Merge pull request #870 from cmu-delphi/release/delphi-epidata-0.3.13

Release Delphi Epidata 0.3.13

Author: krivard

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.3.12
+current_version = 0.3.13
 commit = False
 tag = False
 

src/acquisition/covidcast/csv_importer.py

@@ -43,9 +43,9 @@ class CsvImporter:
     "val": float,
     "se": float,
     "sample_size": float,
-    "missing_val": int,
-    "missing_se": int,
-    "missing_sample_size": int
+    "missing_val": "Int64",
+    "missing_se": "Int64",
+    "missing_sample_size": "Int64"
   }
 
   # NOTE: this should be a Python 3.7+ `dataclass`, but the server is on 3.4

src/acquisition/covidcast/database.py

@@ -326,6 +326,7 @@ def delete_batch(self, cc_deletions):
 '''
 
     drop_tmp_table_sql = f'DROP TABLE {tmp_table_name}'
+    total = None
     try:
       self._cursor.execute(create_tmp_table_sql)
       self._cursor.execute(amend_tmp_table_sql)
@@ -337,12 +338,18 @@ def delete_batch(self, cc_deletions):
         raise Exception(f"Bad deletions argument: need a filename or a list of tuples; got a {type(cc_deletions)}")
       self._cursor.execute(add_id_sql)
       self._cursor.execute(delete_sql)
+      total = self._cursor.rowcount
       self._cursor.execute(fix_latest_issue_sql)
       self._connection.commit()
+
+      if total == -1:
+        # the SQL connector does not support returning number of rows affected (see PEP 249)
+        total = None
     except Exception as e:
       raise e
     finally:
       self._cursor.execute(drop_tmp_table_sql)
+    return total
 
   def compute_covidcast_meta(self, table_name='covidcast', use_index=True):
     """Compute and return metadata on all non-WIP COVIDcast signals."""

src/acquisition/covidcast/delete_batch.py

@@ -2,6 +2,7 @@
 
 # standard library
 import argparse
+import glob
 import os
 import time
 
@@ -22,19 +23,21 @@ def get_argument_parser():
       help="filename for log output (defaults to stdout)")
     return parser
 
-def handle_file(deletion_file, database):
+def handle_file(deletion_file, database, logger):
     logger.info("Deleting from csv file", filename=deletion_file)
     rows = []
     with open(deletion_file) as f:
         for line in f:
-            rows.append(line.strip().split(","))
+            fields = line.strip().split(",")
+            if len(fields) < 9: continue
+            rows.append(fields + ["day"])
     rows = rows[1:]
     try:
         n = database.delete_batch(rows)
         logger.info("Deleted database rows", row_count=n)
         return n
     except Exception as e:
-        logger.exception('Exception while deleting rows:', e)
+        logger.exception('Exception while deleting rows', exception=e)
         database.rollback()
     return 0
 
@@ -49,7 +52,11 @@ def main(args):
 
     try:
         for deletion_file in sorted(glob.glob(os.path.join(args.deletion_dir, '*.csv'))):
-            all_n += handle_file(deletion_file)
+            n = handle_file(deletion_file, database, logger)
+            if n is not None:
+                all_n += n
+            else:
+                all_n = "rowcount unsupported"
     finally:
         database.disconnect(True)
 

src/client/delphi_epidata.R

@@ -15,7 +15,7 @@ Epidata <- (function() {
   # API base url
   BASE_URL <- 'https://delphi.cmu.edu/epidata/api.php'
 
-  client_version <- '0.3.12'
+  client_version <- '0.3.13'
 
   # Helper function to cast values and/or ranges to strings
   .listitem <- function(value) {

src/client/delphi_epidata.js

@@ -22,7 +22,7 @@
   }
 })(this, function (exports, fetchImpl, jQuery) {
   const BASE_URL = "https://delphi.cmu.edu/epidata/";
-  const client_version = "0.3.12";
+  const client_version = "0.3.13";
 
   // Helper function to cast values and/or ranges to strings
   function _listitem(value) {

src/client/packaging/npm/package.json

@@ -2,7 +2,7 @@
   "name": "delphi_epidata",
   "description": "Delphi Epidata API Client",
   "authors": "Delphi Group",
-  "version": "0.3.12",
+  "version": "0.3.13",
   "license": "MIT",
   "homepage": "https://github.com/cmu-delphi/delphi-epidata",
   "bugs": {

src/client/packaging/pypi/delphi_epidata/__init__.py

@@ -1,4 +1,4 @@
 from .delphi_epidata import Epidata
 
 name = 'delphi_epidata'
-__version__ = '0.3.12'
+__version__ = '0.3.13'

src/client/packaging/pypi/setup.py

@@ -5,7 +5,7 @@
 
 setuptools.setup(
     name="delphi_epidata",
-    version="0.3.12",
+    version="0.3.13",
     author="David Farrow",
     author_email="[email protected]",
     description="A programmatic interface to Delphi's Epidata API.",

src/server/_config.py

@@ -5,7 +5,7 @@
 
 load_dotenv()
 
-VERSION = "0.3.12"
+VERSION = "0.3.13"
 
 MAX_RESULTS = int(10e6)
 MAX_COMPATIBILITY_RESULTS = int(3650)