From 7a4660ddf8aeecb3c274538b0fb7d60bf6189486 Mon Sep 17 00:00:00 2001
From: Florian Spreckelsen <f.spreckelsen@indiscale.com>
Date: Mon, 17 Feb 2025 15:14:36 +0100
Subject: [PATCH] ENH: Use configurable server URL in sample export
---
.../src/ext/js/ext_samplemanagement.js | 2 +-
.../scripting/bin/export_sample_csv.py | 68 +++++++------------
2 files changed, 24 insertions(+), 46 deletions(-)
diff --git a/sample-management-custom/caosdb-server/caosdb-webui/src/ext/js/ext_samplemanagement.js b/sample-management-custom/caosdb-server/caosdb-webui/src/ext/js/ext_samplemanagement.js
index 92a854e..ba4dcb4 100644
--- a/sample-management-custom/caosdb-server/caosdb-webui/src/ext/js/ext_samplemanagement.js
+++ b/sample-management-custom/caosdb-server/caosdb-webui/src/ext/js/ext_samplemanagement.js
@@ -94,7 +94,7 @@ const ext_samplemanagement = function($, navbar, log, form_elements, form_panel,
script: "export_sample_csv.py",
fields: [{
type: "text",
- name: "bis_ids",
+ name: "ids",
label: sample_id_label,
required: false,
pattern: "((([0-9]+\\s*-\\s*){0,1}[0-9]+)\\s*,\\s*)*(([0-9]+\\s*-\\s*){0,1}[0-9]+)",
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 4b79fdd..41ca25f 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
@@ -25,33 +25,28 @@ import logging
import os
import sys
import urllib
-from datetime import date, datetime
-from typing import List
import linkahead as db
import pandas as pd
-from caosadvancedtools.datainconsistency import DataInconsistencyError
from caosadvancedtools.serverside import helper
from caosadvancedtools.table_export import BaseTableExporter
-from caosadvancedtools.table_importer import CSVImporter
-from caoscrawler import Crawler, SecurityMode
-from caoscrawler.crawl import ForbiddenTransaction
-from caoscrawler.identifiable_adapters import CaosDBIdentifiableAdapter
+from caoscrawler.config import get_config_setting
from caoscrawler.logging import configure_server_side_logging
from linkahead.cached import cached_get_entity_by, cached_query as cquery
from linkahead.common.datatype import get_id_of_datatype
from linkahead.exceptions import (EmptyUniqueQueryError, QueryNotUniqueError,
TransactionError)
-from dateutil import parser as dateparser
-from dateutil.parser import isoparse
from bis_utils import (create_email_with_link_text,
get_description_row, get_email_from_username,
- get_options_row, send_mail_with_defaults,
- SPECIAL_TREATMENT_SAMPLE as SPECIAL_TREATMENT)
+ get_options_row, send_mail_with_defaults)
from export_container_csv import (generate_label_text,
extract_storage_chain as container_storage_chain)
-from upload_sample_template import DATATYPE_DEFINITIONS
+from sample_helpers.sample_upload_column_definitions import (
+ DATATYPE_DEFINITIONS, SPECIAL_TREATMENT_SAMPLE as SPECIAL_TREATMENT)
+from sample_helpers.utils import (CONSTANTS, get_column_header_name,
+ get_entity_name)
+
# suppress warning of diff function
apilogger = logging.getLogger("linkahead.apiutils")
@@ -59,8 +54,8 @@ apilogger.setLevel(logging.ERROR)
logger = logging.getLogger("caosadvancedtools")
-ERROR_PREFIX = 'Something went wrong: '
-ERROR_SUFFIX = ' Please conatct <a href="mailto:biosamples@geomar.de">biosamples@geomar.de</a> if you encounter this issue.'
+ERROR_PREFIX = CONSTANTS["error_prefix"]
+ERROR_SUFFIX = CONSTANTS["error_suffix"]
def cached_record(i):
@@ -283,7 +278,7 @@ def extract_hol(record, key):
def extract_bis_url(record, key):
# base_uri = db.get_config().get("Connection", "url")
- base_uri = "https://biosamples.geomar.de/"
+ base_uri = get_config_setting("public_host_url")
return urllib.parse.urljoin(base_uri, f"Entity/{record.id}")
@@ -336,7 +331,7 @@ def extract_event_url(record, key):
if not events:
return None
if len(events) == 1:
- return urllib.parse.urljoin("https://biosamples.geomar.de", f"Entity/{events[0].id}")
+ return urllib.parse.urljoin(get_config_setting("public_host_url"), f"Entity/{events[0].id}")
logger.debug(f"Sample {record.id} has multiple events.")
return None
@@ -347,10 +342,6 @@ EXTRACTORS = {
"Parent BIS ID": extract_parent_sample,
"AphiaID": default_find,
"Collection": extract_reference_name,
- "Date collected start": extract_date,
- "Date collected stop": extract_date,
- "Date sampled start": extract_date,
- "Date sampled stop": extract_date,
"Main User": extract_person,
"Sampling Person": extract_person,
"PI": extract_person,
@@ -402,14 +393,14 @@ IGNORE_KEYS = [
# Additional list of keys to be ignored when extracting parent sample information
IGNORE_KEYS_PARENT = IGNORE_KEYS + [
- "BIS ID",
+ "LinkAhead ID",
]
# List of columns to be exported although they are not known to or ignored by
# the import.
ADDITIONAL_EXPORTS = [
- "BIS URL",
- "Parent BIS ID",
+ "LinkAhead URL",
+ "Parent LinkAhead ID",
"Storage chain",
]
@@ -540,25 +531,25 @@ def to_csv(samples):
def retrieve_samples(data):
container = []
not_found = []
- for bis_id in data:
- if isinstance(bis_id, int):
+ for eid in data:
+ if isinstance(eid, int):
try:
container.append(
- cached_get_entity_by(query=f"FIND RECORD SAMPLE WITH id='{bis_id}'"))
+ cached_get_entity_by(query=f"FIND RECORD SAMPLE WITH id='{eid}'"))
except EmptyUniqueQueryError as e:
# we want to warn about these
- not_found.append(bis_id)
+ not_found.append(eid)
else:
found_at_least_one_in_range = False
- for next_bis_id in bis_id:
+ for next_eid in eid:
try:
container.append(
- cached_get_entity_by(query=f"FIND RECORD Sample WITH id='{next_bis_id}'"))
+ cached_get_entity_by(query=f"FIND RECORD Sample WITH id='{next_eid}'"))
found_at_least_one_in_range = True
except EmptyUniqueQueryError as e:
pass
if not found_at_least_one_in_range:
- not_found.append(f"{bis_id.start}-{bis_id.stop-1}")
+ not_found.append(f"{eid.start}-{eid.stop-1}")
return container, not_found
@@ -626,19 +617,6 @@ def main():
logger.info("Removing empty columns from export")
no_empty_columns = True
- if "from_date" in form_data:
- # Inserted after ...
- data = [el.id for el in db.execute_query(
- "SELECT id FROM sample WHICH REFERENCES A SourceEvent "
- "WHICH HAS AN IGSN AND "
- f"(WHICH WAS INSERTED SINCE {form_data['from_date']})")
- ]
- # ... + update after
- data += [el.id for el in db.execute_query(
- "SELECT id FROM sample WHICH REFERENCES A SourceEvent "
- "WHICH HAS AN IGSN AND "
- f"(WHICH WAS UPDATED SINCE {form_data['from_date']})")
- ]
elif "query_string" in form_data and form_data["query_string"]:
query_string = form_data["query_string"]
if not query_string.lower().startswith("find ") and not query_string.lower().startswith("select "):
@@ -657,11 +635,11 @@ def main():
)
return
else:
- if not form_data["bis_ids"]:
+ if not form_data["ids"]:
logger.error(
"Please specify the samples to be exported either by query or by id(s).")
return
- tmp = form_data["bis_ids"].split(",")
+ tmp = form_data["ids"].split(",")
data = []
for d in tmp:
if "-" in d:
--
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