From f423f21cf47b40fe5a0fa6d33dbbbe1348521c36 Mon Sep 17 00:00:00 2001
From: vermeul <swen@ethz.ch>
Date: Fri, 29 Jan 2021 00:59:57 +0100
Subject: [PATCH] fixed datasets list, added search feature
---
pybis/src/python/pybis/pybis.py | 38 +++++++++++++++++----------------
1 file changed, 20 insertions(+), 18 deletions(-)
diff --git a/pybis/src/python/pybis/pybis.py b/pybis/src/python/pybis/pybis.py
index 8493abd3c6b..38a730226fd 100644
--- a/pybis/src/python/pybis/pybis.py
+++ b/pybis/src/python/pybis/pybis.py
@@ -416,14 +416,23 @@ def _subcriteria_for_is_finished(is_finished):
def _subcriteria_for_properties(prop, value, entity):
-
+ """This internal method creates the JSON RPC criterias for searching
+ in properties. It distinguishes between numbers, dates and strings
+ and uses the comparative operator (< > >= <=), if available.
+ creationDate and modificationDate attributes can be searched as well.
+ To search in the properties of parents, children, etc. the user has to
+ prefix the propery accordingly:
+
+ - parent_propertyName
+ - child_propertyName
+ - container_propertyName
+ """
search_types = {
'sample': {
'parent' : "as.dto.sample.search.SampleParentsSearchCriteria",
'child' : "as.dto.sample.search.SampleChildrenSearchCriteria",
'container' : "as.dto.sample.search.SampleContainerSearchCriteria",
- 'component' : "as.dto.sample.search.SampleContainerSearchCriteria",
},
'dataset': {
'parent' : "as.dto.dataset.search.DataSetParentsSearchCriteria",
@@ -441,10 +450,10 @@ def _subcriteria_for_properties(prop, value, entity):
if 'date' in prop.lower() and re.search(r'\d{4}\-\d{2}\-\d{2}', value):
is_date = True
eq_type = "as.dto.common.search.DateEqualToValue"
- if prop.lower() =='registrationdate':
+ if prop.lower().endswith('registrationdate'):
str_type = "as.dto.common.search.RegistrationDateSearchCriteria"
fieldType = "ATTRIBUTE"
- elif prop.lower() =='modificationdate':
+ elif prop.lower().endswith('modificationdate'):
str_type = "as.dto.common.search.ModificationDateSearchCriteria"
fieldType = "ATTRIBUTE"
else:
@@ -504,23 +513,14 @@ def _subcriteria_for_properties(prop, value, entity):
eq_type = "as.dto.common.search.StringLessThanOrEqualToValue"
else:
eq_type = "as.dto.common.search.StringEqualToValue"
- return {
- "@type": str_type,
- "fieldName": prop.upper(),
- "fieldType": fieldType,
- "fieldValue": {
- "value": value,
- "@type": eq_type
- }
- }
# searching for parent/child/container identifier
- elif any(relation == prop.lower() for relation in ['parent','child','container']):
+ if any(relation == prop.lower() for relation in ['parent','child','container']):
relation=prop.lower()
if is_identifier(value):
identifier_search_type = "as.dto.common.search.IdentifierSearchCriteria"
- # find any parent, child or container
+ # find any parent, child, container
elif value == '*':
return {
"@type": search_types[entity][relation],
@@ -562,7 +562,7 @@ def _subcriteria_for_properties(prop, value, entity):
{
"@type": str_type,
"fieldName": property_name.upper(),
- "fieldType": "PROPERTY",
+ "fieldType": fieldType,
"fieldValue": {
"@type": eq_type,
"value": value,
@@ -1034,7 +1034,6 @@ class Openbis:
raise ValueError("Your session expired, please log in again")
if DEBUG_LEVEL >=LOG_DEBUG: print(json.dumps(request))
- #print(json.dumps(request))
resp = requests.post(
full_url,
@@ -2273,7 +2272,7 @@ class Openbis:
search_criteria['criteria'] = sub_criteria
search_criteria['operator'] = 'AND'
- fetchopts = get_fetchoptions('dataSet', including=['type','parents'])
+ fetchopts = get_fetchoptions('dataSet', including=['type','parents','children','containers','components'])
fetchopts['from'] = start_with
fetchopts['count'] = count
@@ -3840,6 +3839,9 @@ class Openbis:
datasets['sample'] = datasets['sample'].map(extract_nested_identifier)
datasets['type'] = datasets['type'].map(extract_code)
datasets['permId'] = datasets['code']
+ for column in ['parents','children','components','containers']:
+ if column in datasets:
+ datasets[column] = datasets[column].map(extract_identifiers)
datasets['size'] = datasets['physicalData'].map(lambda x: x.get('size') if x else '')
datasets['status'] = datasets['physicalData'].map(lambda x: x.get('status') if x else '')
datasets['presentInArchive'] = datasets['physicalData'].map(lambda x: x.get('presentInArchive') if x else '')
--
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