From d80236fd055590df8260c66aa8d9b2f248707718 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Fr=C3=A9d=C3=A9ric=20Haziza?= Date: Mon, 10 Dec 2018 15:42:13 +0100 Subject: [PATCH 1/7] docker -> deploy --- .travis.yml | 10 +++++----- {docker => deploy}/.gitignore | 0 {docker => deploy}/Makefile | 0 {docker => deploy}/README.md | 0 {docker => deploy}/bootstrap/boot.sh | 0 {docker => deploy}/bootstrap/cega.sh | 0 {docker => deploy}/bootstrap/defs.sh | 0 {docker => deploy}/bootstrap/lega.sh | 0 {docker => deploy}/bootstrap/settings.rc | 0 {docker => deploy}/bootstrap/troubleshooting.md | 0 {docker => deploy}/images/Makefile | 0 {docker => deploy}/images/README.md | 0 {docker => deploy}/images/base/Dockerfile | 0 {docker => deploy}/images/cega/eureka.py | 0 {docker => deploy}/images/cega/server.py | 0 {docker => deploy}/images/cega/users.html | 0 {docker => deploy}/images/db/download.sql | 0 {docker => deploy}/images/db/ebi.sql | 0 {docker => deploy}/images/db/entrypoint.sh | 0 {docker => deploy}/images/db/grants.sql | 0 {docker => deploy}/images/db/main.sql | 0 {docker => deploy}/images/db/postgresql.conf | 0 {docker => deploy}/images/db/qc.sql | 0 {docker => deploy}/images/inbox/Dockerfile | 0 {docker => deploy}/images/inbox/entrypoint.sh | 0 {docker => deploy}/images/mq/defs.json | 0 {docker => deploy}/images/mq/entrypoint.sh | 0 {docker => deploy}/images/mq/rabbitmq.config | 0 {docker => deploy}/images/os/Dockerfile | 0 {docker => deploy}/test/.gitignore | 0 {docker => deploy}/test/Makefile | 2 +- {docker => deploy}/test/README.md | 0 {docker => deploy}/test/rabbitmqadmin | 0 {docker => deploy}/tests/.gitignore | 0 {docker => deploy}/tests/README.md | 0 {docker => deploy}/tests/pom.xml | 0 .../src/test/java/se/nbis/lega/cucumber/Context.java | 0 .../java/se/nbis/lega/cucumber/IngestionTests.java | 0 .../java/se/nbis/lega/cucumber/OutgestionTests.java | 0 .../java/se/nbis/lega/cucumber/RobustnessTests.java | 0 .../src/test/java/se/nbis/lega/cucumber/Utils.java | 0 .../se/nbis/lega/cucumber/hooks/BeforeAfterHooks.java | 0 .../java/se/nbis/lega/cucumber/pojo/FileStatus.java | 0 .../java/se/nbis/lega/cucumber/publisher/Checksum.java | 0 .../java/se/nbis/lega/cucumber/publisher/Message.java | 0 .../se/nbis/lega/cucumber/steps/Authentication.java | 0 .../java/se/nbis/lega/cucumber/steps/Ingestion.java | 0 .../java/se/nbis/lega/cucumber/steps/Outgetsion.java | 0 .../java/se/nbis/lega/cucumber/steps/Robustness.java | 0 .../java/se/nbis/lega/cucumber/steps/Uploading.java | 0 .../tests/src/test/resources/config.properties | 0 .../resources/cucumber/features/authentication.feature | 0 .../test/resources/cucumber/features/checksums.feature | 0 .../test/resources/cucumber/features/ingestion.feature | 0 .../resources/cucumber/features/outgestion.feature | 0 .../resources/cucumber/features/robustness.feature | 0 .../test/resources/cucumber/features/uploading.feature | 0 .../tests/src/test/resources/simplelogger.properties | 0 tox.ini | 2 +- 59 files changed, 7 insertions(+), 7 deletions(-) rename {docker => deploy}/.gitignore (100%) rename {docker => deploy}/Makefile (100%) rename {docker => deploy}/README.md (100%) rename {docker => deploy}/bootstrap/boot.sh (100%) rename {docker => deploy}/bootstrap/cega.sh (100%) rename {docker => deploy}/bootstrap/defs.sh (100%) rename {docker => deploy}/bootstrap/lega.sh (100%) rename {docker => deploy}/bootstrap/settings.rc (100%) rename {docker => deploy}/bootstrap/troubleshooting.md (100%) rename {docker => deploy}/images/Makefile (100%) rename {docker => deploy}/images/README.md (100%) rename {docker => deploy}/images/base/Dockerfile (100%) rename {docker => deploy}/images/cega/eureka.py (100%) rename {docker => deploy}/images/cega/server.py (100%) rename {docker => deploy}/images/cega/users.html (100%) rename {docker => deploy}/images/db/download.sql (100%) rename {docker => deploy}/images/db/ebi.sql (100%) rename {docker => deploy}/images/db/entrypoint.sh (100%) rename {docker => deploy}/images/db/grants.sql (100%) rename {docker => deploy}/images/db/main.sql (100%) rename {docker => deploy}/images/db/postgresql.conf (100%) rename {docker => deploy}/images/db/qc.sql (100%) rename {docker => deploy}/images/inbox/Dockerfile (100%) rename {docker => deploy}/images/inbox/entrypoint.sh (100%) rename {docker => deploy}/images/mq/defs.json (100%) rename {docker => deploy}/images/mq/entrypoint.sh (100%) rename {docker => deploy}/images/mq/rabbitmq.config (100%) rename {docker => deploy}/images/os/Dockerfile (100%) rename {docker => deploy}/test/.gitignore (100%) rename {docker => deploy}/test/Makefile (99%) rename {docker => deploy}/test/README.md (100%) rename {docker => deploy}/test/rabbitmqadmin (100%) rename {docker => deploy}/tests/.gitignore (100%) rename {docker => deploy}/tests/README.md (100%) rename {docker => deploy}/tests/pom.xml (100%) rename {docker => deploy}/tests/src/test/java/se/nbis/lega/cucumber/Context.java (100%) rename {docker => deploy}/tests/src/test/java/se/nbis/lega/cucumber/IngestionTests.java (100%) rename {docker => deploy}/tests/src/test/java/se/nbis/lega/cucumber/OutgestionTests.java (100%) rename {docker => deploy}/tests/src/test/java/se/nbis/lega/cucumber/RobustnessTests.java (100%) rename {docker => deploy}/tests/src/test/java/se/nbis/lega/cucumber/Utils.java (100%) rename {docker => deploy}/tests/src/test/java/se/nbis/lega/cucumber/hooks/BeforeAfterHooks.java (100%) rename {docker => deploy}/tests/src/test/java/se/nbis/lega/cucumber/pojo/FileStatus.java (100%) rename {docker => deploy}/tests/src/test/java/se/nbis/lega/cucumber/publisher/Checksum.java (100%) rename {docker => deploy}/tests/src/test/java/se/nbis/lega/cucumber/publisher/Message.java (100%) rename {docker => deploy}/tests/src/test/java/se/nbis/lega/cucumber/steps/Authentication.java (100%) rename {docker => deploy}/tests/src/test/java/se/nbis/lega/cucumber/steps/Ingestion.java (100%) rename {docker => deploy}/tests/src/test/java/se/nbis/lega/cucumber/steps/Outgetsion.java (100%) rename {docker => deploy}/tests/src/test/java/se/nbis/lega/cucumber/steps/Robustness.java (100%) rename {docker => deploy}/tests/src/test/java/se/nbis/lega/cucumber/steps/Uploading.java (100%) rename {docker => deploy}/tests/src/test/resources/config.properties (100%) rename {docker => deploy}/tests/src/test/resources/cucumber/features/authentication.feature (100%) rename {docker => deploy}/tests/src/test/resources/cucumber/features/checksums.feature (100%) rename {docker => deploy}/tests/src/test/resources/cucumber/features/ingestion.feature (100%) rename {docker => deploy}/tests/src/test/resources/cucumber/features/outgestion.feature (100%) rename {docker => deploy}/tests/src/test/resources/cucumber/features/robustness.feature (100%) rename {docker => deploy}/tests/src/test/resources/cucumber/features/uploading.feature (100%) rename {docker => deploy}/tests/src/test/resources/simplelogger.properties (100%) diff --git a/.travis.yml b/.travis.yml index 12612275..c2e56154 100644 --- a/.travis.yml +++ b/.travis.yml @@ -32,7 +32,7 @@ jobs: script: tox - stage: image build before_script: - - cd docker + - cd deploy script: - echo "$DOCKER_PASSWORD" | docker login -u "$DOCKER_USER" --password-stdin - ../extras/travis_check_image_change.sh os @@ -45,7 +45,7 @@ jobs: - docker push nbisweden/ega-inbox:"PR${TRAVIS_PULL_REQUEST}" - stage: integration tests before_script: - - cd docker + - cd deploy - ../extras/travis_push_docker_hub.sh - make bootstrap ARGS='--inbox mina --keyserver ega' - sudo chown -R travis private @@ -57,7 +57,7 @@ jobs: - mvn test -Dtest=IngestionTests -B - stage: integration tests before_script: - - cd docker + - cd deploy - ../extras/travis_push_docker_hub.sh - make bootstrap ARGS='--inbox mina --keyserver ega' - sudo chown -R travis private @@ -69,7 +69,7 @@ jobs: - mvn test -Dtest=OutgestionTests -B - stage: integration tests before_script: - - cd docker + - cd deploy - ../extras/travis_push_docker_hub.sh - make bootstrap ARGS='--inbox mina --keyserver ega' - sudo chown -R travis private @@ -81,7 +81,7 @@ jobs: - mvn test -Dtest=RobustnessTests -B - stage: integration tests before_script: - - cd docker + - cd deploy - ../extras/travis_push_docker_hub.sh - make bootstrap - sudo chown -R travis private diff --git a/docker/.gitignore b/deploy/.gitignore similarity index 100% rename from docker/.gitignore rename to deploy/.gitignore diff --git a/docker/Makefile b/deploy/Makefile similarity index 100% rename from docker/Makefile rename to deploy/Makefile diff --git a/docker/README.md b/deploy/README.md similarity index 100% rename from docker/README.md rename to deploy/README.md diff --git a/docker/bootstrap/boot.sh b/deploy/bootstrap/boot.sh similarity index 100% rename from docker/bootstrap/boot.sh rename to deploy/bootstrap/boot.sh diff --git a/docker/bootstrap/cega.sh b/deploy/bootstrap/cega.sh similarity index 100% rename from docker/bootstrap/cega.sh rename to deploy/bootstrap/cega.sh diff --git a/docker/bootstrap/defs.sh b/deploy/bootstrap/defs.sh similarity index 100% rename from docker/bootstrap/defs.sh rename to deploy/bootstrap/defs.sh diff --git a/docker/bootstrap/lega.sh b/deploy/bootstrap/lega.sh similarity index 100% rename from docker/bootstrap/lega.sh rename to deploy/bootstrap/lega.sh diff --git a/docker/bootstrap/settings.rc b/deploy/bootstrap/settings.rc similarity index 100% rename from docker/bootstrap/settings.rc rename to deploy/bootstrap/settings.rc diff --git a/docker/bootstrap/troubleshooting.md b/deploy/bootstrap/troubleshooting.md similarity index 100% rename from docker/bootstrap/troubleshooting.md rename to deploy/bootstrap/troubleshooting.md diff --git a/docker/images/Makefile b/deploy/images/Makefile similarity index 100% rename from docker/images/Makefile rename to deploy/images/Makefile diff --git a/docker/images/README.md b/deploy/images/README.md similarity index 100% rename from docker/images/README.md rename to deploy/images/README.md diff --git a/docker/images/base/Dockerfile b/deploy/images/base/Dockerfile similarity index 100% rename from docker/images/base/Dockerfile rename to deploy/images/base/Dockerfile diff --git a/docker/images/cega/eureka.py b/deploy/images/cega/eureka.py similarity index 100% rename from docker/images/cega/eureka.py rename to deploy/images/cega/eureka.py diff --git a/docker/images/cega/server.py b/deploy/images/cega/server.py similarity index 100% rename from docker/images/cega/server.py rename to deploy/images/cega/server.py diff --git a/docker/images/cega/users.html b/deploy/images/cega/users.html similarity index 100% rename from docker/images/cega/users.html rename to deploy/images/cega/users.html diff --git a/docker/images/db/download.sql b/deploy/images/db/download.sql similarity index 100% rename from docker/images/db/download.sql rename to deploy/images/db/download.sql diff --git a/docker/images/db/ebi.sql b/deploy/images/db/ebi.sql similarity index 100% rename from docker/images/db/ebi.sql rename to deploy/images/db/ebi.sql diff --git a/docker/images/db/entrypoint.sh b/deploy/images/db/entrypoint.sh similarity index 100% rename from docker/images/db/entrypoint.sh rename to deploy/images/db/entrypoint.sh diff --git a/docker/images/db/grants.sql b/deploy/images/db/grants.sql similarity index 100% rename from docker/images/db/grants.sql rename to deploy/images/db/grants.sql diff --git a/docker/images/db/main.sql b/deploy/images/db/main.sql similarity index 100% rename from docker/images/db/main.sql rename to deploy/images/db/main.sql diff --git a/docker/images/db/postgresql.conf b/deploy/images/db/postgresql.conf similarity index 100% rename from docker/images/db/postgresql.conf rename to deploy/images/db/postgresql.conf diff --git a/docker/images/db/qc.sql b/deploy/images/db/qc.sql similarity index 100% rename from docker/images/db/qc.sql rename to deploy/images/db/qc.sql diff --git a/docker/images/inbox/Dockerfile b/deploy/images/inbox/Dockerfile similarity index 100% rename from docker/images/inbox/Dockerfile rename to deploy/images/inbox/Dockerfile diff --git a/docker/images/inbox/entrypoint.sh b/deploy/images/inbox/entrypoint.sh similarity index 100% rename from docker/images/inbox/entrypoint.sh rename to deploy/images/inbox/entrypoint.sh diff --git a/docker/images/mq/defs.json b/deploy/images/mq/defs.json similarity index 100% rename from docker/images/mq/defs.json rename to deploy/images/mq/defs.json diff --git a/docker/images/mq/entrypoint.sh b/deploy/images/mq/entrypoint.sh similarity index 100% rename from docker/images/mq/entrypoint.sh rename to deploy/images/mq/entrypoint.sh diff --git a/docker/images/mq/rabbitmq.config b/deploy/images/mq/rabbitmq.config similarity index 100% rename from docker/images/mq/rabbitmq.config rename to deploy/images/mq/rabbitmq.config diff --git a/docker/images/os/Dockerfile b/deploy/images/os/Dockerfile similarity index 100% rename from docker/images/os/Dockerfile rename to deploy/images/os/Dockerfile diff --git a/docker/test/.gitignore b/deploy/test/.gitignore similarity index 100% rename from docker/test/.gitignore rename to deploy/test/.gitignore diff --git a/docker/test/Makefile b/deploy/test/Makefile similarity index 99% rename from docker/test/Makefile rename to deploy/test/Makefile index eb90184b..50f99ae2 100644 --- a/docker/test/Makefile +++ b/deploy/test/Makefile @@ -19,7 +19,7 @@ get_shasum = \ ############################## -DOCKER_PATH=$(MAIN_REPO)/docker +DOCKER_PATH=$(MAIN_REPO)/deploy CEGA_USERS=$(DOCKER_PATH)/private/cega/users INSTANCE_PORT=$(shell awk -F= '/DOCKER_PORT_inbox/ {print $$2}' $(DOCKER_PATH)/bootstrap/settings.rc) diff --git a/docker/test/README.md b/deploy/test/README.md similarity index 100% rename from docker/test/README.md rename to deploy/test/README.md diff --git a/docker/test/rabbitmqadmin b/deploy/test/rabbitmqadmin similarity index 100% rename from docker/test/rabbitmqadmin rename to deploy/test/rabbitmqadmin diff --git a/docker/tests/.gitignore b/deploy/tests/.gitignore similarity index 100% rename from docker/tests/.gitignore rename to deploy/tests/.gitignore diff --git a/docker/tests/README.md b/deploy/tests/README.md similarity index 100% rename from docker/tests/README.md rename to deploy/tests/README.md diff --git a/docker/tests/pom.xml b/deploy/tests/pom.xml similarity index 100% rename from docker/tests/pom.xml rename to deploy/tests/pom.xml diff --git a/docker/tests/src/test/java/se/nbis/lega/cucumber/Context.java b/deploy/tests/src/test/java/se/nbis/lega/cucumber/Context.java similarity index 100% rename from docker/tests/src/test/java/se/nbis/lega/cucumber/Context.java rename to deploy/tests/src/test/java/se/nbis/lega/cucumber/Context.java diff --git a/docker/tests/src/test/java/se/nbis/lega/cucumber/IngestionTests.java b/deploy/tests/src/test/java/se/nbis/lega/cucumber/IngestionTests.java similarity index 100% rename from docker/tests/src/test/java/se/nbis/lega/cucumber/IngestionTests.java rename to deploy/tests/src/test/java/se/nbis/lega/cucumber/IngestionTests.java diff --git a/docker/tests/src/test/java/se/nbis/lega/cucumber/OutgestionTests.java b/deploy/tests/src/test/java/se/nbis/lega/cucumber/OutgestionTests.java similarity index 100% rename from docker/tests/src/test/java/se/nbis/lega/cucumber/OutgestionTests.java rename to deploy/tests/src/test/java/se/nbis/lega/cucumber/OutgestionTests.java diff --git a/docker/tests/src/test/java/se/nbis/lega/cucumber/RobustnessTests.java b/deploy/tests/src/test/java/se/nbis/lega/cucumber/RobustnessTests.java similarity index 100% rename from docker/tests/src/test/java/se/nbis/lega/cucumber/RobustnessTests.java rename to deploy/tests/src/test/java/se/nbis/lega/cucumber/RobustnessTests.java diff --git a/docker/tests/src/test/java/se/nbis/lega/cucumber/Utils.java b/deploy/tests/src/test/java/se/nbis/lega/cucumber/Utils.java similarity index 100% rename from docker/tests/src/test/java/se/nbis/lega/cucumber/Utils.java rename to deploy/tests/src/test/java/se/nbis/lega/cucumber/Utils.java diff --git a/docker/tests/src/test/java/se/nbis/lega/cucumber/hooks/BeforeAfterHooks.java b/deploy/tests/src/test/java/se/nbis/lega/cucumber/hooks/BeforeAfterHooks.java similarity index 100% rename from docker/tests/src/test/java/se/nbis/lega/cucumber/hooks/BeforeAfterHooks.java rename to deploy/tests/src/test/java/se/nbis/lega/cucumber/hooks/BeforeAfterHooks.java diff --git a/docker/tests/src/test/java/se/nbis/lega/cucumber/pojo/FileStatus.java b/deploy/tests/src/test/java/se/nbis/lega/cucumber/pojo/FileStatus.java similarity index 100% rename from docker/tests/src/test/java/se/nbis/lega/cucumber/pojo/FileStatus.java rename to deploy/tests/src/test/java/se/nbis/lega/cucumber/pojo/FileStatus.java diff --git a/docker/tests/src/test/java/se/nbis/lega/cucumber/publisher/Checksum.java b/deploy/tests/src/test/java/se/nbis/lega/cucumber/publisher/Checksum.java similarity index 100% rename from docker/tests/src/test/java/se/nbis/lega/cucumber/publisher/Checksum.java rename to deploy/tests/src/test/java/se/nbis/lega/cucumber/publisher/Checksum.java diff --git a/docker/tests/src/test/java/se/nbis/lega/cucumber/publisher/Message.java b/deploy/tests/src/test/java/se/nbis/lega/cucumber/publisher/Message.java similarity index 100% rename from docker/tests/src/test/java/se/nbis/lega/cucumber/publisher/Message.java rename to deploy/tests/src/test/java/se/nbis/lega/cucumber/publisher/Message.java diff --git a/docker/tests/src/test/java/se/nbis/lega/cucumber/steps/Authentication.java b/deploy/tests/src/test/java/se/nbis/lega/cucumber/steps/Authentication.java similarity index 100% rename from docker/tests/src/test/java/se/nbis/lega/cucumber/steps/Authentication.java rename to deploy/tests/src/test/java/se/nbis/lega/cucumber/steps/Authentication.java diff --git a/docker/tests/src/test/java/se/nbis/lega/cucumber/steps/Ingestion.java b/deploy/tests/src/test/java/se/nbis/lega/cucumber/steps/Ingestion.java similarity index 100% rename from docker/tests/src/test/java/se/nbis/lega/cucumber/steps/Ingestion.java rename to deploy/tests/src/test/java/se/nbis/lega/cucumber/steps/Ingestion.java diff --git a/docker/tests/src/test/java/se/nbis/lega/cucumber/steps/Outgetsion.java b/deploy/tests/src/test/java/se/nbis/lega/cucumber/steps/Outgetsion.java similarity index 100% rename from docker/tests/src/test/java/se/nbis/lega/cucumber/steps/Outgetsion.java rename to deploy/tests/src/test/java/se/nbis/lega/cucumber/steps/Outgetsion.java diff --git a/docker/tests/src/test/java/se/nbis/lega/cucumber/steps/Robustness.java b/deploy/tests/src/test/java/se/nbis/lega/cucumber/steps/Robustness.java similarity index 100% rename from docker/tests/src/test/java/se/nbis/lega/cucumber/steps/Robustness.java rename to deploy/tests/src/test/java/se/nbis/lega/cucumber/steps/Robustness.java diff --git a/docker/tests/src/test/java/se/nbis/lega/cucumber/steps/Uploading.java b/deploy/tests/src/test/java/se/nbis/lega/cucumber/steps/Uploading.java similarity index 100% rename from docker/tests/src/test/java/se/nbis/lega/cucumber/steps/Uploading.java rename to deploy/tests/src/test/java/se/nbis/lega/cucumber/steps/Uploading.java diff --git a/docker/tests/src/test/resources/config.properties b/deploy/tests/src/test/resources/config.properties similarity index 100% rename from docker/tests/src/test/resources/config.properties rename to deploy/tests/src/test/resources/config.properties diff --git a/docker/tests/src/test/resources/cucumber/features/authentication.feature b/deploy/tests/src/test/resources/cucumber/features/authentication.feature similarity index 100% rename from docker/tests/src/test/resources/cucumber/features/authentication.feature rename to deploy/tests/src/test/resources/cucumber/features/authentication.feature diff --git a/docker/tests/src/test/resources/cucumber/features/checksums.feature b/deploy/tests/src/test/resources/cucumber/features/checksums.feature similarity index 100% rename from docker/tests/src/test/resources/cucumber/features/checksums.feature rename to deploy/tests/src/test/resources/cucumber/features/checksums.feature diff --git a/docker/tests/src/test/resources/cucumber/features/ingestion.feature b/deploy/tests/src/test/resources/cucumber/features/ingestion.feature similarity index 100% rename from docker/tests/src/test/resources/cucumber/features/ingestion.feature rename to deploy/tests/src/test/resources/cucumber/features/ingestion.feature diff --git a/docker/tests/src/test/resources/cucumber/features/outgestion.feature b/deploy/tests/src/test/resources/cucumber/features/outgestion.feature similarity index 100% rename from docker/tests/src/test/resources/cucumber/features/outgestion.feature rename to deploy/tests/src/test/resources/cucumber/features/outgestion.feature diff --git a/docker/tests/src/test/resources/cucumber/features/robustness.feature b/deploy/tests/src/test/resources/cucumber/features/robustness.feature similarity index 100% rename from docker/tests/src/test/resources/cucumber/features/robustness.feature rename to deploy/tests/src/test/resources/cucumber/features/robustness.feature diff --git a/docker/tests/src/test/resources/cucumber/features/uploading.feature b/deploy/tests/src/test/resources/cucumber/features/uploading.feature similarity index 100% rename from docker/tests/src/test/resources/cucumber/features/uploading.feature rename to deploy/tests/src/test/resources/cucumber/features/uploading.feature diff --git a/docker/tests/src/test/resources/simplelogger.properties b/deploy/tests/src/test/resources/simplelogger.properties similarity index 100% rename from docker/tests/src/test/resources/simplelogger.properties rename to deploy/tests/src/test/resources/simplelogger.properties diff --git a/tox.ini b/tox.ini index 229e2a21..99cf337b 100644 --- a/tox.ini +++ b/tox.ini @@ -4,7 +4,7 @@ envlist = unit_tests, flake8 [flake8] ignore = E226,D203,D212,D213,D404,D100,D104 exclude = - docker, + deploy, extras, .tox max-line-length = 160 From d096111d135c10a63c4fb529b4eeb917816e3193 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Fr=C3=A9d=C3=A9ric=20Haziza?= Date: Mon, 10 Dec 2018 15:43:12 +0100 Subject: [PATCH 2/7] Commenting out my integration test --- .travis.yml | 34 +++++++++++++++++----------------- 1 file changed, 17 insertions(+), 17 deletions(-) diff --git a/.travis.yml b/.travis.yml index c2e56154..af7359fd 100644 --- a/.travis.yml +++ b/.travis.yml @@ -79,23 +79,23 @@ jobs: script: - cd tests - mvn test -Dtest=RobustnessTests -B - - stage: integration tests - before_script: - - cd deploy - - ../extras/travis_push_docker_hub.sh - - make bootstrap - - sudo chown -R travis private - - docker network create cega - - docker-compose up -d #--scale ingest=3 --scale verify=5 - - docker-compose ps - script: - - sleep 5 - - pip install -r https://raw.githubusercontent.com/NBISweden/LocalEGA-cryptor/master/requirements.txt - - pip install git+https://github.com/NBISweden/LocalEGA-cryptor.git - - pip install pika - - make -C test - - sleep 10 - - make -C test check + # - stage: integration tests + # before_script: + # - cd deploy + # - ../extras/travis_push_docker_hub.sh + # - make bootstrap + # - sudo chown -R travis private + # - docker network create cega + # - docker-compose up -d #--scale ingest=3 --scale verify=5 + # - docker-compose ps + # script: + # - sleep 5 + # - pip install -r https://raw.githubusercontent.com/NBISweden/LocalEGA-cryptor/master/requirements.txt + # - pip install git+https://github.com/NBISweden/LocalEGA-cryptor.git + # - pip install pika + # - make -C test + # - sleep 10 + # - make -C test check - stage: tag image script: ./extras/travis_push_docker_hub.sh From f1272d2cb98d8fe66e9102a2628ce0e738d965f7 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Fr=C3=A9d=C3=A9ric=20Haziza?= Date: Mon, 10 Dec 2018 15:09:27 +0100 Subject: [PATCH 3/7] Renaming components --- README.md | 2 +- deploy/bootstrap/lega.sh | 28 +++++++++---------- .../src/test/resources/config.properties | 2 +- docs/code.rst | 4 +-- lega/{mapper.py => finalize.py} | 0 setup.py | 2 +- tests/{test_mapper.py => test_finalize.py} | 18 ++++++------ 7 files changed, 28 insertions(+), 28 deletions(-) rename lega/{mapper.py => finalize.py} (100%) rename tests/{test_mapper.py => test_finalize.py} (61%) diff --git a/README.md b/README.md index fff6082b..e4eacf6e 100644 --- a/README.md +++ b/README.md @@ -27,6 +27,6 @@ containers or as virtual machines. | ingesters | Split the Crypt4GH header and move the remainder to the storage backend. No cryptographic task, nor connection to the keyserver. | | verifiers | Connect to the keyserver (via SSL) and decrypt the stored files and checksum them against their embedded checksum. | | vault | Storage backend: as a regular file system or as a S3 object store. | -| ID mapper | Handles the so-called _Stable ID_ filename mappings from CentralEGA. | +| Finalize | Handles the so-called _Stable ID_ filename mappings from CentralEGA. | Find the [LocalEGA documentation](http://localega.readthedocs.io) hosted on [ReadTheDocs.org](https://readthedocs.org/). diff --git a/deploy/bootstrap/lega.sh b/deploy/bootstrap/lega.sh index a736d498..18dd3892 100755 --- a/deploy/bootstrap/lega.sh +++ b/deploy/bootstrap/lega.sh @@ -84,7 +84,7 @@ chroot_sessions = True [vault] driver = S3Storage -url = http://s3:9000 +url = http://vault:9000 access_key = ${S3_ACCESS_KEY} secret_key = ${S3_SECRET_KEY} #region = lega @@ -235,20 +235,20 @@ fi cat >> ${PRIVATE}/lega.yml <> ${PRIVATE}/lega.yml <> ${PRIVATE}/lega.yml <> ${PRIVATE}/lega.yml <> ${PRIVATE}/lega.yml < Date: Fri, 7 Dec 2018 18:05:01 +0100 Subject: [PATCH 4/7] Adding flake8 in the tox dependencies --- tests/requirements.txt | 1 + tox.ini | 1 + 2 files changed, 2 insertions(+) diff --git a/tests/requirements.txt b/tests/requirements.txt index 6c3bf9e5..e31862b1 100644 --- a/tests/requirements.txt +++ b/tests/requirements.txt @@ -4,3 +4,4 @@ aioresponses testfixtures coveralls git+https://github.com/NBISweden/LocalEGA-cryptor.git +flake8 diff --git a/tox.ini b/tox.ini index 99cf337b..fb6086f2 100644 --- a/tox.ini +++ b/tox.ini @@ -6,6 +6,7 @@ ignore = E226,D203,D212,D213,D404,D100,D104 exclude = deploy, extras, + tmp, .tox max-line-length = 160 max-complexity = 10 From ab05d03b3658cc2ce2e98891a4f999e9bb41c33a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Fr=C3=A9d=C3=A9ric=20Haziza?= Date: Mon, 10 Dec 2018 12:00:29 +0100 Subject: [PATCH 5/7] Fixing a naming issue with no.uio.ifi --- deploy/tests/pom.xml | 2 +- .../src/test/java/se/nbis/lega/cucumber/steps/Uploading.java | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/deploy/tests/pom.xml b/deploy/tests/pom.xml index 58ffba14..a5f9ca15 100644 --- a/deploy/tests/pom.xml +++ b/deploy/tests/pom.xml @@ -62,7 +62,7 @@ no.uio.ifi crypt4gh - 1.0.0 + 1.2.0 test diff --git a/deploy/tests/src/test/java/se/nbis/lega/cucumber/steps/Uploading.java b/deploy/tests/src/test/java/se/nbis/lega/cucumber/steps/Uploading.java index b2e1a068..312471a0 100644 --- a/deploy/tests/src/test/java/se/nbis/lega/cucumber/steps/Uploading.java +++ b/deploy/tests/src/test/java/se/nbis/lega/cucumber/steps/Uploading.java @@ -3,7 +3,7 @@ import cucumber.api.java8.En; import lombok.extern.slf4j.Slf4j; import net.schmizz.sshj.sftp.RemoteResourceInfo; -import no.ifi.uio.crypt4gh.stream.Crypt4GHOutputStream; +import no.uio.ifi.crypt4gh.stream.Crypt4GHOutputStream; import org.apache.commons.codec.binary.Hex; import org.apache.commons.codec.digest.DigestUtils; import org.apache.commons.io.FileUtils; From 6634124139a1f670ffabe9e2b08ef799e8b306e3 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Fr=C3=A9d=C3=A9ric=20Haziza?= Date: Mon, 10 Dec 2018 17:12:21 +0100 Subject: [PATCH 6/7] Adding a -dev to bootstrap to use dummy passwords. --- deploy/Makefile | 4 ++-- deploy/bootstrap/defs.sh | 8 +++++++- deploy/bootstrap/settings.rc | 8 ++++++++ 3 files changed, 17 insertions(+), 3 deletions(-) diff --git a/deploy/Makefile b/deploy/Makefile index 2fa05ad3..cfb4ff37 100644 --- a/deploy/Makefile +++ b/deploy/Makefile @@ -7,8 +7,8 @@ help: @echo "where is: 'bootstrap', 'up' 'ps', 'down', 'network' or 'clean'\n" # If DEPLOY_DEV is yes, we use dummy passwords -bootstrap: ENVS=--env DEPLOY_DEV=yes -private/cega.yml private/lega.yml private bootstrap: +bootstrap-dev: ENVS=--env DEPLOY_DEV=yes +private/cega.yml private/lega.yml private bootstrap bootstrap-dev: @docker run --rm -it \ -v /dev/urandom:/dev/random \ ${ENVS} \ diff --git a/deploy/bootstrap/defs.sh b/deploy/bootstrap/defs.sh index db501f52..a2763d74 100644 --- a/deploy/bootstrap/defs.sh +++ b/deploy/bootstrap/defs.sh @@ -51,7 +51,13 @@ function rm_politely { } function generate_password { + local force=${2:-no} + if [[ "${force}" != "force" ]] && [[ "${DEPLOY_DEV}" = "yes" ]]; then + echo "dummy" + return 0 # early return + fi + # Otherwise local size=${1:-16} # defaults to 16 characters - python3.6 -c "import secrets,string;print(''.join(secrets.choice(string.ascii_letters + string.digits) for i in range(${size})))" + ${PYTHON:-python3.6} -c "import secrets,string;print(''.join(secrets.choice(string.ascii_letters + string.digits) for i in range(${size})))" } diff --git a/deploy/bootstrap/settings.rc b/deploy/bootstrap/settings.rc index f2c1a2f6..6a647b98 100644 --- a/deploy/bootstrap/settings.rc +++ b/deploy/bootstrap/settings.rc @@ -25,6 +25,14 @@ PGP_PASSPHRASE=$(generate_password 16) S3_ACCESS_KEY=$(generate_password 16) S3_SECRET_KEY=$(generate_password 32) +# Special cases +# - Access key length should be between minimum 3 characters in length. +# - Secret key should be in between 8 and 40 characters. +if [[ "${DEPLOY_DEV}" = "yes" ]]; then + S3_ACCESS_KEY="dummyaccesskey" + S3_SECRET_KEY="dummysecretkey" +fi + LOG_LEVEL=DEBUG LEGA_PASSWORD=$(generate_password 32) From 6df4698dfa29a5fea7b87d0d0fa790bb7aa5d270 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Fr=C3=A9d=C3=A9ric=20Haziza?= Date: Tue, 11 Dec 2018 13:47:01 +0100 Subject: [PATCH 7/7] Temporary fix: idna's version is 2.7 --- .travis.yml | 35 ++++++++++++++++++----------------- 1 file changed, 18 insertions(+), 17 deletions(-) diff --git a/.travis.yml b/.travis.yml index af7359fd..d512cd07 100644 --- a/.travis.yml +++ b/.travis.yml @@ -79,23 +79,24 @@ jobs: script: - cd tests - mvn test -Dtest=RobustnessTests -B - # - stage: integration tests - # before_script: - # - cd deploy - # - ../extras/travis_push_docker_hub.sh - # - make bootstrap - # - sudo chown -R travis private - # - docker network create cega - # - docker-compose up -d #--scale ingest=3 --scale verify=5 - # - docker-compose ps - # script: - # - sleep 5 - # - pip install -r https://raw.githubusercontent.com/NBISweden/LocalEGA-cryptor/master/requirements.txt - # - pip install git+https://github.com/NBISweden/LocalEGA-cryptor.git - # - pip install pika - # - make -C test - # - sleep 10 - # - make -C test check + - stage: integration tests + before_script: + - cd deploy + - ../extras/travis_push_docker_hub.sh + - make bootstrap + - sudo chown -R travis private + - docker network create cega + - docker-compose up -d #--scale ingest=3 --scale verify=5 + - docker-compose ps + script: + - sleep 5 + - pip install idna==2.7 + - pip install -r https://raw.githubusercontent.com/NBISweden/LocalEGA-cryptor/master/requirements.txt + - pip install git+https://github.com/NBISweden/LocalEGA-cryptor.git + - pip install pika + - make -C test + - sleep 10 + - make -C test check - stage: tag image script: ./extras/travis_push_docker_hub.sh