From 3f1ae46722f130e6cb58ff817915542bb6c0620f Mon Sep 17 00:00:00 2001 From: utku-ozturk Date: Mon, 15 May 2023 11:50:27 +0300 Subject: [PATCH 1/4] port term grouping changes to cgap --- package-lock.json | 1369 +++++++++-------- package.json | 2 +- src/encoded/search/lucene_builder.py | 28 +- src/encoded/search/search.py | 15 +- .../tests/data/master-inserts/user.json | 11 + 5 files changed, 740 insertions(+), 685 deletions(-) diff --git a/package-lock.json b/package-lock.json index 5911d408e1..4bd0fd93f2 100644 --- a/package-lock.json +++ b/package-lock.json @@ -13,7 +13,7 @@ "@gmod/tabix": "^1.5.3", "@gmod/vcf": "^5.0.6", "@hms-dbmi-bgm/react-workflow-viz": "0.1.5", - "@hms-dbmi-bgm/shared-portal-components": "git+https://github.com/4dn-dcic/shared-portal-components#0.1.63", + "@hms-dbmi-bgm/shared-portal-components": "git+https://github.com/4dn-dcic/shared-portal-components#0.1.64b15", "auth0-lock": "^11.33.0", "d3": "^5.16.0", "date-fns": "^2.28.0", @@ -114,9 +114,9 @@ } }, "node_modules/@babel/cli": { - 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"@hms-dbmi-bgm/shared-portal-components": "git+https://github.com/4dn-dcic/shared-portal-components#0.1.63", + "@hms-dbmi-bgm/shared-portal-components": "git+https://github.com/4dn-dcic/shared-portal-components#0.1.64b15", "auth0-lock": "^11.33.0", "d3": "^5.16.0", "date-fns": "^2.28.0", diff --git a/src/encoded/search/lucene_builder.py b/src/encoded/search/lucene_builder.py index a63c62401b..4b464d731c 100644 --- a/src/encoded/search/lucene_builder.py +++ b/src/encoded/search/lucene_builder.py @@ -950,13 +950,29 @@ def _add_range_aggregation(cls, facet, query_field, search_filters, string_query @staticmethod def _build_terms_aggregation(query_field, facet, requested_values=None, nested=False): """ Builds a terms aggregation, specifically requesting counts for any selected values. """ - agg = { - TERMS: { - 'size': MAX_FACET_COUNTS, - 'field': query_field, - 'missing': facet.get('missing_value_replacement', 'No value') + if 'group_by_field' not in facet: + agg = { + TERMS: { + 'size': MAX_FACET_COUNTS, + 'field': query_field, + 'missing': facet.get('missing_value_replacement', 'No value') + } + } + else : + agg = { + TERMS: { + 'size': MAX_FACET_COUNTS, + 'field': "embedded." + facet['group_by_field'] + ".raw", + 'missing': facet.get('missing_value_replacement', 'No value') + }, + 'aggs': { + "sub_terms" : { + "terms" : { + "field": query_field, + } + } + } } - } if requested_values: # getall returns [], not None agg[TERMS]['include'] = requested_values if nested: diff --git a/src/encoded/search/search.py b/src/encoded/search/search.py index eae3b8b4a3..69786adf92 100644 --- a/src/encoded/search/search.py +++ b/src/encoded/search/search.py @@ -651,10 +651,6 @@ def initialize_facets(self): split_field = field.strip().split('.') use_field = '.'.join(split_field[1:]) # e.g. "experiments_in_set.files.file_size.from" - if use_field in used_facet_fields or use_field in disabled_facet_fields: - # Cancel if already in facets or is disabled (first check, before more broad check re: agg_type:stats, etc) - continue - # Use the last part of the split field to get the field title title_field = split_field[-1] @@ -672,6 +668,9 @@ def initialize_facets(self): else: is_object_title = False + if use_field in used_facet_fields or use_field in disabled_facet_fields or use_field in used_facet_fields: + # Cancel if already in facets or is disabled (first check, before more broad check re: agg_type:stats, etc) + continue # 'terms' is the default per-term bucket aggregation for all non-schema facets if self.item_type_es_mapping and find_nested_path(field, self.item_type_es_mapping): @@ -900,6 +899,14 @@ def extract_buckets(path): result_facet['terms'] = list(term_to_bucket.values()) + if 'group_by_field' in result_facet: + for term in result_facet['terms']: + if 'sub_terms' not in term: + continue + term['terms'] = term['sub_terms']['buckets'] + del result_facet['group_by_field'] + result_facet['has_group_by'] = True + # XXX: not clear this functions as intended - Will 2/17/2020 if len(aggregations[full_agg_name].keys()) > 2: result_facet['extra_aggs'] = {k: v for k, v in aggregations[full_agg_name].items() if diff --git a/src/encoded/tests/data/master-inserts/user.json b/src/encoded/tests/data/master-inserts/user.json index fc5e654d23..6fe22d632b 100644 --- a/src/encoded/tests/data/master-inserts/user.json +++ b/src/encoded/tests/data/master-inserts/user.json @@ -420,5 +420,16 @@ ], "user_institution": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "uuid": "74fef71a-dfc1-4aa4-acc0-cedcb7ac1d68" + }, + { + "email": "ozturkutku@gmail.com", + "first_name": "Serkan Utku", + "last_name": "Öztürk", + "uuid": "42cd3586-0ae7-43bd-9d9c-14a03572e3ad", + "groups": ["admin"], + "project": "12a92962-8265-4fc0-b2f8-cf14f05db58b", + "project_roles": [{"project": "12a92962-8265-4fc0-b2f8-cf14f05db58b", + "role": "developer"}], + "user_institution": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989" } ] From 56c9c7dff5114eecab885c3ce39d1b75a74695b4 Mon Sep 17 00:00:00 2001 From: utku-ozturk Date: Wed, 17 May 2023 00:58:57 +0300 Subject: [PATCH 2/4] remove sub_terms --- package-lock.json | 429 +++++++++++++++-------------------- src/encoded/search/search.py | 1 + 2 files changed, 182 insertions(+), 248 deletions(-) diff --git a/package-lock.json b/package-lock.json index 4bd0fd93f2..f6e6019b6b 100644 --- a/package-lock.json +++ b/package-lock.json @@ -2557,9 +2557,9 @@ } }, "node_modules/@npmcli/fs/node_modules/semver": { - "version": "7.5.0", - "resolved": "https://registry.npmjs.org/semver/-/semver-7.5.0.tgz", - "integrity": "sha512-+XC0AD/R7Q2mPSRuy2Id0+CGTZ98+8f+KvwirxOKIEyid+XSx6HbC63p+O4IndTHuX5Z+JxQ0TghCkO5Cg/2HA==", + "version": "7.5.1", + "resolved": "https://registry.npmjs.org/semver/-/semver-7.5.1.tgz", + "integrity": 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"https://registry.npmjs.org/terser/-/terser-5.17.4.tgz", + "integrity": "sha512-jcEKZw6UPrgugz/0Tuk/PVyLAPfMBJf5clnGueo45wTweoV8yh7Q7PEkhkJ5uuUbC7zAxEcG3tqNr1bstkQ8nw==", "dev": true, "requires": { "@jridgewell/source-map": "^0.3.2", diff --git a/src/encoded/search/search.py b/src/encoded/search/search.py index 69786adf92..97e0492f4d 100644 --- a/src/encoded/search/search.py +++ b/src/encoded/search/search.py @@ -904,6 +904,7 @@ def extract_buckets(path): if 'sub_terms' not in term: continue term['terms'] = term['sub_terms']['buckets'] + del term['sub_terms'] del result_facet['group_by_field'] result_facet['has_group_by'] = True From 278a74b6da6aaaee6b67bc577089075cdab19e17 Mon Sep 17 00:00:00 2001 From: utku-ozturk Date: Thu, 18 May 2023 01:48:10 +0300 Subject: [PATCH 3/4] SPC upgrade (0.1.64b16) --- package-lock.json | 44 ++++++++++++++++++++++---------------------- package.json | 2 +- 2 files changed, 23 insertions(+), 23 deletions(-) diff --git a/package-lock.json b/package-lock.json index f6e6019b6b..46602fc3f4 100644 --- a/package-lock.json +++ b/package-lock.json @@ -13,7 +13,7 @@ "@gmod/tabix": "^1.5.3", "@gmod/vcf": "^5.0.6", "@hms-dbmi-bgm/react-workflow-viz": "0.1.5", - "@hms-dbmi-bgm/shared-portal-components": "git+https://github.com/4dn-dcic/shared-portal-components#0.1.64b15", + "@hms-dbmi-bgm/shared-portal-components": "git+https://github.com/4dn-dcic/shared-portal-components#0.1.64b16", "auth0-lock": "^11.33.0", "d3": "^5.16.0", "date-fns": "^2.28.0", @@ -2351,7 +2351,7 @@ }, "node_modules/@hms-dbmi-bgm/shared-portal-components": { "version": "0.1.64", - "resolved": "git+ssh://git@github.com/4dn-dcic/shared-portal-components.git#b875b0f902bfd8cdf8fad9fb128a06f8f5ba80b6", + "resolved": "git+ssh://git@github.com/4dn-dcic/shared-portal-components.git#e50b0443cfdca2537db7d6ad508b61be29c76c82", "license": "MIT", "dependencies": { "@4dn-dcic/react-infinite": "github:4dn-dcic/react-infinite#1.1.9", @@ -5395,9 +5395,9 @@ } }, 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