14,39 @@ class CreateRelease:
     new_performances = {}
     new_traits = set()
 
-    def __init__(self, release_tomorrow=None):
-        self.release_tomorrow = release_tomorrow
+    def __init__(self, release_date=date.today()):
+        self.release_date = release_date
         self.new_publications = Publication.objects.filter(date_released__isnull=True, curation_status="C")
 
+    @classmethod
+    def tomorrow(cls) -> Self:
+        return cls.on(date.today() + timedelta(days=1))
 
-    def get_release_date(self):
-        release_date = date.today()
-        if self.release_tomorrow:
-            release_date = release_date + timedelta(days=1)
-        self.new_release_date = release_date
+    @classmethod
+    def on(cls, release_date: date) -> Self:
+        return cls(release_date=release_date)
 
+    def get_release_date(self):
+        return self.release_date
 
     def update_data_to_release(self):
         """
         Update data ready for the release (scores, performances and publications)
         by adding a date in the 'date_released' columns
         """
-        self.get_release_date()
+        release_date = 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 ####
+        #### Add release date for each publication and dependent models ####
         for publication in self.new_publications:
-            publication.date_released = self.new_release_date
+            publication.date_released = release_date
             publication.save()
 
             # Scores
             scores_list = Score.objects.filter(date_released__isnull=True, publication=publication)
             for score in scores_list:
                 self.new_scores[score.id] = 1
                 # Update date_release
-                score.date_released = self.new_release_date
+                score.date_released = release_date
                 score.save()
                 # Get new traits
                 score_traits = {efotrait.id for efotrait in score.trait_efo.all()}
@@ -53,16 +57,15 @@ def update_data_to_release(self):
             for performance in performances_list:
                 self.new_performances[performance.id] = 1
                 # Update date_release
-                performance.date_released = self.new_release_date
+                performance.date_released = release_date
                 performance.save()
 
-
     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), {} 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,
+                date=self.get_release_date(),
                 performance_count=len(self.new_performances.keys()),
                 publication_count=len(self.new_publications),
                 score_count=len(self.new_scores.keys()),
@@ -71,7 +74,6 @@ def create_new_release(self):
               )
         return release
 
-
     def check_ftp(self):
         """ Check that all the PGSs have a corresponding Scoring file in the PGS FTP. """
         files_list = []
@@ -113,17 +115,38 @@ def check_ftp(self):
 
 ################################################################################
 
-def run():
+def parse_arguments(args):
+    """Parse runscript --script-args arguments and return them as a dictionary
+    Must be a list of key=value pairs.
+    eg: python manage.py runscript CreateRelease --script-args date=2024-12-25"""
+    try:
+        return dict(map(lambda s: s.split('='), args))
+    except ValueError:
+        raise Exception("Invalid arguments: must be key=value pairs")
+
+
+def create_new_release_from_args(args) -> CreateRelease:
+    """Parse the runscript arguments for the CreateRelease command.
+    Expected argument: date=<iso-format-date YYYY-MM-DD>, to choose a particular date for the release.
+    If no argument is given, the release will be planned for tomorrow."""
+    parsed_args = parse_arguments(args)
+
+    if 'date' in parsed_args:
+        release = CreateRelease.on(date.fromisoformat(parsed_args['date']))
+    else:
+        release = CreateRelease.tomorrow()
+    release.update_data_to_release()
+    return release
 
-    lastest_release = Release.objects.latest('date').date
 
-    release = CreateRelease(release_tomorrow=1)
-    release.update_data_to_release()
-    new_release = release.create_new_release()
+def run(*args):
 
+    latest_release = Release.objects.latest('date').date
+    release = create_new_release_from_args(args)
+    new_release = release.create_new_release()
 
     # Just a bunch of prints
-    print("Latest release: "+str(lastest_release))
+    print("Latest release: "+str(latest_release))
     print("New release: "+str(new_release.date))
     print("Number of new Scores: "+str(new_release.score_count))
     print(', '.join(release.new_scores.keys()))

release/scripts/run_release_script.py

@@ -1,8 +1,6 @@
-import sys, os.path, shutil, glob
-from datetime import date
 from catalog.models import *
 from release.scripts.UpdateGwasStudies import UpdateGwasStudies
-from release.scripts.CreateRelease import CreateRelease
+from release.scripts.CreateRelease import create_new_release_from_args
 from release.scripts.EuropePMCLinkage import EuropePMCLinkage
 from curation_tracker.models import CurationPublicationAnnotation
 
@@ -11,10 +9,12 @@
 output_prefix = '  > '
 
 
-def run():
+def run(*args):
     """
         Main method executed by the Django command:
         `python manage.py runscript run_release_script`
+        To choose a particular release date, use the command:
+        `python manage.py runscript run_release_script --script-args date=YYYY-MM-DD`
     """
 
     #-------------#
@@ -45,8 +45,8 @@ def run():
 
     print("\n\n#### Start the database release ####")
 
-    # Create release
-    call_create_release()
+    # Create release (default date is tomorrow, otherwise the value of the runscript argument 'date')
+    call_create_release(args)
 
     # Update Curation Tracker
     update_curation_tracker()
@@ -164,18 +164,16 @@ def update_gwas_studies():
     gwas_studies.update_studies()
 
 
-def call_create_release():
+def call_create_release(args):
     """ Create a new PGS Catalog release """
     report_header("Create a new PGS Catalog release")
 
-    lastest_release = Release.objects.latest('date').date
-
-    release = CreateRelease(release_tomorrow=1)
-    release.update_data_to_release()
+    latest_release = Release.objects.latest('date').date
+    release = create_new_release_from_args(args)
     new_release = release.create_new_release()
 
     # Just a bunch of prints
-    output_report("Latest release: "+str(lastest_release))
+    output_report("Latest release: "+str(latest_release))
     output_report("New release: "+str(new_release.date))
     output_report("Number of new Scores: "+str(new_release.score_count))
     output_report(', '.join(release.new_scores.keys()))