Merge pull request #3 from zkhan12/dev

dockerize application

Author: zkhan12

Dockerfile

@@ -0,0 +1,27 @@
+FROM ubuntu:18.04
+
+USER root
+
+RUN apt-get update \
+    && apt-get -y install curl \
+    && chmod 777 /opt
+
+ENV PATH="/opt/miniconda-latest/bin:$PATH"
+
+RUN useradd --create-home --shell /bin/bash coder
+USER coder
+
+RUN export PATH="/opt/miniconda-latest/bin:$PATH" \
+    && conda_installer="/tmp/miniconda.sh" \
+    && curl -fsSL --retry 5 -o "$conda_installer" https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh \
+    && bash "$conda_installer" -b -p /opt/miniconda-latest \
+    && mkdir /home/coder/projects
+
+WORKDIR /home/coder/projects
+
+COPY --chown=coder . /home/coder/projects/
+
+RUN conda env create -f environment.yml
+RUN bash -c 'conda init && . /home/coder/.bashrc'
+
+ENTRYPOINT ["/opt/miniconda-latest/envs/log/bin/python", "./logToHtml.py"]

README.md

@@ -1 +1,20 @@
-# log-html
+# log-html
+Log-html is a command line tool which generates html summary files for directories with log files.
+
+# Usage
+Log-html can be run 
+## Python (via conda)
+Options inside of <> are where user specific information is entered
+- Create conda environment (inside cloned directory): `conda env create -f environment.yml`
+- Activate conda environment: `conda activate log`
+- Run script: `python logToHtml.py <location of log directory> <location of output file> <location of template file> <path to log directory on rdss (note this may be different than the first path to the log directory)>`
+- Example run script command: `python logToHtml.py ${PWD}/logs/ ${PWD}/outputs/summary.html templates/temp.tpl /home/user/Accelerometer/logs/`
+
+## Docker
+Options inside of <> are where user specific information is entered
+- Build docker image (inside cloned directory): `docker build -t <image tag> .`
+- Run docker container: `docker run -v <path to log directory>:/home/coder/projects/logs -v <path to where outputs should be stored>:/home/coder/projects/outputs <image tag> /home/coder/projects/logs/ /home/coder/projects/outputs/<name of output html file> /home/coder/projects/templates/temp.tpl <path to log directory on rdss where output file will be opened from (note: this may be different than the first path to the log directory)>`
+- Example run command: `docker run -v ${PWD}/logs/:/home/coder/projects/logs -v ${PWD}/outputs/:/home/coder/projects/outputs htmllog:latest /home/coder/projects/logs/ /home/coder/projects/outputs/summary.html /home/coder/projects/templates/temp.tpl /home/user/Accelerometer/logs/`
+
+## Singularity
+This image is available on dockerhub at: `hbclab/log-html` and can be pulled to run with singularity.

environment.yml

@@ -0,0 +1,27 @@
+name: log
+channels:
+  - defaults
+dependencies:
+  - _libgcc_mutex=0.1
+  - ca-certificates=2020.1.1
+  - certifi=2020.4.5.2
+  - ld_impl_linux-64=2.33.1
+  - libedit=3.1.20181209
+  - libffi=3.3
+  - libgcc-ng=9.1.0
+  - libstdcxx-ng=9.1.0
+  - ncurses=6.2
+  - openssl=1.1.1g
+  - pip=20.1.1
+  - python=3.7.7
+  - readline=8.0
+  - setuptools=47.3.0
+  - sqlite=3.31.1
+  - tk=8.6.8
+  - wheel=0.34.2
+  - xz=5.2.5
+  - zlib=1.2.11
+  - pip:
+    - jinja2==2.11.2
+    - markupsafe==1.1.1
+

logToHtml.py

@@ -9,9 +9,11 @@ def build_parser():
                     formatter_class=RawTextHelpFormatter
                     )
     parser.add_argument('log_dir', help='(must be absolute path) directory where log '
-                                        'files are kept')
+                                        'files are mounted')
     parser.add_argument('output_file', help='location of the html output')
     parser.add_argument('template_file', help='location of the html template')
+    parser.add_argument('rdss_log_dir', help='(must be absolute path) directory on '
+                                             'rdss drive containing logs')
 
     return parser
 
@@ -40,10 +42,10 @@ def __init__(self, filename, status, path, date, time):
     time = contents[11:19]
     if 'ERROR' in contents:
         accel_files.append(Accel(fil, 'ERROR', 'file:///' +
-                                 os.path.join(opts.log_dir, fil), date, time))
+                                 os.path.join(opts.rdss_log_dir, fil), date, time))
     else:
         accel_files.append(Accel(fil, 'SUCCESS', 'file:///' +
-                                 os.path.join(opts.log_dir, fil), date, time))
+                                 os.path.join(opts.rdss_log_dir, fil), date, time))
 
 env = jinja2.Environment(
     loader=jinja2.FileSystemLoader(searchpath=os.path.dirname(opts.template_file))