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Merge pull request #385 from medizininformatik-initiative/feature/341…
…-add-elastic-search-to-github-integration-tests #341 - Add elastic search to github integration tests
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,7 +1,7 @@ | ||
| #!/bin/bash -e | ||
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| mkdir --parents .github/integration-test/ontology/ui_profiles .github/integration-test/ontology/migration | ||
| curl -L https://github.com/medizininformatik-initiative/fhir-ontology-generator/raw/v3.0.0-test.1/example/fdpg-ontology/backend.zip -o .github/integration-test/ontology/backend.zip | ||
| curl -L https://github.com/medizininformatik-initiative/fhir-ontology-generator/raw/${ONTOLOGY_GIT_TAG}/example/fdpg-ontology/backend.zip -o .github/integration-test/ontology/backend.zip | ||
| unzip -jod .github/integration-test/ontology/ui_profiles/ .github/integration-test/ontology/backend.zip | ||
| mv .github/integration-test/ontology/ui_profiles/R__Load_latest_ui_profile.sql .github/integration-test/ontology/migration/ | ||
| rm .github/integration-test/ontology/backend.zip |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,46 @@ | ||
| #!/bin/bash -e | ||
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| ABSOLUTE_FILEPATH="${ELASTIC_FILEPATH//TAGPLACEHOLDER/$ONTOLOGY_GIT_TAG}$ELASTIC_FILENAME" | ||
| echo "Downloading $ABSOLUTE_FILEPATH" | ||
| response_onto_dl=$(curl --write-out "%{http_code}" -sLO "$ABSOLUTE_FILEPATH") | ||
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| if [ "$response_onto_dl" -ne 200 ]; then | ||
| echo "Could not download ontology file. Maybe the tag $ONTOLOGY_GIT_TAG does not exist? Error code was $response_onto_dl" | ||
| exit 1 | ||
| fi | ||
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| unzip -o "$ELASTIC_FILENAME" | ||
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| echo "(Trying to) delete existing indices" | ||
| curl --request DELETE "$ELASTIC_HOST/ontology" | ||
| curl --request DELETE "$ELASTIC_HOST/codeable_concept" | ||
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| echo "Creating ontology index..." | ||
| response_onto=$(curl --write-out "%{http_code}" -s --output /dev/null -XPUT -H 'Content-Type: application/json' "$ELASTIC_HOST/ontology" -d @elastic/ontology_index.json) | ||
| echo "Creating codeable concept index..." | ||
| response_cc=$(curl --write-out "%{http_code}" -s --output /dev/null -XPUT -H 'Content-Type: application/json' "$ELASTIC_HOST/codeable_concept" -d @elastic/codeable_concept_index.json) | ||
| echo "Done." | ||
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| for FILE in elastic/*; do | ||
| if [ -f "$FILE" ]; then | ||
| BASENAME=$(basename "$FILE") | ||
| if [[ $BASENAME == onto_es__ontology* && $BASENAME == *.json ]]; then | ||
| if [[ "$response_onto" -eq 200 || "$OVERRIDE_EXISTING" = "true" ]]; then | ||
| echo "Uploading $BASENAME" | ||
| curl -s --output /dev/null -XPOST -H 'Content-Type: application/json' --data-binary @"$FILE" "$ELASTIC_HOST/ontology/_bulk" | ||
| else | ||
| echo "Skipping $BASENAME because index was already existing. Set OVERRIDE_EXISTING to true to force creating a new index" | ||
| fi | ||
| fi | ||
| if [[ $BASENAME == onto_es__codeable_concept* && $BASENAME == *.json ]]; then | ||
| if [[ "$response_cc" -eq 200 || "$OVERRIDE_EXISTING" = "true" ]]; then | ||
| echo "Uploading $BASENAME" | ||
| curl -s --output /dev/null -XPOST -H 'Content-Type: application/json' --data-binary @"$FILE" "$ELASTIC_HOST/codeable_concept/_bulk" | ||
| else | ||
| echo "Skipping $BASENAME because index was already existing. Set OVERRIDE_EXISTING to true to force creating a new index" | ||
| fi | ||
| fi | ||
| fi | ||
| done | ||
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| echo "All done" |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,96 @@ | ||
| #!/bin/bash -e | ||
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| curl "$ELASTIC_HOST/_cat/indices" | ||
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| response=$(curl -s -w "%{http_code}" -o response_body "$ELASTIC_HOST/ontology/_doc/9c2328b0-ac4e-3d69-8f2f-d8b905875348") | ||
| http_code="${response: -3}" | ||
| json_body=$(cat response_body) | ||
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| if [ "$http_code" -eq 200 ]; then | ||
| if echo "$json_body" | jq '.found == true' | grep -q true; then | ||
| echo "Ontology Document found in elastic search" | ||
| else | ||
| echo "Empty or nonexistent response from elastic search" | ||
| exit 1 | ||
| fi | ||
| else | ||
| echo "Response code $http_code" | ||
| exit 1 | ||
| fi | ||
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| response=$(curl -s -w "%{http_code}" -o response_body "$ELASTIC_HOST/codeable_concept/_doc/d676be36-7f34-3ea6-9838-c0c9e1ca3dcc") | ||
| http_code="${response: -3}" | ||
| json_body=$(cat response_body) | ||
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| if [ "$http_code" -eq 200 ]; then | ||
| if echo "$json_body" | jq '.found == true' | grep -q true; then | ||
| echo "Codeable Concept Document found in elastic search" | ||
| else | ||
| echo "Empty or nonexistent response from elastic search" | ||
| exit 1 | ||
| fi | ||
| else | ||
| echo "Response code $http_code" | ||
| exit 1 | ||
| fi | ||
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| access_token="$(curl -s --request POST \ | ||
| --url http://localhost:8083/auth/realms/dataportal/protocol/openid-connect/token \ | ||
| --header 'Content-Type: application/x-www-form-urlencoded' \ | ||
| --data grant_type=password \ | ||
| --data client_id=dataportal-webapp \ | ||
| --data username=testuser \ | ||
| --data password=testpassword \ | ||
| --data scope=openid | jq '.access_token' | tr -d '"')" | ||
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| response=$(curl -s -w "%{http_code}" --header "Authorization: Bearer $access_token" -o response_body "http://localhost:8091/api/v4/terminology/entry/search?searchterm=Blutdruck") | ||
| http_code="${response: -3}" | ||
| json_body=$(cat response_body) | ||
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| if [ "$http_code" -eq 200 ]; then | ||
| if echo "$json_body" | jq '.totalHits > 0' | grep -q true; then | ||
| echo "OK response with non-empty array" | ||
| else | ||
| echo "Empty or nonexistent response" | ||
| exit 1 | ||
| fi | ||
| else | ||
| echo "Response code $http_code" | ||
| exit 1 | ||
| fi | ||
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| response=$(curl -s -w "%{http_code}" --header "Authorization: Bearer $access_token" -o response_body "http://localhost:8091/api/v4/codeable-concept/entry/search?searchterm=Vectorcardiogram") | ||
| http_code="${response: -3}" | ||
| json_body=$(cat response_body) | ||
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| if [ "$http_code" -eq 200 ]; then | ||
| if echo "$json_body" | jq '.totalHits > 0' | grep -q true; then | ||
| echo "OK response with non-empty array" | ||
| else | ||
| echo "Empty or nonexistent response" | ||
| exit 1 | ||
| fi | ||
| else | ||
| echo "Response code $http_code" | ||
| exit 1 | ||
| fi | ||
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| response=$(curl -s -w "%{http_code}" --header "Authorization: Bearer $access_token" -o response_body "http://localhost:8091/api/v4/codeable-concept/entry/d676be36-7f34-3ea6-9838-c0c9e1ca3dcc") | ||
| http_code="${response: -3}" | ||
| json_body=$(cat response_body) | ||
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| if [ "$http_code" -eq 200 ]; then | ||
| if echo "$json_body" | jq -e '.code and .code != ""' | grep -q true; then | ||
| echo "OK response with non-empty array" | ||
| else | ||
| echo "Empty or nonexistent response" | ||
| exit 1 | ||
| fi | ||
| else | ||
| echo "Response code $http_code" | ||
| exit 1 | ||
| fi | ||
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| echo "All elastic search tests completed" | ||
| exit 0 |
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