merge gh-pages

CDCgov · Nov 21, 2024 · 6d42208 · 6d42208
2 parents a814769 + db4b1bc
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diff --git a/.dockerignore b/.dockerignore
@@ -1,3 +1,29 @@
-/shiny/*
 /vignettes/*
 /docs/*
+
+# ignore file extensions
+*.DS_Store
+*.Rmd
+*.html
+*.md
+*.Rhistory
+*.gitignore
+*.Rbuildignore
+*.Rproj
+DESCRIPTION
+
+# ignore folders
+**.git
+**.github
+**.Rproj.user
+*docs
+*vignettes
+*man
+*inst
+*pkgdown
+
+# ignore specific files
+docker-compose.yml
+docker-compose-*.yml
+_pkgdown.yml
+NAMESPACE
diff --git a/Dockerfile b/Dockerfile
@@ -1,102 +1,92 @@
-# Create an argument to pull a particular version of micromamba image
-ARG micromamba_version
-ARG micromamba_version=${micromamba_version:-1.5.3}
-
-############# base image ##################
-FROM --platform=$BUILDPLATFORM ubuntu:focal as base
-
-# local apt mirror support
-# start every stage with updated apt sources
-ARG APT_MIRROR_NAME=
-RUN if [ -n "$APT_MIRROR_NAME" ]; then sed -i.bak -E '/security/! s^https?://.+?/(debian|ubuntu)^http://'"$APT_MIRROR_NAME"'/\1^' /etc/apt/sources.list && grep '^deb' /etc/apt/sources.list; fi
-RUN apt-get update --allow-releaseinfo-change --fix-missing
-
-############# micromamba image ##################
-
-FROM --platform=$BUILDPLATFORM mambaorg/micromamba:${micromamba_version} as micromamba
-RUN echo "Getting micromamba image"
-
-############# Build Stage: Final ##################
-
-# Build the final image 
-FROM base as final
-
-# if image defaults to a non-root user, then we may want to make the
-# next 3 ARG commands match the values in our image. 
-ENV MAMBA_USER=$MAMBA_USER
-ENV MAMBA_USER_ID=$MAMBA_USER_ID
-ENV MAMBA_USER_GID=$MAMBA_USER_GID
-ENV MAMBA_ROOT_PREFIX="/opt/conda"
-ENV MAMBA_EXE="/bin/micromamba"
-
-COPY --from=micromamba "$MAMBA_EXE" "$MAMBA_EXE"
-COPY --from=micromamba /usr/local/bin/_activate_current_env.sh /usr/local/bin/_activate_current_env.sh
-COPY --from=micromamba /usr/local/bin/_dockerfile_shell.sh /usr/local/bin/_dockerfile_shell.sh
-COPY --from=micromamba /usr/local/bin/_entrypoint.sh /usr/local/bin/_entrypoint.sh
-COPY --from=micromamba /usr/local/bin/_dockerfile_initialize_user_accounts.sh /usr/local/bin/_dockerfile_initialize_user_accounts.sh
-COPY --from=micromamba /usr/local/bin/_dockerfile_setup_root_prefix.sh /usr/local/bin/_dockerfile_setup_root_prefix.sh
-
-# Install system dependencies
-ARG DEBIAN_FRONTEND=noninteractive
-
-# Install system libraries of general use
-RUN apt-get update --allow-releaseinfo-change --fix-missing \
-  && apt-get install --no-install-recommends -y \
-  dos2unix \
-  ca-certificates \
-  && apt clean autoclean \
-  && apt autoremove --yes \
-  && rm -rf /var/lib/{apt,dpkg,cache,log}/
-
-# Create working directory 
-ENV WORKDIR=/data
-
-# Set up volume directory
-VOLUME ${WORKDIR}
-
-# Set up working directory
-WORKDIR ${WORKDIR}
-
-# Allow permission to read and write to working directory
-RUN chmod -R a+rwx ${WORKDIR}
-
-# Create a program variable
-ENV PROJECT_DIR=/seqsender
-
-# Set up a volume directory 
-VOLUME ${PROJECT_DIR}
-
-# Copy all files to project directory
-COPY . ${PROJECT_DIR}
-
-############ Set-up micromamba environment ##################
-
-# Copy requirement files to program directory
-COPY env.yaml "${PROJECT_DIR}/env.yaml"
-
-# Set up environments
-RUN micromamba install --yes --name base -f "${PROJECT_DIR}/env.yaml" \
-    && micromamba clean --all --yes
-
-############# Launch PROGRAM ##################
-
-# Copy bash script to run PROGRAM to docker image
-COPY seqsender-kickoff "${PROJECT_DIR}/seqsender-kickoff"
-
-# Convert bash script from Windows style line endings to Unix-like control characters
-RUN dos2unix "${PROJECT_DIR}/seqsender-kickoff"
-
-# Allow permission to excute the bash script
-RUN chmod a+x "${PROJECT_DIR}/seqsender-kickoff"
-
-# Allow permission to read and write to program directory
-RUN chmod a+rwx ${PROJECT_DIR}
-
-# Export bash script to path
-ENV PATH="$PATH:${PROJECT_DIR}"
-
-# Activate conda environment
-ENV PATH="$PATH:${MAMBA_ROOT_PREFIX}/bin"
-
-# Execute the pipeline 
-ENTRYPOINT ["tail", "-f", "/dev/null"]
+# Create an argument to pull a particular version of micromamba image
+ARG micromamba_version
+ARG micromamba_version=${micromamba_version:-1.5.3}
+
+############# micromamba image ##################
+
+FROM mambaorg/micromamba:${micromamba_version} as micromamba
+RUN echo "Getting micromamba image"
+
+############# base image ##################
+
+FROM ubuntu:focal as base
+
+# if image defaults to a non-root user, then we may want to make the
+# next 3 ARG commands match the values in our image. 
+ENV MAMBA_USER=$MAMBA_USER
+ENV MAMBA_USER_ID=$MAMBA_USER_ID
+ENV MAMBA_USER_GID=$MAMBA_USER_GID
+ENV MAMBA_ROOT_PREFIX="/opt/conda"
+ENV MAMBA_EXE="/bin/micromamba"
+
+COPY --from=micromamba "$MAMBA_EXE" "$MAMBA_EXE"
+COPY --from=micromamba /usr/local/bin/_activate_current_env.sh /usr/local/bin/_activate_current_env.sh
+COPY --from=micromamba /usr/local/bin/_dockerfile_shell.sh /usr/local/bin/_dockerfile_shell.sh
+COPY --from=micromamba /usr/local/bin/_entrypoint.sh /usr/local/bin/_entrypoint.sh
+COPY --from=micromamba /usr/local/bin/_dockerfile_initialize_user_accounts.sh /usr/local/bin/_dockerfile_initialize_user_accounts.sh
+COPY --from=micromamba /usr/local/bin/_dockerfile_setup_root_prefix.sh /usr/local/bin/_dockerfile_setup_root_prefix.sh
+
+# Install system dependencies
+ARG DEBIAN_FRONTEND=noninteractive
+
+# local apt mirror support
+# start every stage with updated apt sources
+ARG APT_MIRROR_NAME=
+RUN if [ -n "$APT_MIRROR_NAME" ]; then sed -i.bak -E '/security/! s^https?://.+?/(debian|ubuntu)^http://'"$APT_MIRROR_NAME"'/\1^' /etc/apt/sources.list && grep '^deb' /etc/apt/sources.list; fi
+RUN apt-get update --allow-releaseinfo-change --fix-missing \
+  && apt-get install --no-install-recommends -y \
+  dos2unix \
+  ca-certificates \
+  && apt clean autoclean \
+  && apt autoremove --yes \
+  && rm -rf /var/lib/{apt,dpkg,cache,log}/
+
+# Create working directory 
+ENV WORKDIR=/data
+
+# Set up volume directory
+VOLUME ${WORKDIR}
+
+# Set up working directory
+WORKDIR ${WORKDIR}
+
+# Allow permission to read and write to working directory
+RUN chmod -R a+rwx ${WORKDIR}
+
+# Create a program variable
+ENV PROJECT_DIR=/seqsender
+
+# Set up a volume directory 
+VOLUME ${PROJECT_DIR}
+
+# Copy all files to project directory
+COPY . ${PROJECT_DIR}
+
+############ Set-up micromamba environment ##################
+
+# Copy requirement files to program directory
+COPY env.yaml "${PROJECT_DIR}/env.yaml"
+
+# Set up environments
+RUN micromamba install --yes --name base -f "${PROJECT_DIR}/env.yaml" \
+    && micromamba clean --all --yes
+
+############# Launch PROGRAM ##################
+
+# Copy bash script to run PROGRAM to docker image
+COPY seqsender-kickoff "${PROJECT_DIR}/seqsender-kickoff"
+
+# Convert bash script from Windows style line endings to Unix-like control characters
+RUN dos2unix "${PROJECT_DIR}/seqsender-kickoff"
+
+# Allow permission to excute the bash script
+RUN chmod a+x "${PROJECT_DIR}/seqsender-kickoff"
+
+# Allow permission to read and write to program directory
+RUN chmod a+rwx ${PROJECT_DIR}
+
+# Export bash script to path
+ENV PATH="$PATH:${PROJECT_DIR}"
+
+# Activate conda environment
+ENV PATH="$PATH:${MAMBA_ROOT_PREFIX}/bin"
diff --git a/README.Rmd b/README.Rmd
@@ -26,7 +26,7 @@ github_pages_url <- description$GITHUB_PAGES
 
 <p style="font-size: 16px;"><em>Public Database Submission Pipeline</em></p>
 
-**Beta Version**: v1.2.3. This pipeline is currently in Beta testing, and issues could appear during submission. Please use it at your own risk. Feedback and suggestions are welcome! 
+**Beta Version**: v1.2.5. This pipeline is currently in Beta testing, and issues could appear during submission. Please use it at your own risk. Feedback and suggestions are welcome! 
 
 **General Disclaimer**: This repository was created for use by CDC programs to collaborate on public health related projects in support of the [CDC mission](https://www.cdc.gov/about/organization/mission.htm).  GitHub is not hosted by the CDC, but is a third party website used by CDC and its partners to share information and collaborate on software. CDC use of GitHub does not imply an endorsement of any one particular service, product, or enterprise.
 

diff --git a/README.md b/README.md
@@ -5,7 +5,17 @@
 ![Docker image size](https://img.shields.io/docker/image-size/cdcgov/seqsender)
 ![GitHub last commit](https://img.shields.io/github/last-commit/cdcgov/seqsender)
 
-**Beta Version**: 1.2.3. This pipeline is currently in Beta testing, and
+<!-- ![GitHub issues](https://img.shields.io/github/issues/montilab/cadra) -->
+
+<!-- ![GitHub last commit](https://img.shields.io/github/last-commit/montilab/cadra) -->
+
+<p style="font-size: 16px;">
+
+<em>Public Database Submission Pipeline</em>
+
+</p>
+
+**Beta Version**: 1.2.5. This pipeline is currently in Beta testing, and
 issues could appear during submission. Please use it at your own risk.
 Feedback and suggestions are welcome\!
 

diff --git a/config/seqsender/config_file/gisaid_schema.py b/config/seqsender/config_file/gisaid_schema.py
@@ -10,19 +10,19 @@
                     'Username': {
                         'required': False,
                         'type': 'string',
-                        'regex': '^[a-zA-Z0-9_.+-]+',
+                        'regex': '\s*[\S]+\s*',
                         'nullable': True
                     },
                     'Password': {
                         'required': False,
                         'type': 'string',
-                        'regex': '^[a-zA-Z0-9_.+-]+',
+                        'regex': '\s*[\S]+\s*',
                         'nullable': True
                     },
                     'Spuid_Namespace': {
                         'required': False,
                         'type': 'string',
-                        'regex': '^[a-zA-Z0-9_.+-]+',
+                        'regex': '\s*[\S]+\s*',
                         'nullable': True
                     },
                     'BioSample_Package': {
@@ -191,12 +191,12 @@
                     'Username': {
                         'required': True,
                         'type': 'string',
-                        'regex': '^[a-zA-Z0-9_.+-]+'
+                        'regex': '\s*[\S]+\s*'
                     },
                     'Password': {
                         'required': True,
                         'type': 'string',
-                        'regex': '^[a-zA-Z0-9_.+-]+'
+                        'regex': '\s*[\S]+\s*'
                     },
                     'Submission_Position': {
                         'required': False,

diff --git a/config/seqsender/config_file/ncbi_gisaid_schema.py b/config/seqsender/config_file/ncbi_gisaid_schema.py
@@ -10,17 +10,17 @@
                     'Username': {
                         'required': True,
                         'type': 'string',
-                        'regex': '^[a-zA-Z0-9_.+-]+'
+                        'regex': '\s*[\S]+\s*'
                     },
                     'Password': {
                         'required': True,
                         'type': 'string',
-                        'regex': '^[a-zA-Z0-9_.+-]+'
+                        'regex': '\s*[\S]+\s*'
                     },
                     'Spuid_Namespace': {
                         'required': True,
                         'type': 'string',
-                        'regex': '^[a-zA-Z0-9_.+-]+'
+                        'regex': '\s*[\S]+\s*'
                     },
                     'BioSample_Package': {
                         'required': False,
@@ -173,12 +173,12 @@
                     'Username': {
                         'required': True,
                         'type': 'string',
-                        'regex': '^[a-zA-Z0-9_.+-]+'
+                        'regex': '\s*[\S]+\s*'
                     },
                     'Password': {
                         'required': True,
                         'type': 'string',
-                        'regex': '^[a-zA-Z0-9_.+-]+'
+                        'regex': '\s*[\S]+\s*'
                     },
                     'Submission_Position': {
                         'required': True,

diff --git a/config/seqsender/config_file/ncbi_schema.py b/config/seqsender/config_file/ncbi_schema.py
@@ -10,17 +10,17 @@
                     'Username': {
                         'required': True,
                         'type': 'string',
-                        'regex': '^[a-zA-Z0-9_.+-]+'
+                        'regex': '\s*[\S]+\s*'
                     },
                     'Password': {
                         'required': True,
                         'type': 'string',
-                        'regex': '^[a-zA-Z0-9_.+-]+'
+                        'regex': '\s*[\S]+\s*'
                     },
                     'Spuid_Namespace': {
                         'required': True,
                         'type': 'string',
-                        'regex': '^[a-zA-Z0-9_.+-]+'
+                        'regex': '\s*[\S]+\s*'
                     },
                     'BioSample_Package': {
                         'required': False,
@@ -174,13 +174,13 @@
                     'Username': {
                         'required': False,
                         'type': 'string',
-                        'regex': '^[a-zA-Z0-9_.+-]+',
+                        'regex': '\s*[\S]+\s*',
                         'nullable': True
                     },
                     'Password': {
                         'required': False,
                         'type': 'string',
-                        'regex': '^[a-zA-Z0-9_.+-]+',
+                        'regex': '\s*[\S]+\s*',
                         'nullable': True
                     },
                     'Submission_Position': {

diff --git a/docker-compose.yaml b/docker-compose.yaml
@@ -3,14 +3,19 @@ version: "3.9"
 x-data-volumes:
   &data-volume
   type: bind
-  source: $HOME/Github/Testings/seqsender
+  source: $HOME
   target: /data
 
 services:
-  seqsender: 
+  seqsender:
     container_name: seqsender
-    image: cdcgov/seqsender:latest
+    image: seqsender:latest
+    build:
+      context: .
+      dockerfile: Dockerfile
+      args:
+        - micromamba_version=1.5.3
     restart: always
-    volumes: 
+    volumes:
       - *data-volume
-    command: tail -f /dev/null 
+    command: tail -f /dev/null
diff --git a/docs/app.json b/docs/app.json