Merge pull request #8 from HBClab/octothorpe

[REF] Refactor Code

Author: zkhan12

.gitignore

@@ -1,2 +1,141 @@
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# user defined
 *.html
-*.log
+

.travis.yml

@@ -0,0 +1,16 @@
+anguage: python
+
+services:
+  - docker
+
+before_install:
+  - docker build -t hbclab/log-html .
+
+script:
+  - docker run --entrypoint /bin/bash hbclab/log-html -c ". activate log && pytest /home/coder/projects/log-html"
+
+deploy:
+  provider: script
+  script: bash docker_push.sh
+  on:
+    all_branches: true

Dockerfile

@@ -24,4 +24,4 @@ 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", "/home/coder/projects/logToHtml.py"]
+ENTRYPOINT ["/opt/miniconda-latest/envs/log/bin/python", "/home/coder/projects/log-html/logToHtml.py"]

docker_push.sh

@@ -0,0 +1,13 @@
+ 
+echo "$DOCKER_PASS" | docker login --username "$DOCKER_USERNAME" --password-stdin
+# if tag is defined
+if [[ ! -z "$TRAVIS_TAG" ]]; then
+    docker tag hbclab/log-html:latest hbclab/log-html:$TRAVIS_TAG
+    docker push hbclab/log-html:$TRAVIS_TAG
+# if the build is on the master branch
+elif [[ "$TRAVIS_BRANCH" == "master" ]]; then
+    docker tag hbclab/log-html:latest hbclab/log-html:unstable
+    docker push hbclab/log-html:unstable
+else
+    echo "This build is not on the master branch or a tagged release"
+fi

environment.yml

@@ -21,6 +21,7 @@ dependencies:
   - wheel=0.34.2
   - xz=5.2.5
   - zlib=1.2.11
+  - pytest
   - pip:
     - jinja2==2.11.2
     - markupsafe==1.1.1

log-html/__init__.py

@@ -1,8 +1,24 @@
 import os
+import re
 import jinja2
 from argparse import ArgumentParser, RawTextHelpFormatter
 from glob import glob
 
+DEFAULT_TEMPLATE = os.path.join(os.path.dirname(__file__), "templates", "temp.tpl")
+
+
+class Accel():
+        def __init__(self, filename, status, path, date, time):
+            self.filename = filename
+            self.status = status
+            if status == 'ERROR':
+                self.css = 'redtext'
+            else:
+                self.css = 'greentext'
+            self.path = path
+            self.date = date
+            self.time = time
+
 
 def build_parser():
     parser = ArgumentParser(
@@ -11,25 +27,45 @@ def build_parser():
                     )
     parser.add_argument('log_dir', help='(abs path) directory where log '
                                         'files are mounted')
-    parser.add_argument('output_file', help='location of the html output')
+    parser.add_argument('output_file', help='name of the HTML file')
     parser.add_argument('--template-file', help='location of the html template',
-                        required=False, default='templates/temp.tpl')
+                        required=False, default=DEFAULT_TEMPLATE)
 
     return parser
 
+def parse_log_file(fil):
+
+    # read all contents of log file
+    contents = open(fil, 'r').read()
+
+    # assume log entries are separated by at least 5 #'s
+    try:
+        entry_separator = re.search(r"[#]{5,}", contents).group()
+    except AttributeError:
+        raise ValueError("Cannot find at least 5 #'s separating log entries")
+    
+    # assume the last entry is the most recent
+    last_entry = contents.split(entry_separator)[-1]
+
+    # find the date
+    try:
+        date = re.search("[0-9]{4}-[0-9]{2}-[0-9]{2}", last_entry).group()
+    except AttributeError:
+        raise ValueError("Cannot find date formatted YYYY-MM-DD")
+    
+    # find the time
+    try:
+        time = re.search("[0-9]{2}:[0-9]{2}:[0-9]{2}", last_entry).group()
+    except AttributeError:
+        raise ValueError("Cannot find time formatted HH:MM:SS")
+
+    if 'ERROR' in last_entry:
+        return (date, time, "ERROR")
+    else:
+        return (date, time, "SUCCESS")
+        
 
 def main():
-    class Accel():
-        def __init__(self, filename, status, path, date, time):
-            self.filename = filename
-            self.status = status
-            if status == 'ERROR':
-                self.css = 'redtext'
-            else:
-                self.css = 'greentext'
-            self.path = path
-            self.date = date
-            self.time = time
 
     opts = build_parser().parse_args()
     # converting relative paths to absolute
@@ -45,15 +81,11 @@ def __init__(self, filename, status, path, date, time):
     accel_files = []
 
     for fil in filenames:
-        contents = open(fil, 'r').read()
-        date = contents[0:10]
-        time = contents[11:19]
-        if 'ERROR' in contents:
-            accel_files.append(Accel(os.path.basename(fil), 'ERROR', 'file:' +
-                                     fil, date, time))
-        else:
-            accel_files.append(Accel(os.path.basename(fil), 'SUCCESS', 'file:' +
-                                     fil, date, time))
+        date, time, status = parse_log_file(fil)
+
+        accel_files.append(Accel(os.path.basename(fil), status, 'file:' +
+                                    fil, date, time))
+    
 
     env = jinja2.Environment(
         loader=jinja2.FileSystemLoader(searchpath=os.path.dirname(template_file))

logToHtml.py renamed to log-html/logToHtml.py

@@ -0,0 +1,35 @@
+
+###############################
+
+2020-05-14 07:31:12,110 - accel_code.run - ERROR - could not get subject id from redcap for 827 (2018-10-02 00:00:00)
+Traceback (most recent call last):
+  File "/opt/miniconda-latest/envs/accel/lib/python3.7/site-packages/redcap/project.py", line 57, in configure
+    self.metadata = self.__md()
+  File "/opt/miniconda-latest/envs/accel/lib/python3.7/site-packages/redcap/project.py", line 93, in __md
+    return self._call_api(p_l, 'metadata')[0]
+  File "/opt/miniconda-latest/envs/accel/lib/python3.7/site-packages/redcap/project.py", line 155, in _call_api
+    return rcr.execute(**request_kwargs)
+  File "/opt/miniconda-latest/envs/accel/lib/python3.7/site-packages/redcap/request.py", line 125, in execute
+    self.raise_for_status(r)
+  File "/opt/miniconda-latest/envs/accel/lib/python3.7/site-packages/redcap/request.py", line 166, in raise_for_status
+    r.raise_for_status()
+  File "/opt/miniconda-latest/envs/accel/lib/python3.7/site-packages/requests/models.py", line 941, in raise_for_status
+    raise HTTPError(http_error_msg, response=self)
+requests.exceptions.HTTPError: 400 Client Error: Bad Request for url: https://redcap.icts.uiowa.edu/redcap/api/
+
+During handling of the above exception, another exception occurred:
+
+Traceback (most recent call last):
+  File "/home/coder/projects/accel_code/run.py", line 81, in main
+    sub_id = redcap_query.redcap_query(lab_id, project, opts.api_key)
+  File "/home/coder/projects/accel_code/redcap_query.py", line 14, in redcap_query
+    project = redcap.Project(api_url, api_key)
+  File "/opt/miniconda-latest/envs/accel/lib/python3.7/site-packages/redcap/project.py", line 53, in __init__
+    self.configure()
+  File "/opt/miniconda-latest/envs/accel/lib/python3.7/site-packages/redcap/project.py", line 59, in configure
+    raise RedcapError("Exporting metadata failed. Check your URL and token.")
+requests.exceptions.RequestException: Exporting metadata failed. Check your URL and token.
+
+###############################
+
+2020-05-14 12:35:52,510 - accel_code.run - INFO - /mnt/nfs/lss/vosslabhpc/Projects/Accelerometer/3-Data/827/827 (2018-10-02)RAW.csv -> /mnt/nfs/lss/vosslabhpc/Projects/BikeExtend/3-Experiment/2-Data/BIDS/sub-2103/ses-accel1/beh/sub-2103_ses-accel1_accel.csv