From fc2d6441596e547ba8d8c9957b092724d8bb9ae3 Mon Sep 17 00:00:00 2001 From: jwansek Date: Thu, 28 Apr 2022 17:52:47 +0100 Subject: Started writing documentation --- README.md | 9 +------- Smarker/assessments.py | 28 +++++++++++++++++++++++ Smarker/database.py | 34 +++++++++++++++++++++++++++ Smarker/reflect.py | 2 +- Smarker/requirements.txt | 1 + Smarker/templates/tex.jinja2 | 15 +++++++----- Smarker/templates/text.jinja2 | Bin 28 -> 0 bytes docs/Makefile | 20 ++++++++++++++++ docs/deploy.sh | 6 +++++ docs/source/conf.py | 52 ++++++++++++++++++++++++++++++++++++++++++ docs/source/configfile.rst | 39 +++++++++++++++++++++++++++++++ docs/source/database.rst | 5 ++++ docs/source/docker.rst | 44 +++++++++++++++++++++++++++++++++++ docs/source/index.rst | 34 +++++++++++++++++++++++++++ docs/source/reflect.rst | 5 ++++ 15 files changed, 279 insertions(+), 15 deletions(-) mode change 100644 => 120000 README.md delete mode 100644 Smarker/templates/text.jinja2 create mode 100644 docs/Makefile create mode 100644 docs/deploy.sh create mode 100644 docs/source/conf.py create mode 100644 docs/source/configfile.rst create mode 100644 docs/source/database.rst create mode 100644 docs/source/docker.rst create mode 100644 docs/source/index.rst create mode 100644 docs/source/reflect.rst diff --git a/README.md b/README.md deleted file mode 100644 index 0253245..0000000 --- a/README.md +++ /dev/null @@ -1,8 +0,0 @@ -# Smarker -An automated marking system for UEA programming assessments - -## Running in docker - -`sudo docker run -v "$(pwd)/../wsData.txt":/wsData.txt -v "$(pwd)/100301654.zip":/tmp/100301654.zip -v "$(pwd)/out/":/out/ -e submission=/tmp/100301654.zip -e assessment=example -e SMARKERDEPS=matplotlib -e format=pdf -e output=/out/100301654.pdf --rm smarker` - -`sudo docker run -it --entrypoint python --rm smarker assessments.py --list yes` \ No newline at end of file diff --git a/README.md b/README.md new file mode 120000 index 0000000..57b939d --- /dev/null +++ b/README.md @@ -0,0 +1 @@ +docs/source/index.rst \ No newline at end of file diff --git a/Smarker/assessments.py b/Smarker/assessments.py index d5c8daf..a6c4df8 100644 --- a/Smarker/assessments.py +++ b/Smarker/assessments.py @@ -1,11 +1,29 @@ import misc_classes import configparser import jinja_helpers +import pycode_similar +import operator import database import argparse +import tempfile import yaml import os +def generate_plagarism_report(codes): + for file_name, codes in codes.items(): + with tempfile.TemporaryDirectory() as td: + un_added_student_nos = {i[0] for i in codes.keys()} + # print(un_added_student_nos) + for k, v in sorted(codes.keys(), key=operator.itemgetter(0, 1), reverse=True): + if k in un_added_student_nos: + with open(os.path.join(td, "%i.py" % k), "w") as f: + f.write(codes[(k, v)]) + + # print("Written %s at %s" % (k, v)) + un_added_student_nos.remove(k) + input("%s..." % td) + print(pycode_similar.detect(os.listdir(td))) + if __name__ == "__main__": config = configparser.ConfigParser() config.read(os.path.join(os.path.split(__file__)[0], "smarker.conf")) @@ -47,6 +65,13 @@ if __name__ == "__main__": help = "Add a student in the form e.g. 123456789,Eden,Attenborough,E.Attenborough@uea.ac.uk", required = False ) + parser.add_argument( + "-p", "--plagarism_report", + action = misc_classes.EnvDefault, + envvar = "plagarism_report", + help = "Generate a plagarism report for the given assessment", + required = False + ) for option in config.options("mysql"): parser.add_argument( @@ -91,6 +116,9 @@ if __name__ == "__main__": print("Added student %s" % name) + if args["plagarism_report"] is not None: + generate_plagarism_report(db.get_submission_codes(args["plagarism_report"])) + # print(db.get_assessment_yaml("CMP-4009B-2020-A2")) diff --git a/Smarker/database.py b/Smarker/database.py index 38af6a7..c1b1df0 100644 --- a/Smarker/database.py +++ b/Smarker/database.py @@ -111,6 +111,8 @@ class SmarkerDatabase: def remove_assessment(self, name): with self.__connection.cursor() as cursor: + cursor.execute("DELETE FROM submitted_files WHERE submission_id IN (SELECT submission_id FROM submissions WHERE assessment_name = %s);", (name, )) + cursor.execute("DELETE FROM submissions WHERE assessment_name = %s;", (name, )) cursor.execute("DELETE FROM assessment_file WHERE assessment_name = %s;", (name, )) cursor.execute("DELETE FROM assessment WHERE assessment_name = %s;", (name, )) self.__connection.commit() @@ -153,3 +155,35 @@ class SmarkerDatabase: submission_id, file_name, file_contents )) self.__connection.commit() + + def get_submission_codes(self, assessment_name): + out = {} + with self.__connection.cursor() as cursor: + cursor.execute("SELECT file_id, file_name FROM assessment_file WHERE assessment_name = %s;", (assessment_name, )) + for file_id, file_name in cursor.fetchall(): + out[file_name] = {} + + cursor.execute(""" + SELECT + submitted_files.file_text, + submissions.student_no, + submissions.submission_dt + FROM submitted_files + INNER JOIN submissions + ON submissions.submission_id = submitted_files.submission_id + WHERE submitted_files.file_id = %s; + """, (file_id, )) + + for code, student_no, dt in cursor.fetchall(): + out[file_name][(int(student_no), dt)] = code + return out + + def get_most_recent_submission_report(self, assessment_name): + with self.__connection.cursor() as cursor: + cursor.execute("SELECT MAX(submission_id), student_no FROM submissions WHERE assessment_name = %s GROUP BY student_no;", (assessment_name, )) + return [(int(i[0]), int(i[1]), yaml.safe_load(i[2])) for i in cursor.fetchall()] + + +if __name__ == "__main__": + with SmarkerDatabase(host = "vps.eda.gay", user="root", passwd=input("Input password: "), db="Smarker", port=3307) as db: + print(db.get_most_recent_submission_report("simple_assessment")) diff --git a/Smarker/reflect.py b/Smarker/reflect.py index 2a1f552..44d69de 100644 --- a/Smarker/reflect.py +++ b/Smarker/reflect.py @@ -376,7 +376,7 @@ def gen_reflection_report(client_code_path, assessment_struct, student_no, confi lines = lines.replace("\r", "") matches = {} for regex_ in contents["regexes"]: - matches[regex_] = re.findall(regex_, lines) + matches[regex_] = re.findall(str(regex_), lines) required_files_features["run"][j][cmd]["regexes"] = matches required_files_features["run"][j][cmd]["full_output"] = lines diff --git a/Smarker/requirements.txt b/Smarker/requirements.txt index 944b77a..a8fef17 100644 --- a/Smarker/requirements.txt +++ b/Smarker/requirements.txt @@ -9,3 +9,4 @@ junit2html pdfkit lxml pymysql +pycode_similar diff --git a/Smarker/templates/tex.jinja2 b/Smarker/templates/tex.jinja2 index eaa7db7..5985875 100644 --- a/Smarker/templates/tex.jinja2 +++ b/Smarker/templates/tex.jinja2 @@ -57,7 +57,7 @@ breaklines=true \newcommand{\errortext}[1]{\textcolor{red}{\textbf{#1}}} \author{((( student_no )))} -\title{((( name ))) - Automatic marking report} +\title{((( tex_escape(name) ))) - Automatic marking report} \begin{document} @@ -70,16 +70,19 @@ breaklines=true \begin{figure}[H] \centering - \begin{forest} + ((# \begin{forest} ((( recurse_class_tree_forest(class_tree)|indent(8, False) ))) - \end{forest} + \end{forest} #)) + \begin{lstlisting} +((( recurse_class_tree_text(class_tree) ))) + \end{lstlisting} \caption{Class inheritance tree} \end{figure} \section{File Analysis} ((* set flat_files = flatten_struct(files) *)) ((* for filename, files_contents in flat_files.items() *)) - \subsection{\texttt{((( filename )))}} + \subsection{\texttt{((( tex_escape(filename) )))}} ((* if files_contents["present"] *)) ((* if files_contents["has_exception"] *)) \errortext{File cannot be run - has compile time exception.} @@ -87,9 +90,9 @@ breaklines=true Please note that this file cannot be analysed or have tests preformed upon it- this can lead to the whole test suite failing if another module imports this. - \textbf{Exception Type:} \texttt{((( files_contents["exception"]["type"] )))} + \textbf{Exception Type:} \texttt{((( tex_escape(files_contents["exception"]["type"]) )))} - \textbf{Exception String:} \texttt{((( files_contents["exception"]["str"] )))} + \textbf{Exception String:} \texttt{((( tex_escape(files_contents["exception"]["str"]) )))} \textbf{Full Traceback:} diff --git a/Smarker/templates/text.jinja2 b/Smarker/templates/text.jinja2 deleted file mode 100644 index eca6ebd..0000000 Binary files a/Smarker/templates/text.jinja2 and /dev/null differ diff --git a/docs/Makefile b/docs/Makefile new file mode 100644 index 0000000..d0c3cbf --- /dev/null +++ b/docs/Makefile @@ -0,0 +1,20 @@ +# Minimal makefile for Sphinx documentation +# + +# You can set these variables from the command line, and also +# from the environment for the first two. +SPHINXOPTS ?= +SPHINXBUILD ?= sphinx-build +SOURCEDIR = source +BUILDDIR = build + +# Put it first so that "make" without argument is like "make help". +help: + @$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O) + +.PHONY: help Makefile + +# Catch-all target: route all unknown targets to Sphinx using the new +# "make mode" option. $(O) is meant as a shortcut for $(SPHINXOPTS). +%: Makefile + @$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O) diff --git a/docs/deploy.sh b/docs/deploy.sh new file mode 100644 index 0000000..d43e998 --- /dev/null +++ b/docs/deploy.sh @@ -0,0 +1,6 @@ +tar czvf build.tar.gz build/ +scp build.tar.gz eden@vps.eda.gay:/home/eden/SmarkerDocs/build.tar.gz +rm build.tar.gz +ssh eden@vps.eda.gay "rm -rf /home/eden/SmarkerDocs/build/" +ssh eden@vps.eda.gay "tar xvf /home/eden/SmarkerDocs/build.tar.gz -C /home/eden/SmarkerDocs" +ssh eden@vps.eda.gay "rm /home/eden/SmarkerDocs/build.tar.gz" \ No newline at end of file diff --git a/docs/source/conf.py b/docs/source/conf.py new file mode 100644 index 0000000..fd85d58 --- /dev/null +++ b/docs/source/conf.py @@ -0,0 +1,52 @@ +# Configuration file for the Sphinx documentation builder. +# +# This file only contains a selection of the most common options. For a full +# list see the documentation: +# https://www.sphinx-doc.org/en/master/usage/configuration.html + +# -- Path setup -------------------------------------------------------------- + +# If extensions (or modules to document with autodoc) are in another directory, +# add these directories to sys.path here. If the directory is relative to the +# documentation root, use os.path.abspath to make it absolute, like shown here. +# +import os +import sys +sys.path.insert(0, os.path.abspath(os.path.join("..", "..", "Smarker"))) +# print(os.listdir(os.path.abspath(os.path.join("..", "..", "Smarker")))) + + +# -- Project information ----------------------------------------------------- + +project = 'Smarker' +copyright = '2022, Eden Attenborough' +author = 'Eden Attenborough' + + +# -- General configuration --------------------------------------------------- + +# Add any Sphinx extension module names here, as strings. They can be +# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom +# ones. +extensions = ['sphinx.ext.autodoc', 'sphinx.ext.coverage', 'sphinx.ext.napoleon'] + +# Add any paths that contain templates here, relative to this directory. +templates_path = ['_templates'] + +# List of patterns, relative to source directory, that match files and +# directories to ignore when looking for source files. +# This pattern also affects html_static_path and html_extra_path. +exclude_patterns = [] + + +# -- Options for HTML output ------------------------------------------------- + +# The theme to use for HTML and HTML Help pages. See the documentation for +# a list of builtin themes. +# +html_theme = 'alabaster' + +# Add any paths that contain custom static files (such as style sheets) here, +# relative to this directory. They are copied after the builtin static files, +# so a file named "default.css" will overwrite the builtin "default.css". +html_static_path = ['_static'] \ No newline at end of file diff --git a/docs/source/configfile.rst b/docs/source/configfile.rst new file mode 100644 index 0000000..646230f --- /dev/null +++ b/docs/source/configfile.rst @@ -0,0 +1,39 @@ +.. _configfile: + +``smarker.conf``: Configuration File +==================================== + +Here is what it should look like. It needs to be in the same directory as the +source code. Its a standard .ini format. + +Once it's been created, you can safely forget about it since all of the options +can be over-ridden in command line arguments.:: + + [mysql] + host = vps.eda.gay + port = 3307 + user = root + passwd = ************ + + [tex] + columns = 1 + show_full_docs = True + show_source = True + show_all_regex_occurrences = True + show_all_run_output = True + + [md] + show_full_docs = False + show_source = False + show_all_regex_occurrences = True + show_all_run_output = False + + [txt] + show_full_docs = False + show_source = False + show_all_regex_occurrences = True + show_all_run_output = False + +The first block configures where your SQL server is. The other options are +the default options when generating reports. ``[tex]`` options are inherited +for rendering to PDF. \ No newline at end of file diff --git a/docs/source/database.rst b/docs/source/database.rst new file mode 100644 index 0000000..663c596 --- /dev/null +++ b/docs/source/database.rst @@ -0,0 +1,5 @@ +``database.py``: Interfacing with the database +============================================== + +.. automodule:: database + :members: \ No newline at end of file diff --git a/docs/source/docker.rst b/docs/source/docker.rst new file mode 100644 index 0000000..7c3237a --- /dev/null +++ b/docs/source/docker.rst @@ -0,0 +1,44 @@ +.. _docker: + +Running in docker +================= + +Running the system in docker has many advantages: + +* Don't have to worry about getting dependencies- the system requires many libraries to be avaliable on the PATH + +* Isolation: we are running remote code supplied by anyone, which can potentially be very dangerous. Docker isolates the dangerous code, a significant security concern + +* Makes the system be able to be used in Windows- Smarker has been tested in docker for windows using WSL for the backend + +Using docker +------------ + +We have a ``Dockerfile`` ready for use: ``sudo docker build -t smarker .`` + +To input files and get the output report we use docker volumes ``-v``. Unfortunately +docker seems to be rather buggy passing through single files, so we recommend making +a directory to pass through instead. + +Command line arguments can be replaced with environment variables, using the ``-e`` +flag in a ``key=value`` format. There is the additional environment variable ``SMARKERDEPS`` +which will pip install pypi modules at the start, deliminated with commas. + +.. code-block:: bash + + sudo docker run \ + -v "$(pwd)/../wsData.txt":/wsData.txt \ + -v "$(pwd)/100301654.zip":/tmp/100301654.zip \ + -v "$(pwd)/out/":/out/ \ + -e submission=/tmp/100301654.zip \ + -e assessment=example \ + -e SMARKERDEPS=matplotlib \ + -e format=pdf \ + -e output=/out/100301654.pdf \ + --rm smarker + +To list assessments in the database using docker: + +.. code-block:: bash + + sudo docker run -it --entrypoint python --rm smarker assessments.py --list yes \ No newline at end of file diff --git a/docs/source/index.rst b/docs/source/index.rst new file mode 100644 index 0000000..c238253 --- /dev/null +++ b/docs/source/index.rst @@ -0,0 +1,34 @@ +Welcome to Smarker's documentation! +=================================== + +Setting up +---------- + +* Set up a MySQL/MariaDB server. The database will be generated automatically. +* Add ``smarker.conf`` to the root directory of the code. See :ref:`configfile` for the structure of this file. +* Decide how you want to run the program: with or without docker. + +.. toctree:: + :maxdepth: 2 + :caption: Modules: + + reflect.rst + database.rst + +.. toctree:: + :maxdepth: 2 + :caption: Other Pages: + + configfile.rst + docker.rst + + + + + +Indices and tables +================== + +* :ref:`genindex` +* :ref:`modindex` +* :ref:`search` diff --git a/docs/source/reflect.rst b/docs/source/reflect.rst new file mode 100644 index 0000000..c059206 --- /dev/null +++ b/docs/source/reflect.rst @@ -0,0 +1,5 @@ +``reflect.py``: Getting information about code +============================================== + +.. automodule:: reflect + :members: \ No newline at end of file -- cgit v1.2.3