Flu download fix

docker-compose.cloudsql.prod.yml

@@ -1,8 +1,6 @@
 # docker compose --env-file .cloudsql_env -f docker-compose.cloudsql.yml -p cgcloudsql build
 # docker compose --env-file .cloudsql_env -f docker-compose.cloudsql.yml -p cgcloudsql up -d
 
-version: "3.7"
-
 services:
   server:
     build:

docker-compose.cloudsql.yml

@@ -1,8 +1,6 @@
 # docker compose --env-file .cloudsql_env -f docker-compose.cloudsql.yml -p cgcloudsql build
 # docker compose --env-file .cloudsql_env -f docker-compose.cloudsql.yml -p cgcloudsql up -d
 
-version: "3.7"
-
 services:
   server:
     build:

docker-compose.flu.genbank.yml

@@ -1,6 +1,5 @@
 # docker compose -f docker-compose.flu.genbank.yml up -d
 name: pathmut-flu-genbank
-version: "3.7"
 
 services:
   server:

docker-compose.flu.gisaid.yml

@@ -1,6 +1,5 @@
 # docker compose -f docker-compose.flu.gisaid.yml up -d
 name: pathmut-flu-gisaid
-version: "3.7"
 
 services:
   server:

docker-compose.rsv.yml

@@ -1,6 +1,5 @@
 # docker compose -f docker-compose.rsv.yml up -d
 name: pathmut-rsv
-version: "3.7"
 
 services:
   server:

docker-compose.sars2.yml

@@ -1,6 +1,5 @@
 # docker compose -f docker-compose.sars2.yml up -d
 name: pathmut-sars2
-version: "3.7"
 
 services:
   server:

docker-compose.yml

@@ -1,5 +1,4 @@
 name: pathmut-all
-version: "3.7"
 
 services:
   cg-frontend:

services/server/cg_server/download/metadata.py

@@ -33,9 +33,9 @@ def download_metadata(conn, req):
             req.get("subm_end_date", None),
             req.get("selected_metadata_fields", None),
             req.get("selected_group_fields", None),
+            selected_reference,
             req.get("sequence_length", None),
             req.get("percent_ambiguous", None),
-            selected_reference,
         )
 
         # Fields that the user wants
@@ -45,7 +45,7 @@ def download_metadata(conn, req):
         )
 
         sequence_cols = [
-            "Accession ID",
+            "isolate_id",
             "collection_date",
             "submission_date",
         ]
@@ -122,10 +122,10 @@ def download_metadata(conn, req):
                 sql.SQL(
                     """
                 INNER JOIN (
-                    SELECT "sequence_id", "reference", "mutations"
+                    SELECT "isolate_id", "reference", "mutations"
                     FROM {mutation_table}
                 ) {mutation_table_short} ON 
-                    {mutation_table_short}."sequence_id" = m."sequence_id" AND
+                    {mutation_table_short}."isolate_id" = m."isolate_id" AND
                     {mutation_table_short}."reference" = {reference_name}
                 """
                 ).format(

services/server/cg_server/query/group_mutation_frequencies.py

@@ -114,9 +114,9 @@ def query_group_mutation_frequencies_dynamic(conn, req):
         req.get("subm_end_date", None),
         req.get("selected_metadata_fields", None),
         req.get("selected_group_fields", None),
+        selected_reference,
         req.get("sequence_length", None),
         req.get("percent_ambiguous", None),
-        selected_reference,
     )
     sequence_mutation_table = "sequence_" + mutation_table
 
@@ -129,16 +129,16 @@ def query_group_mutation_frequencies_dynamic(conn, req):
             sql.SQL(
                 """
             WITH "group_counts" AS (
-                SELECT {group_col}, COUNT("sequence_id")
+                SELECT {group_col}, COUNT("isolate_id")
                 FROM {sequence_mutation_table}
                 WHERE {sequence_where_filter}
                 GROUP BY {group_col}
             ),
             "group_muts" AS (
                 SELECT
-                    {group_col}, "mutation", COUNT("sequence_id")
+                    {group_col}, "mutation", COUNT("isolate_id")
                 FROM (
-                    SELECT "sequence_id", {group_col}, UNNEST("mutations") as "mutation"
+                    SELECT "isolate_id", {group_col}, UNNEST("mutations") as "mutation"
                     FROM {sequence_mutation_table}
                     WHERE {sequence_where_filter}
                 ) "group_muts"

services/server/cg_server/query/report.py

@@ -91,7 +91,7 @@ def generate_report(conn, req):
                 GROUP BY "region", "mutation_id"
             ),
             region_counts AS (
-                SELECT "region", COUNT("sequence_id")
+                SELECT "region", COUNT("isolate_id")
                 FROM "metadata" m
                 WHERE
                     "collection_date" >= %(start_date)s AND
@@ -195,7 +195,7 @@ def generate_report(conn, req):
                 """
             WITH seq_cooc AS (
                 SELECT
-                    seq_mut."sequence_id",
+                    seq_mut."isolate_id",
                     seq_mut."region",
                     ("mutations" & (
                         SELECT ARRAY_AGG("id")
@@ -204,7 +204,7 @@ def generate_report(conn, req):
                     )) as "mutations",
                     m.{group}
                 FROM "sequence_gene_aa_mutation" seq_mut
-                INNER JOIN "metadata" m ON seq_mut."sequence_id" = m."sequence_id"
+                INNER JOIN "metadata" m ON seq_mut."isolate_id" = m."isolate_id"
                 WHERE
                     seq_mut."collection_date" >= %(start_date)s AND
                     seq_mut."collection_date" <= %(end_date)s
@@ -218,7 +218,7 @@ def generate_report(conn, req):
                     SELECT
                         "mutations",
                         {group},
-                        COUNT("sequence_id") as "count"
+                        COUNT("isolate_id") as "count"
                     FROM seq_cooc
                     GROUP BY "mutations", {group}
                 ) cooc_group
@@ -228,14 +228,14 @@ def generate_report(conn, req):
                 SELECT
                     seq_cooc."region",
                     "mutations",
-                    COUNT(seq_cooc."sequence_id") AS "count"
+                    COUNT(seq_cooc."isolate_id") AS "count"
                 FROM seq_cooc
                 GROUP BY seq_cooc."mutations", seq_cooc."region"
             ),
             region_counts AS (
                 SELECT
                     seq_cooc."region",
-                    COUNT(seq_cooc."sequence_id") as "count"
+                    COUNT(seq_cooc."isolate_id") as "count"
                 FROM seq_cooc
                 GROUP BY seq_cooc."region"
             )
@@ -321,7 +321,7 @@ def generate_report(conn, req):
             WITH region_counts AS (
                 SELECT
                     m."region",
-                    COUNT(m."sequence_id") as "count"
+                    COUNT(m."isolate_id") as "count"
                 FROM "metadata" m
                 WHERE
                     m."collection_date" >= %(start_date)s AND
@@ -332,7 +332,7 @@ def generate_report(conn, req):
                 SELECT
                     m."region",
                     m.{group},
-                    COUNT(m."sequence_id") AS "count"
+                    COUNT(m."isolate_id") AS "count"
                 FROM "metadata" m
                 WHERE
                     m."collection_date" >= %(start_date)s AND

services/server/cg_server/query/variant_table.py

@@ -41,6 +41,7 @@ def build_variant_table(conn, req):
         raise Exception("No reference specified")
 
     with conn.cursor() as cur:
+
         sequence_where_filter = build_sequence_location_where_filter(
             constants["GROUP_MUTATION"],
             get_loc_level_ids(req),
@@ -50,10 +51,11 @@ def build_variant_table(conn, req):
             req.get("subm_end_date", None),
             req.get("selected_metadata_fields", None),
             req.get("selected_group_fields", None),
+            selected_reference,
             req.get("sequence_length", None),
             req.get("percent_ambiguous", None),
-            selected_reference,
         )
+
 
         (mutation_filter, mutation_table) = build_coordinate_filters(
             conn,
@@ -73,7 +75,7 @@ def build_variant_table(conn, req):
 
         # Get grouping columns, metadata columns
         metadata_cols = [
-            "Accession ID",
+            "isolate_id",
             "collection_date",
             "submission_date",
         ]
@@ -126,7 +128,7 @@ def build_variant_table(conn, req):
                 sm."mutations"
             FROM (
                 SELECT
-                    sst."sequence_id",
+                    sst."isolate_id",
                     sst."reference",
                     (sst.mutations & (
                         SELECT ARRAY_AGG("id")
@@ -136,9 +138,9 @@ def build_variant_table(conn, req):
                 FROM {sequence_mutation_table} sst
                 WHERE {sequence_where_filter}
             ) sm
-            INNER JOIN "metadata" m ON sm."sequence_id" = m."sequence_id"
+            INNER JOIN "metadata" m ON sm."isolate_id" = m."isolate_id"
             {joins}
-            ORDER BY m."Accession ID" ASC
+            ORDER BY m."isolate_id" ASC
             """
         ).format(
             metadata_cols_expr=sql.SQL(",").join(metadata_cols_expr),
@@ -155,7 +157,7 @@ def build_variant_table(conn, req):
             # cur.fetchall(), columns=metadata_cols + ["mutation_name", "pos"]
             cur.fetchall(),
             columns=metadata_cols + ["reference", "mutations"],
-        ).set_index("Accession ID")
+        ).set_index("isolate_id")
 
         mutation_name_field = "mutation_str"
         if mutation_format == constants["MUTATION_FORMAT"]["POS_REF_ALT"]:
@@ -208,7 +210,7 @@ def build_variant_table(conn, req):
                         .fillna("N/A")
                     )
                 ),
-                index=["Accession ID"],
+                index=["isolate_id"],
                 columns="mutations",
                 values="val",
             )

src/stores/dataStore.js

@@ -317,6 +317,12 @@ export class DataStore {
           (field) => selectedFields[field]
         ),
         mutation_format: mutationFormat,
+        sequence_length: toJS(
+          rootStoreInstance.configStore.sequenceLengthRange
+        ),
+        percent_ambiguous: toJS(
+          rootStoreInstance.configStore.percentAmbiguousRange
+        ),
       }),
     })
       .then((res) => {
@@ -372,6 +378,12 @@ export class DataStore {
         end_date: toJS(rootStoreInstance.configStore.endDate),
         subm_start_date: toJS(rootStoreInstance.configStore.submStartDate),
         subm_end_date: toJS(rootStoreInstance.configStore.submEndDate),
+        sequence_length: toJS(
+          rootStoreInstance.configStore.sequenceLengthRange
+        ),
+        percent_ambiguous: toJS(
+          rootStoreInstance.configStore.percentAmbiguousRange
+        ),
         compress,
       }),
     })
@@ -734,6 +746,12 @@ export class DataStore {
           (field) => selectedFields[field]
         ),
         mutation_format: mutationFormat,
+        sequence_length: toJS(
+          rootStoreInstance.configStore.sequenceLengthRange
+        ),
+        percent_ambiguous: toJS(
+          rootStoreInstance.configStore.percentAmbiguousRange
+        ),
       }),
     })
       .then((res) => {