From 1843ff3fd0c27fcf1611ae7b3d75a7011335e753 Mon Sep 17 00:00:00 2001
From: "Janet L. Goldstein" <jgoldste@nrao.edu>
Date: Mon, 22 Nov 2021 09:39:08 -0700
Subject: [PATCH] Core sampler: make the -e option accept an SDM name rather
than an execution_block_id
---
.../core_sampler/core_sampler/core_sampler.py | 40 ++++++++++++-----
.../core_sampler/test/test_core_sampler.py | 43 ++++++++++++++++---
2 files changed, 65 insertions(+), 18 deletions(-)
diff --git a/apps/cli/utilities/core_sampler/core_sampler/core_sampler.py b/apps/cli/utilities/core_sampler/core_sampler/core_sampler.py
index bd4c5deb9..c756f0f8f 100644
--- a/apps/cli/utilities/core_sampler/core_sampler/core_sampler.py
+++ b/apps/cli/utilities/core_sampler/core_sampler/core_sampler.py
@@ -28,9 +28,6 @@ import argparse
import psycopg2 as pg
from psycopg2 import extras
-
-# pylint: disable=C0103, E0402, R0201
-
from pycapo import CapoConfig
from .database import PGTable
@@ -41,6 +38,8 @@ from .row_writer import (
UniquifyingRowWriter,
)
+# pylint: disable=C0103, E0402, R0201, R0903
+
# stolen shamelessly from aat_wrest
class MDDBConnector:
"""Use this connection to interrogate this science product locator"""
@@ -105,16 +104,18 @@ class CoreSampler:
self.save(requested)
self.writer.close()
- def sample_eb(self, exec_block_id: int):
+ def sample_eb(self, sdm_name: str):
"""
Pull execution block metadata from the archive database.
- :param exec_block_id: execution_block_id of interest
+ :param sdm_name: SDM of interest
:return:
"""
ebs = self.table("execution_blocks")
- requested = ebs.fetch({"execution_block_id": exec_block_id})
+ finder = ExecBlockFinder(self.connection)
+ eb_id = finder.find_eb_id(sdm_name)
+ requested = ebs.fetch({"execution_block_id": eb_id})
self.save(requested)
self.writer.close()
@@ -155,6 +156,23 @@ class CoreSampler:
rows.write_to(self.writer)
+class ExecBlockFinder:
+ """Looks up execution block ID for an SDM"""
+
+ def __init__(self, connection: MDDBConnector):
+ self.connection = connection
+
+ def find_eb_id(self, sdm_name: str) -> int:
+ cursor = self.connection.cursor()
+ sql = """
+SELECT execution_block_id FROM execution_blocks
+WHERE ngas_fileset_id=%(sdm_name)s
+ """
+ cursor.execute(sql, {"sdm_name": sdm_name})
+ data = cursor.fetchone()
+ return data["execution_block_id"]
+
+
def main():
parser = argparse.ArgumentParser()
group = parser.add_mutually_exclusive_group(required=True)
@@ -163,18 +181,18 @@ def main():
)
group.add_argument(
"-e",
- "--exec_block_id",
- type=int,
+ "--sdm_name",
+ type=str,
nargs=1,
- help="execution_block_id of SDM for which to pull a core sample",
+ help="name of SDM for which to pull a core sample, e.g., 21A-409.sb39530397.eb39561636.59309.07888592593",
action="store",
)
ns = parser.parse_args()
if ns.project_code:
CoreSampler(MDDBConnector()).sample_project(ns.project_code[0])
- elif ns.exec_block_id:
- CoreSampler(MDDBConnector()).sample_eb(int(ns.exec_block_id[0]))
+ elif ns.sdm_name:
+ CoreSampler(MDDBConnector()).sample_eb(ns.sdm_name[0])
return 0
diff --git a/apps/cli/utilities/core_sampler/test/test_core_sampler.py b/apps/cli/utilities/core_sampler/test/test_core_sampler.py
index e1623fcc2..0651b0b89 100644
--- a/apps/cli/utilities/core_sampler/test/test_core_sampler.py
+++ b/apps/cli/utilities/core_sampler/test/test_core_sampler.py
@@ -16,31 +16,49 @@
# You should have received a copy of the GNU General Public License
# along with Workspaces. If not, see <https://www.gnu.org/licenses/>.
#
-""" Tests for core sampler"""
+""" Tests for core sampler """
+import logging
import sys
from io import StringIO
+from logging import getLogger
from unittest.mock import patch
-import core_sampler
-import pytest
from core_sampler.core_sampler import main
+logger = logging.getLogger("core_sampler")
+logger.setLevel(logging.INFO)
+logger.addHandler(logging.StreamHandler(sys.stdout))
+
+import pytest
+
def test_gets_eb_as_expected():
"""
- Do we get the output we expect for this 20A-465 execution block?
+ Do we get the output we expect for this 21A-409 execution block?
:return:
"""
sys.argv.append("-e")
- sys.argv.append("148839")
+ sys.argv.append("21A-409.sb39530397.eb39561636.59309.07888592593")
with patch("sys.stdout", new=StringIO()) as fake_out:
main()
output = fake_out.getvalue()
rows = output.split("\n")
- assert len(rows) == 86
+
+ found = False
+ for row in rows:
+ if "156759763" in row and "23142018" in row:
+ found = True
+ break
+ assert found
+
+ if len(rows) == 181:
+ # sometimes we get an extra blank line
+ assert len(rows[-1]) == 0
+ else:
+ assert len(rows) == 180
sys.argv.pop()
sys.argv.pop()
@@ -59,6 +77,17 @@ def test_gets_project_as_expected():
main()
output = fake_out.getvalue()
rows = output.split("\n")
- assert len(rows) == 704
+ if len(rows) == 705:
+ # sometimes we get an extra blank line
+ assert len(rows[-1]) == 0
+ else:
+ assert len(rows) == 704
+ found = False
+ for row in rows:
+ if "uid____evla_bdf_1589728351957.bdf" in row and "121847" in row:
+ found = True
+ break
+ assert found
+
sys.argv.pop()
sys.argv.pop()
--
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