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update all dependencies and resolve all warnings and security vulnerabilities #203

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ocshawn wants to merge 22 commits into from
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update all dependencies and resolve all warnings and security vulnerabilities #203

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209b1b4
feat(es7): make guppy comapatible with es7
thanh-nguyen-dang Apr 21, 2023
234c665
fix(type): remove type param from mapping
thanh-nguyen-dang Jun 22, 2023
e433b1a
fix(test): fix mock data
thanh-nguyen-dang Jun 22, 2023
ece2bfc
fix(test): fix array-config test
thanh-nguyen-dang Jun 22, 2023
5e31ec6
fix(log): add debug info
thanh-nguyen-dang Jun 22, 2023
c8eaaf2
fix(missing): change to use missing_bucket
thanh-nguyen-dang Jun 26, 2023
d7529ea
fix(debug): add more debug info
thanh-nguyen-dang Jun 27, 2023
2c758f7
fix(no_data): using missing_bucket and replace null with no_data
thanh-nguyen-dang Jun 28, 2023
1bbdda8
fix(totalCount): fix totalCount agg
thanh-nguyen-dang Jun 29, 2023
30f22d2
fix(docker): correct version in docker files
thanh-nguyen-dang Jun 30, 2023
dce3b02
fix(command): correct payload to ES
thanh-nguyen-dang Jun 30, 2023
bf8a6af
update all dependencies and resolve all warnings and security vulnera…
Jun 30, 2023
d9c69ea
use npm 8.5.5 to generate pakage-lock
Jun 30, 2023
311b5da
update node revert package lock to newer version
Jun 30, 2023
685ee62
revert package lock to v2
Jun 30, 2023
1562dde
update order of items
Jun 30, 2023
1681f59
update es server error handaling
Jun 30, 2023
60aee76
Merge branch 'feat/es7' into chore/updateAllDep
Jun 30, 2023
fb1eff3
updating more
Jun 30, 2023
31ec932
more updates
Jun 30, 2023
cc6fb9a
removed unused dependency
Jun 30, 2023
805e0a0
removed unused dependency
Jun 30, 2023
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2 changes: 1 addition & 1 deletion .travis.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,7 @@ language: node_js
git:
depth: 1
node_js:
- "14"
- "16"

services:
- docker
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2 changes: 1 addition & 1 deletion Dockerfile
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Expand Up @@ -11,7 +11,7 @@ RUN apt-get update \
sudo \
vim \
libcap2-bin \
&& curl -sL https://deb.nodesource.com/setup_14.x | bash - \
&& curl -sL https://deb.nodesource.com/setup_16.x | bash - \
&& apt-get install -y --no-install-recommends nodejs \
&& rm -rf /var/lib/apt/lists/* \
&& npm install -g [email protected]
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16 changes: 11 additions & 5 deletions devHelper/docker/esearch.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -3,7 +3,7 @@ version: "3.3"
services:
# see https://www.elastic.co/guide/en/elasticsearch/reference/current/docker.html#docker-cli-run-prod-mode
elasticsearch:
image: docker.elastic.co/elasticsearch/elasticsearch-oss:6.8.12
image: docker.elastic.co/elasticsearch/elasticsearch-oss:7.10.0
ports:
- "9200:9200"
- "9300:9300"
Expand All @@ -12,9 +12,12 @@ services:
volumes:
- "esdata:/usr/share/elasticsearch/data"
environment:
"cluster.name": "localdev"
"discovery.type": "single-node"
ES_JAVA_OPTS: "-Xms1g -Xmx1g"
- cluster.name=localdev
- bootstrap.memory_lock=false
- ES_JAVA_OPTS=-Xms1g -Xmx1g
- discovery.type=single-node
- network.host=0.0.0.0
- http.port=9200
deploy:
replicas: 1
restart_policy:
Expand All @@ -24,7 +27,7 @@ services:
window: 120s

kibana:
image: docker.elastic.co/kibana/kibana-oss:6.5.4
image: docker.elastic.co/kibana/kibana-oss:7.10.0
ports:
- "5601:5601"
logging:
Expand All @@ -38,6 +41,9 @@ services:
- elasticsearch
environment:
LOGGING_QUIET: "true"
SERVER_NAME: elasticsearch
ELASTICSEARCH_URL: http://elasticsearch:9200
network.host: 0.0.0.0

volumes:
esdata:
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94 changes: 44 additions & 50 deletions devHelper/scripts/commands.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -42,7 +42,7 @@ curl -iv -X PUT "${ESHOST}/${indexName}" \
"ngram_tokenizer": {
"type": "ngram",
"min_gram": 2,
"max_gram": 20,
"max_gram": 3,
"token_chars": [ "letter", "digit" ]
}
},
Expand All @@ -64,46 +64,44 @@ curl -iv -X PUT "${ESHOST}/${indexName}" \
}
},
"mappings": {
"subject": {
"properties": {
"subject_id": { "type": "keyword", "fields": { "analyzed": {"type": "text", "analyzer": "ngram_analyzer", "search_analyzer": "search_analyzer", "term_vector": "with_positions_offsets"} } },
"name": { "type": "keyword", "fields": { "analyzed": {"type": "text", "analyzer": "ngram_analyzer", "search_analyzer": "search_analyzer", "term_vector": "with_positions_offsets"} } },
"project": { "type": "keyword", "fields": { "analyzed": {"type": "text", "analyzer": "ngram_analyzer", "search_analyzer": "search_analyzer", "term_vector": "with_positions_offsets"} } },
"study": { "type": "keyword", "fields": { "analyzed": {"type": "text", "analyzer": "ngram_analyzer", "search_analyzer": "search_analyzer", "term_vector": "with_positions_offsets"} } },
"visits": {
"type": "nested",
"properties": {
"days_to_visit": { "type": "integer" },
"visit_label": { "type": "keyword", "fields": { "analyzed": {"type": "text", "analyzer": "ngram_analyzer", "search_analyzer": "search_analyzer", "term_vector": "with_positions_offsets"} } },
"follow_ups": {
"type": "nested",
"properties": {
"days_to_follow_up": { "type": "integer" },
"follow_up_label": { "type": "keyword", "fields": { "analyzed": {"type": "text", "analyzer": "ngram_analyzer", "search_analyzer": "search_analyzer", "term_vector": "with_positions_offsets"} } }
}
"properties": {
"subject_id": { "type": "keyword", "fields": { "analyzed": {"type": "text", "analyzer": "ngram_analyzer", "search_analyzer": "search_analyzer", "term_vector": "with_positions_offsets"} } },
"name": { "type": "keyword", "fields": { "analyzed": {"type": "text", "analyzer": "ngram_analyzer", "search_analyzer": "search_analyzer", "term_vector": "with_positions_offsets"} } },
"project": { "type": "keyword", "fields": { "analyzed": {"type": "text", "analyzer": "ngram_analyzer", "search_analyzer": "search_analyzer", "term_vector": "with_positions_offsets"} } },
"study": { "type": "keyword", "fields": { "analyzed": {"type": "text", "analyzer": "ngram_analyzer", "search_analyzer": "search_analyzer", "term_vector": "with_positions_offsets"} } },
"visits": {
"type": "nested",
"properties": {
"days_to_visit": { "type": "integer" },
"visit_label": { "type": "keyword", "fields": { "analyzed": {"type": "text", "analyzer": "ngram_analyzer", "search_analyzer": "search_analyzer", "term_vector": "with_positions_offsets"} } },
"follow_ups": {
"type": "nested",
"properties": {
"days_to_follow_up": { "type": "integer" },
"follow_up_label": { "type": "keyword", "fields": { "analyzed": {"type": "text", "analyzer": "ngram_analyzer", "search_analyzer": "search_analyzer", "term_vector": "with_positions_offsets"} } }
}
}
},
"gender": { "type": "keyword", "fields": { "analyzed": {"type": "text", "analyzer": "ngram_analyzer", "search_analyzer": "search_analyzer", "term_vector": "with_positions_offsets"} } },
"race": { "type": "keyword", "fields": { "analyzed": {"type": "text", "analyzer": "ngram_analyzer", "search_analyzer": "search_analyzer", "term_vector": "with_positions_offsets"} } },
"ethnicity": { "type": "keyword", "fields": { "analyzed": {"type": "text", "analyzer": "ngram_analyzer", "search_analyzer": "search_analyzer", "term_vector": "with_positions_offsets"} } },
"vital_status": { "type": "keyword", "fields": { "analyzed": {"type": "text", "analyzer": "ngram_analyzer", "search_analyzer": "search_analyzer", "term_vector": "with_positions_offsets"} } },
"file_type": { "type": "keyword", "fields": { "analyzed": {"type": "text", "analyzer": "ngram_analyzer", "search_analyzer": "search_analyzer", "term_vector": "with_positions_offsets"} } },
"file_format": { "type": "keyword", "fields": { "analyzed": {"type": "text", "analyzer": "ngram_analyzer", "search_analyzer": "search_analyzer", "term_vector": "with_positions_offsets"} } },
"auth_resource_path": { "type": "keyword", "fields": { "analyzed": {"type": "text", "analyzer": "ngram_analyzer", "search_analyzer": "search_analyzer", "term_vector": "with_positions_offsets"} } },
"file_count": { "type": "integer" },
"whatever_lab_result_value": { "type": "float" },
"some_nested_array_field": {
"type": "nested",
"properties": {
"some_integer_inside_nested": { "type": "integer" },
"some_string_inside_nested": { "type": "keyword", "fields": { "analyzed": {"type": "text", "analyzer": "ngram_analyzer", "search_analyzer": "search_analyzer", "term_vector": "with_positions_offsets"} } }
}
},
"some_integer_field": { "type": "integer" },
"some_long_field": { "type": "long" },
"sensitive": { "type": "keyword" }
}
}
},
"gender": { "type": "keyword", "fields": { "analyzed": {"type": "text", "analyzer": "ngram_analyzer", "search_analyzer": "search_analyzer", "term_vector": "with_positions_offsets"} } },
"race": { "type": "keyword", "fields": { "analyzed": {"type": "text", "analyzer": "ngram_analyzer", "search_analyzer": "search_analyzer", "term_vector": "with_positions_offsets"} } },
"ethnicity": { "type": "keyword", "fields": { "analyzed": {"type": "text", "analyzer": "ngram_analyzer", "search_analyzer": "search_analyzer", "term_vector": "with_positions_offsets"} } },
"vital_status": { "type": "keyword", "fields": { "analyzed": {"type": "text", "analyzer": "ngram_analyzer", "search_analyzer": "search_analyzer", "term_vector": "with_positions_offsets"} } },
"file_type": { "type": "keyword", "fields": { "analyzed": {"type": "text", "analyzer": "ngram_analyzer", "search_analyzer": "search_analyzer", "term_vector": "with_positions_offsets"} } },
"file_format": { "type": "keyword", "fields": { "analyzed": {"type": "text", "analyzer": "ngram_analyzer", "search_analyzer": "search_analyzer", "term_vector": "with_positions_offsets"} } },
"auth_resource_path": { "type": "keyword", "fields": { "analyzed": {"type": "text", "analyzer": "ngram_analyzer", "search_analyzer": "search_analyzer", "term_vector": "with_positions_offsets"} } },
"file_count": { "type": "integer" },
"whatever_lab_result_value": { "type": "float" },
"some_nested_array_field": {
"type": "nested",
"properties": {
"some_integer_inside_nested": { "type": "integer" },
"some_string_inside_nested": { "type": "keyword", "fields": { "analyzed": {"type": "text", "analyzer": "ngram_analyzer", "search_analyzer": "search_analyzer", "term_vector": "with_positions_offsets"} } }
}
},
"some_integer_field": { "type": "integer" },
"some_long_field": { "type": "long" },
"sensitive": { "type": "keyword" }
}
}
}
Expand All @@ -119,13 +117,11 @@ curl -iv -X PUT "${ESHOST}/${fileIndexName}" \
}
},
"mappings": {
"file": {
"properties": {
"file_id": { "type": "keyword" },
"auth_resource_path": { "type": "keyword" },
"subject_id": { "type": "keyword" },
"sensitive": { "type": "keyword" }
}
"properties": {
"file_id": { "type": "keyword" },
"auth_resource_path": { "type": "keyword" },
"subject_id": { "type": "keyword" },
"sensitive": { "type": "keyword" }
}
}
}
Expand All @@ -141,10 +137,8 @@ curl -iv -X PUT "${ESHOST}/${configIndexName}" \
}
},
"mappings": {
"_doc": {
"properties": {
"array": { "type": "keyword" }
}
"properties": {
"array": { "type": "keyword" }
}
}
}
Expand Down
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