Update dependencies

.github/workflows/test.yml

@@ -62,10 +62,12 @@ jobs:
     - name: Run test suites [dev]
       if: matrix.container == 'julienpeloton/fink-ci:dev'
       run: |
+        # TODO: remove me
+        pip install fink-utils==0.13.11
         cd $USRLIBS
         source scripts/start_services.sh --kafka-version ${KAFKA_VERSION} --hbase-version ${HBASE_VERSION}
         cd $FINK_HOME
-        fink_test -c conf/fink.conf.dev --unit-tests
+        fink_test -c conf/fink.conf.dev --unit-tests --db-integration
     - name: Run test suites [prod]
       if: matrix.container == 'julienpeloton/fink-ci:prod'
       run: |

bin/index_archival.py

@@ -1,5 +1,5 @@
 #!/usr/bin/env python
-# Copyright 2020-2023 AstroLab Software
+# Copyright 2020-2024 AstroLab Software
 # Author: Julien Peloton
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
@@ -42,6 +42,7 @@
 from fink_broker.loggingUtils import get_fink_logger, inspect_application
 
 from fink_filters.classification import extract_fink_classification
+from fink_utils.spark.utils import check_status_last_prv_candidates
 
 from fink_tns.utils import download_catalog
 
@@ -88,17 +89,9 @@ def main():
     # This is independent from the final structure
     cf = assign_column_family_names(df_flat, cols_i, cols_d, cols_b)
 
-    # Restrict the input DataFrame to the subset of wanted columns.
-    if 'upper' in args.index_table:
-        df = data.select(
-            F.col('objectId').cast('string').alias('objectId'),
-            F.col('prv_candidates.jd').cast('array<double>').alias('jd'),
-            F.col('prv_candidates.fid').cast('array<int>').alias('fid'),
-            F.col('prv_candidates.magpsf').cast('array<float>').alias('magpsf'),
-            F.col('prv_candidates.sigmapsf').cast('array<float>').alias('sigmapsf'),
-            F.col('prv_candidates.diffmaglim').cast('array<float>').alias('diffmaglim')
-        )
-    else:
+    # Restrict the input DataFrame to the subset of wanted columns,
+    # except for tables containing uppervalid & upper limit data
+    if 'upper' not in args.index_table:
         df = df_flat
 
     # Load common cols (casted)
@@ -212,9 +205,21 @@ def main():
             row_key_name=index_row_key_name
         )
     elif columns[0] == 'upper':
-        # This case is the same as the main table
-        # but we keep only upper limit measurements.
+        # select only data for which there are new recent upper limits
+        data = check_status_last_prv_candidates(data, status='upper')
+        data = data.filter('upper')
+
+        df = data.select(
+            F.col('objectId').cast('string').alias('objectId'),
+            F.col('prv_candidates.jd').cast('array<double>').alias('jd'),
+            F.col('prv_candidates.fid').cast('array<int>').alias('fid'),
+            F.col('prv_candidates.magpsf').cast('array<float>').alias('magpsf'),
+            F.col('prv_candidates.sigmapsf').cast('array<float>').alias('sigmapsf'),
+            F.col('prv_candidates.diffmaglim').cast('array<float>').alias('diffmaglim')
+        )
+
         index_row_key_name = 'objectId_jd'
+
         # explode
         df_ex = df.withColumn(
             "tmp",
@@ -229,30 +234,61 @@ def main():
             F.col("tmp.diffmaglim")
         )
 
-        # take only upper limits
+        # take only upper limits within remaining historical data
         df_index = df_ex.filter(~df_ex['magpsf'].isNotNull())
         # drop NaN columns
         df_index = df_index.drop(*['magpsf', 'sigmapsf'])
     elif columns[0] == 'uppervalid':
-        # This case is the same as the main table
-        # but we keep only upper limit measurements.
+        # select only data for which there are new recent low quality data
+        data = check_status_last_prv_candidates(data, status='uppervalid')
+        data = data.filter('uppervalid')
+
+        df = data.select(
+            F.col('objectId').cast('string').alias('objectId'),
+            F.col('prv_candidates.jd').cast('array<double>').alias('jd'),
+            F.col('prv_candidates.fid').cast('array<int>').alias('fid'),
+            F.col('prv_candidates.magpsf').cast('array<float>').alias('magpsf'),
+            F.col('prv_candidates.sigmapsf').cast('array<float>').alias('sigmapsf'),
+            F.col('prv_candidates.diffmaglim').cast('array<float>').alias('diffmaglim'),
+            F.col('prv_candidates.magnr').cast('array<float>').alias('magnr'),
+            F.col('prv_candidates.sigmagnr').cast('array<float>').alias('sigmagnr'),
+            F.col('prv_candidates.isdiffpos').cast('array<string>').alias('isdiffpos'),
+            F.col('prv_candidates.rb').cast('array<float>').alias('rb'),
+            F.col('prv_candidates.nbad').cast('array<int>').alias('nbad')
+        )
+
         index_row_key_name = 'objectId_jd'
+
         # explode
         df_ex = df.withColumn(
             "tmp",
-            F.arrays_zip("magpsf", "sigmapsf", "diffmaglim", "jd", "fid")
+            F.arrays_zip(
+                "magpsf", "sigmapsf", "diffmaglim", "jd", "fid",
+                "magnr", "sigmagnr", "isdiffpos",
+                "rb", "nbad"
+            )
         ).withColumn("tmp", F.explode("tmp")).select(
             F.concat_ws('_', 'objectId', 'tmp.jd').alias(index_row_key_name),
             "objectId",
             F.col("tmp.jd"),
             F.col("tmp.fid"),
             F.col("tmp.magpsf"),
             F.col("tmp.sigmapsf"),
-            F.col("tmp.diffmaglim")
+            F.col("tmp.diffmaglim"),
+            F.col("tmp.magnr"),
+            F.col("tmp.sigmagnr"),
+            F.col("tmp.isdiffpos"),
+            F.col("tmp.rb"),
+            F.col("tmp.nbad")
         )
 
-        # take only valid measurements from the history
-        df_index = df_ex.filter(df_ex['magpsf'].isNotNull())
+        # take only noisy measurements from the history
+        f1 = (df_ex["rb"] >= 0.55) & (df_ex["nbad"] == 0)
+        cond = ~f1 & df_ex['magpsf'].isNotNull()
+        df_index = df_ex.filter(cond)
+
+        # Remove unused columns
+        df_index = df_index.drop(*["rb", "nbad"])
     elif columns[0] == 'tns':
         with open('{}/tns_marker.txt'.format(args.tns_folder)) as f:
             tns_marker = f.read().replace('\n', '')

deps/requirements.txt

@@ -19,9 +19,9 @@ fastavro==1.6.0
 
 # Fink core
 fink_filters>=3.24
-git+https://github.com/astrolabsoftware/[email protected].1
-fink-utils>=0.13.8
-fink-spins>=0.3.5
+git+https://github.com/astrolabsoftware/[email protected].2
+fink-utils>=0.13.11
+fink-spins>=0.3.7
 fink-tns>=0.9
 
 # Misc