Merge pull request #203 from uc-cdis/chore/update_image_docker

Update Image

.coveragerc

@@ -27,4 +27,4 @@ exclude_also =
     if __name__ == .__main__.:
 
     ; Don't complain about abstract methods, they aren't run:
-    @(abc\.)?abstractmethod
+    @(abc\.)?abstractmethod

.dockerignore

@@ -3,3 +3,7 @@
 **/*.pyc
 **/*.egg-info
 **/__pycache__
+knowledge/
+prof/
+tests/
+tsvs/

.pre-commit-config.yaml

@@ -1,18 +1,18 @@
 repos:
 -   repo: [email protected]:Yelp/detect-secrets
-    rev: v1.4.0
+    rev: v1.5.0
     hooks:
     -   id: detect-secrets
         args: ['--baseline', '.secrets.baseline']
         exclude: poetry.lock
 -   repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v2.5.0
+    rev: v5.0.0
     hooks:
     -   id: trailing-whitespace
     -   id: end-of-file-fixer
     -   id: no-commit-to-branch
         args: [--branch, develop, --branch, master, --pattern, release/.*]
 -   repo: https://github.com/psf/black
-    rev: 22.3.0
+    rev: 25.1.0
     hooks:
     -   id: black

.secrets.baseline

@@ -0,0 +1,159 @@
+{
+  "version": "1.5.0",
+  "plugins_used": [
+    {
+      "name": "ArtifactoryDetector"
+    },
+    {
+      "name": "AWSKeyDetector"
+    },
+    {
+      "name": "AzureStorageKeyDetector"
+    },
+    {
+      "name": "Base64HighEntropyString",
+      "limit": 4.5
+    },
+    {
+      "name": "BasicAuthDetector"
+    },
+    {
+      "name": "CloudantDetector"
+    },
+    {
+      "name": "DiscordBotTokenDetector"
+    },
+    {
+      "name": "GitHubTokenDetector"
+    },
+    {
+      "name": "GitLabTokenDetector"
+    },
+    {
+      "name": "HexHighEntropyString",
+      "limit": 3.0
+    },
+    {
+      "name": "IbmCloudIamDetector"
+    },
+    {
+      "name": "IbmCosHmacDetector"
+    },
+    {
+      "name": "IPPublicDetector"
+    },
+    {
+      "name": "JwtTokenDetector"
+    },
+    {
+      "name": "KeywordDetector",
+      "keyword_exclude": ""
+    },
+    {
+      "name": "MailchimpDetector"
+    },
+    {
+      "name": "NpmDetector"
+    },
+    {
+      "name": "OpenAIDetector"
+    },
+    {
+      "name": "PrivateKeyDetector"
+    },
+    {
+      "name": "PypiTokenDetector"
+    },
+    {
+      "name": "SendGridDetector"
+    },
+    {
+      "name": "SlackDetector"
+    },
+    {
+      "name": "SoftlayerDetector"
+    },
+    {
+      "name": "SquareOAuthDetector"
+    },
+    {
+      "name": "StripeDetector"
+    },
+    {
+      "name": "TelegramBotTokenDetector"
+    },
+    {
+      "name": "TwilioKeyDetector"
+    }
+  ],
+  "filters_used": [
+    {
+      "path": "detect_secrets.filters.allowlist.is_line_allowlisted"
+    },
+    {
+      "path": "detect_secrets.filters.common.is_baseline_file",
+      "filename": ".secrets.baseline"
+    },
+    {
+      "path": "detect_secrets.filters.common.is_ignored_due_to_verification_policies",
+      "min_level": 2
+    },
+    {
+      "path": "detect_secrets.filters.heuristic.is_indirect_reference"
+    },
+    {
+      "path": "detect_secrets.filters.heuristic.is_likely_id_string"
+    },
+    {
+      "path": "detect_secrets.filters.heuristic.is_lock_file"
+    },
+    {
+      "path": "detect_secrets.filters.heuristic.is_not_alphanumeric_string"
+    },
+    {
+      "path": "detect_secrets.filters.heuristic.is_potential_uuid"
+    },
+    {
+      "path": "detect_secrets.filters.heuristic.is_prefixed_with_dollar_sign"
+    },
+    {
+      "path": "detect_secrets.filters.heuristic.is_sequential_string"
+    },
+    {
+      "path": "detect_secrets.filters.heuristic.is_swagger_file"
+    },
+    {
+      "path": "detect_secrets.filters.heuristic.is_templated_secret"
+    }
+  ],
+  "results": {
+    ".github/workflows/ci.yml": [
+      {
+        "type": "Secret Keyword",
+        "filename": ".github/workflows/ci.yml",
+        "hashed_secret": "3e26d6750975d678acb8fa35a0f69237881576b0",
+        "is_verified": false,
+        "line_number": 17
+      }
+    ],
+    "tests/.env": [
+      {
+        "type": "Secret Keyword",
+        "filename": "tests/.env",
+        "hashed_secret": "6ffd8b80f2a76ca670ae33ab196f7936d59fb43b",
+        "is_verified": false,
+        "line_number": 8
+      }
+    ],
+    "tests/tsvs/bdc/bdc_2.tsv": [
+      {
+        "type": "Hex High Entropy String",
+        "filename": "tests/tsvs/bdc/bdc_2.tsv",
+        "hashed_secret": "b6bb1128fca99567fb54d64d76630a9223f4c394",
+        "is_verified": false,
+        "line_number": 2
+      }
+    ]
+  },
+  "generated_at": "2025-01-17T16:26:37Z"
+}

Dockerfile

@@ -1,56 +1,45 @@
-FROM quay.io/cdis/amazonlinux:python3.9-master as build-deps
+ARG AZLINUX_BASE_VERSION=master
 
-USER root
+# Base stage with python-build-base
+FROM quay.io/cdis/python-nginx-al:${AZLINUX_BASE_VERSION} AS base
 
 ENV appname=gen3discoveryai
 
-RUN pip3 install --no-cache-dir --upgrade poetry
+WORKDIR /$appname
 
-RUN yum update -y && yum install -y --setopt install_weak_deps=0 \
-    kernel-devel libffi-devel libxml2-devel libxslt-devel postgresql-devel python3-devel \
-    git && yum clean all
+RUN chown -R gen3:gen3 /${appname}
 
-WORKDIR /$appname
+# Builder stage
+FROM base AS builder
+
+# RUN yum update -y && yum install -y --setopt install_weak_deps=0 \
+#     kernel-devel libffi-devel libxml2-devel libxslt-devel postgresql-devel python3-devel \
+#     git && yum clean all
+
+USER gen3
 
 # copy ONLY poetry artifact, install the dependencies but not gen3discoveryai
 # this will make sure that the dependencies are cached
 COPY poetry.lock pyproject.toml /$appname/
 COPY ./docs/openapi.yaml /$appname/docs/openapi.yaml
-RUN poetry config virtualenvs.in-project true \
-    && poetry install -vv --no-root --only main --no-interaction \
-    && poetry show -v
 
-# copy source code ONLY after installing dependencies
-COPY . /$appname
+RUN poetry install -vv --without dev --no-interaction
 
-# install gen3discoveryai
-RUN poetry config virtualenvs.in-project true \
-    && poetry install -vv --only main --no-interaction \
-    && poetry show -v
+# copy source code and needed files ONLY after installing dependencies
+COPY --chown=gen3:gen3 . /$appname
 
-#Creating the runtime image
-FROM quay.io/cdis/amazonlinux:python3.9-master
+# Run poetry again so this app itself gets installed too
+RUN poetry install --without dev --no-interaction
 
-ENV appname=gen3discoveryai
+# Creating the runtime image
+FROM base
 
-USER root
+USER gen3
 
+COPY --from=builder /${appname} /${appname}
+WORKDIR /${appname}
 EXPOSE 80
 
-RUN pip3 install --no-cache-dir --upgrade poetry
-
-RUN yum update -y && yum install -y --setopt install_weak_deps=0 \
-    postgresql-devel shadow-utils\
-    bash && yum clean all
-
-RUN useradd -ms /bin/bash appuser
-
-COPY --from=build-deps --chown=appuser:appuser /$appname /$appname
-
-WORKDIR /$appname
-
-USER appuser
-
 # Cache the necessary tiktoken encoding file
 RUN poetry run python -c "from langchain.text_splitter import TokenTextSplitter; TokenTextSplitter.from_tiktoken_encoder(chunk_size=100, chunk_overlap=0)"