From e80097017192c733e1ffd820ee86c9b65b7719a8 Mon Sep 17 00:00:00 2001
From: Florian Spreckelsen <f.spreckelsen@indiscale.com>
Date: Fri, 7 Feb 2025 15:54:08 +0100
Subject: [PATCH] WIP: Remove some entries from sample exporter
---
.../scripting/bin/export_sample_csv.py | 55 +------------------
1 file changed, 1 insertion(+), 54 deletions(-)
diff --git a/sample-management-custom/caosdb-server/scripting/bin/export_sample_csv.py b/sample-management-custom/caosdb-server/scripting/bin/export_sample_csv.py
index 4f47b48..4b79fdd 100755
--- a/sample-management-custom/caosdb-server/scripting/bin/export_sample_csv.py
+++ b/sample-management-custom/caosdb-server/scripting/bin/export_sample_csv.py
@@ -63,19 +63,6 @@ ERROR_PREFIX = 'Something went wrong: '
ERROR_SUFFIX = ' Please conatct <a href="mailto:biosamples@geomar.de">biosamples@geomar.de</a> if you encounter this issue.'
-# Declare mapping of different time/date column names to property names
-TIME_NAME_MAPPINGS = {
- "date collected start": "time start",
- "time collected start": "time start",
- "date collected stop": "time stop",
- "time collected stop": "time stop",
- "date sampled start": "time sampled start",
- "time sampled start": "time sampled start",
- "date sampled stop": "time sampled stop",
- "time sampled stop": "time sampled stop",
-}
-
-
def cached_record(i):
return cached_get_entity_by(eid=i)
@@ -212,29 +199,6 @@ def extract_date_time(record, p):
return extract_value_as_list(record, p)
-def extract_date(record, key):
- if key.lower() in TIME_NAME_MAPPINGS.keys():
- time_key = TIME_NAME_MAPPINGS[key.lower()]
- else:
- time_key = key
- date_times = extract_date_time(record, time_key)
- return [isoparse(t).date().isoformat() for t in date_times]
-
-
-def extract_time(record, key):
- if key.lower() in TIME_NAME_MAPPINGS.keys():
- time_key = TIME_NAME_MAPPINGS[key.lower()]
- else:
- time_key = key
- date_times = extract_date_time(record, time_key)
- return [isoparse(t).time().isoformat() for t in date_times]
-
-
-def extract_time_zone(record, key):
- date_times = extract_date_time(record, "Time start")
- return [isoparse(t).tzname() for t in date_times]
-
-
def extract_station_number(record, key):
source_ev = retrieve_source_event(record)
return [e.get_property(key).value for e in source_ev if
@@ -377,7 +341,7 @@ def extract_event_url(record, key):
return None
-# must be same keys as SPECIAL_TREATMENT
+# must include all keys from SPECIAL_TREATMENT
EXTRACTORS = {
"BIS ID": lambda record, key: record.id,
"Parent BIS ID": extract_parent_sample,
@@ -399,11 +363,6 @@ EXTRACTORS = {
"Nagoya case number": extract_nagoya_case_number,
"PDFReport": extract_pdf_id,
"Subevent": extract_source_event_name,
- "Time collected start": extract_time,
- "Time collected stop": extract_time,
- "Time sampled start": extract_time,
- "Time sampled stop": extract_time,
- "Timezone": extract_time_zone,
"Station ID": extract_station_id,
"Station number": extract_station_number,
"Sampling depth start": extract_sampling_depth_start,
@@ -436,14 +395,9 @@ REVERSE_COLUMN_CONVERTER = {
# List of sample properties to be ignored because they are treated
# otherwise. Similar, but not identical to SPECIAL TREATMENT.
IGNORE_KEYS = [
- "NagoyaCase",
"Parent Sample",
"Container",
- "SourceEvent",
"Event",
- "Date",
- "Sampling depth",
- "Water depth"
]
# Additional list of keys to be ignored when extracting parent sample information
@@ -455,15 +409,8 @@ IGNORE_KEYS_PARENT = IGNORE_KEYS + [
# the import.
ADDITIONAL_EXPORTS = [
"BIS URL",
- "Date sampled start",
- "Date sampled stop",
- "IGSN URL",
- "IGSN",
"Parent BIS ID",
"Storage chain",
- "Time sampled start",
- "Time sampled stop",
- "URL SourceEvent"
]
--
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