Bugfix: Prevent Error 500 and Update README.md mentioning new dependencies and pitfalls after merge of "feature boxplot-taskstatistic"

.github/workflows/test.yml

@@ -24,7 +24,7 @@ jobs:
       run: |
         sudo apt-get update
         sudo apt-get install swig libsasl2-dev libssl-dev libpq-dev
-        sudo apt-get install openjdk-8-jdk dejagnu checkstyle # gcj-jdk is not available anymore
+        sudo apt-get install openjdk-8-jdk dejagnu checkstyle
         sudo apt-get install r-base wget
         sudo apt-get install libcunit1-dev libcppunit-dev
         sudo apt-get install apache2-dev  # needed for unit test of praktomat.wsgi , praktomat.wsgi used mod_wsgi, installing mod_wsgi via requirementsfile via pip needs apache2-dev
@@ -59,9 +59,9 @@ jobs:
         ls -la --time-style=long-iso ..
     - name: Run tests
       run: |
-        ./src/manage-test.py test accounts attestation checker configuration solutions tasks hbrs_tests
+        ./src/manage-test.py test accounts attestation checker configuration solutions tasks taskstatistics hbrs_tests
     - name: Run test with code coverage
       run: |
-        coverage run --branch --omit='*/node_modules/*,*/migrations/*' --source='./src' ./src/manage-test.py test accounts attestation checker configuration solutions tasks hbrs_tests
+        coverage run --branch --omit='*/node_modules/*,*/migrations/*' --source='./src' ./src/manage-test.py test accounts attestation checker configuration solutions tasks taskstatistics hbrs_tests
     - name: Coverage report
       run: coverage report

README.md

@@ -7,7 +7,6 @@ In case of bugs or feature requests, please use the [Bug tracker]. There is
 also a moderated [mailing list] for Praktomat administrators:
 [email protected].
 
-
 A note about Python 2
 =============
 Since `pip` will drop support for Python 2 in January 2020,
@@ -25,11 +24,12 @@ Python 3.5
     python-psycopg2
     python-virtualenv
 
+
 General setup
 =============
 
-You need the latest version that is compatible with the Python version used. 
-We also highly recommend to use virtualenv so your system Python installation remains clean.
+You need the latest version of `pip`that is compatible with the Python version used.
+We also highly recommend to use `virtualenv` so your system Python installation remains clean.
 
 If you are having trouble with
 
@@ -64,6 +64,7 @@ Prerequisites: Database and Webserver
     libapache2-mod-xsendfile   (version 0.12; or install version 1.0 manually)
     apache2-dev                (used by pip while installing mod_wsgi)
 
+
 Pitfalls while Systemupgrades
 ============
   In Ubuntu 16 the package `apache2-mpm-worker` has been merged into `apache2`.
@@ -83,13 +84,86 @@ Pitfalls while Systemupgrades
 
   If you don't change that value, apache2 package becomes deleted while upgrading Ubuntu.
 
+Pitfalls after Praktomat-Update (Summer 2022)
+=================
+
+A note about `prlimit`
+----------
+  To make Praktomat compatible with newer Python versions, we introduce a dependency to binary executable program `prlimit`.
+
+    util-linux (containing prlimit)
+
+  If you have installed `util-linux` but the command `prlimit` remain unknown, your linux system may be too old.
+  On some circumstances you can build `prlimit` from scources ( more about this cf. https://github.com/KITPraktomatTeam/Praktomat/pull/342#issuecomment-1219445202 )
+
+
+ A note about SQLite3 and Praktomat's unit tests
+----------
+
+Unit tests which are testing Praktomat code are using `SQLite3` as database backend, depending on settings in `Praktomat/src/settings/test.py`.
+
+Since merge of feature boxplot-taskstatistic (cf https://github.com/KITPraktomatTeam/Praktomat/pull/345 ) at 2022-07-27
+your Python environment is using an too old `SQLite3` version, if tests fails with message:
+
+
+    django.db.utils.OperationalError: near "(": syntax error while migrating migrationfile taskstatistics.0001_initial_TaskStatisticsDBview
+
+
+In example, `SQLite3` version 3.16.2 dated to 2017-01-06 is much too old to handle the handwritten migration file `Praktomat/src/taskstatistics/migrations/0001_initial_TaskStatisticsDBview.py` correctly.
+
+That migration file uses *SQL window functions*, which were standardized in `SQL:2003` and covered by `SQLite3` with version 3.25.0 dated to 2018-09-15. But, because of some bugs inside `SQLite3`, you cannot use that first version supporting *SQL window functions*, too.
+
+Please use `SQLite3` Version 3.38.5 from 2022-05-06, which works for our needs.
+
+Check your Python - SQLite dependency on command line via:
+
+```bash
+$ python -c "import sqlite3; print(\"... uses pysqlite \" + sqlite3.version +\" with SQLite \" + sqlite3.sqlite_version);"
+
+... uses pysqlite 2.6.0 with SQLite 3.38.5
+```
+
+
+A note about Python and dependencies to Tcl/Tk
+----------
+
+ Since merge of feature boxplot-taskstatistic (cf https://github.com/KITPraktomatTeam/Praktomat/pull/345 )
+ users can have a look onto whisker-boxplot diagrams.
+ These diagrams where generated via `matplotlib`, which can be installed via `pip` and is listed in our `requirements` file.
+ `matplotlib` loads transitive `_tkinter` module, which you cannot install via `pip`, and which have dependencies to system libraries for Tcl/Tk. (There exists a package installable via `pip` named `tk` but that package has nothing to do with what you need...)
+
+ You can check, if your Python version and your system fullfill that dependencies in a shell:
+
+     python -c "import lzma" && python -c "import _tkinter" && python -c "import -c"matplotlib.pyplot as plt"
+
+ That commands should not produce any error messages.
+
+ If `lzma` couldn't be imported, then you need to install the system library and dev package:
+
+    apt-get install liblzma-dev lzma -y -q
+
+ If `_tkinter` failed to load, then perhaps on your system the `_tkinter` module can be installed for your Python on a separate way.
+ In example, on Debian you install the tkinter-support via system package manager:
+
+    apt install python-tk -y -q (that is for Python 2)
+    apt install python3-tk -y -q (that is for Python 3)
+
+ And of course you need tcl/tk on the system:
+
+    apt install tk tk-dev
+
+**Hint:** Praktomat's DejaGnuChecker uses `dejagnu`, which is written in `expect`. And `expect` is using `Tcl`.
+
+
+
 Prerequisites: 3rd-Party libraries and programms
 ============
 
   Praktomat requires some 3rd-Party libraries programs to run.
   On a Ubuntu/Debian System, these can be installed by installing the following packages:
 
-    util-linux
+    util-linux (containing prlimit)
+
     libpq-dev
     zlib1g-dev
     libmysqlclient-dev (or: default-libmysqlclient-dev)
@@ -110,8 +184,7 @@ Prerequisites: 3rd-Party libraries and programms
 
     r-base
 
-
-  If youre going to use Praktomat to check Haskell submissions, you will also require the packages:
+  If you're going to use Praktomat to check Haskell submissions, you will also require the packages:
 
     ghc libghc-test-framework-dev libghc-test-framework-hunit-dev libghc-test-framework-quickcheck2-dev
 
@@ -174,7 +247,7 @@ Praktomat/src/checker/scripts/junit.policy
 ```
 
 You can deactivate checkers and compilers in your local Praktomat instance,
-just comment them out in ``` src/checker/checker/__init__.py ``` and ``` src/checker/checker/__init__.py ```.
+just comment them out in ``` src/checker/checker/__init__.py ``` and ``` src/checker/compiler/__init__.py ```.
 Do not forget to create and run a django migration in that case.
 
 If you exchange Praktomat-Tasks (export and import) than the instance, which is used to import the task,
@@ -229,11 +302,11 @@ to run django unit tests
 ```bash
 cd Praktomat
 mkdir ../test-data/
-./src/manage-test.py test accounts attestation checker configuration solutions tasks hbrs_tests
+./src/manage-test.py test accounts attestation checker configuration solutions tasks taskstatistics hbrs_tests
 ```
 
 
-Deployment installation
+Deployment installation (using Apache and PostgreSQL)
 =======================
 
 Like for the development version, clone the Praktomat and install its dependencies:
@@ -250,7 +323,17 @@ Now create a database. Using postgres on Ubuntu, this might work for creating
 a database "praktomat_<PRAKTOMAT_ID>". Also edit `pg_hba.conf` to allow the access.
 Your database-system should be configured to UTF-8.
 
+To find your `pg_hba.conf` run on server commandline
+
 ```bash
+cd / && cat $( sudo -u postgres psql -c 'SHOW config_file' | grep '\.conf') | grep 'pg_hba.conf' && cd ~
+```
+Edit that file to your needs. (Per default only connections to localhost are configured.)
+
+```bash
+sudo systemctl enable postgresql
+sudo systemctl start postgresql
+sudo systemctl status postgresql
 sudo -u postgres createuser -DRS praktomat
 sudo -u postgres createdb --encoding UTF8 -O praktomat praktomat_<PRAKTOMAT_ID>
 ```
@@ -264,8 +347,8 @@ Create the upload directory, populate the database:
 ```bash
 cd Praktomat
 mkdir ../work-data/
-./Praktomat/src/manage-local.py collectstatic --noinput --link
-./Praktomat/src/manage-local.py migrate --noinput
+./src/manage-local.py collectstatic --noinput --link
+./src/manage-local.py migrate --noinput
 ```
 
 It should now be possible to start the deployment server with:
@@ -275,6 +358,29 @@ It should now be possible to start the deployment server with:
 
   If you want to deploy the project using mod_wsgi in apache you could use `documentation/apache_praktomat_wsgi.conf` as a starting point. Don't forget to install `mod_xsendfile` to serve uploaded files.
 
+```bash
+sudo systemctl enable apache2
+sudo a2enmod macro
+sudo a2enmod xsendfile
+sudo a2enmod ssl
+sudo a2ensite default-ssl
+```
+Change /etc/apache2/sites-enabled/default-ssl.conf by inserting information `ServerAdmin` and `ServerName` after line `<VirtualHost _default_:443>`
+
+```
+  ServerAdmin fill in valid e-mail-adress to reach servers admin.
+  ServerName  fill in FQDN of server (matching to HTTPS-Certificate.)
+```
+And copy the complete Apache-Macro `Praktomat` from `documentation/apache_praktomat_wsgi.conf`, with modification for your needs, just before
+the `<VirtualHost _default_:443>`-Entries. Use the `Praktomat` Apache-Macro inside the `<VirtualHost _default_:443>`-Entries like you can see in
+usage example `<VirtualHost *:80>` in `documentation/apache_praktomat_wsgi.conf`.
+
+Start `Apache`.
+```bash
+sudo systemctl start apache2
+sudo systemctl status apache2
+```
+
   And if your Praktomat running on apache should handle non-ASCII filenames correctly, than the easyest way is activating UTF-8 support inside apache.
   Debian runs Apache with the LANG=C locale by default, which breaks uploading files with special characters in their names at least when running with mod_wsgi.
   Activating a UTF-8 locale in /etc/apache2/envvars should resolve the issue. ( see https://code.djangoproject.com/ticket/6009#comment:18 )
@@ -326,6 +432,11 @@ submissions from the system:
    prefixed with `sudo -u tester --`. For this to work you need to add a user
    `tester` which is also a member of the default group of the user that runs
    the praktomat (usually `praktomat`).
+   ```bash
+   sudo adduser tester --disabled-password
+   sudo usermod tester -a -G praktomat
+   sudo usermod www-data -a -G praktomat
+   ```
  * With `USESAFEDOCKER = True`, external commands are prefixed with
    `safe-docker`, which you need to have installed. You can fetch it from
    http://github.com/nomeata/safe-docker
@@ -360,6 +471,18 @@ detection program [jPlag](https://jplag.ipd.kit.edu/). Do enable this support, y
  * Copy the resulting `.jar` file somewhere on the Praktomat server.
  * In the settings, set `JPLAGJAR = /full/path/to/jplag.jar`
 
+Automating the execution of checkers
+=================
+
+To automatically run all checkers for expired tasks where not all checkers are finished yet,
+there is a command called `runallcheckers`:
+```bash
+./Praktomat/src/manage-local.py runallcheckers
+```
+
+Use Cron (or something similar) to automate the execution of this command.
+Tutors can then automatically start attesting solutions without the need of
+an admin or trainer to manually run all checkers after a task expired.
 
 PhpBB integration
 =================

documentation/ExampleChecker.py

@@ -9,40 +9,40 @@
 
 class ExampleChecker(Checker):
 	""" This class is an minimalistic example on how to implement a new checker. """
-	
+
 	# Add fields to configure checker instances. You can use any of the Django fields. (See online documentation)
 	# The fields created, task, public, required and always will be inherited from the abstract base class Checker
 	configuration_field = models.CharField(max_length=100, blank=True, default="I'm a test.", help_text=_("This text will be displayed under Charfield in the admin."))
-	
+
 	def title(self):
 		""" Return the name of this instance of the checker. This will be shown to the user if the checker is public. """
-		return "Exampe Checker"
+		return "Example Checker"
 
 	@classmethod
 	def description():
 		""" Returns a description for this Checker which will be displayed in the admin interface. """
 		return "This class is an minimalistic example on how to implement a new checker."
 
 	#def requires(self):
-		#""" Returns the list of passed Checkers required by this checker. If the returned checker have not been passed this checker will fail automaticly """
+		#""" Returns the list of passed Checkers required by this checker. If the returned checker have not been passed this checker will fail automatically """
 		#from checker.compiler.Builder import Builder
-		#return [ Builder ]	
+		#return [ Builder ]
+
 
-
 	def run(self, env):
-		""" Do whatever this checker is suposed to do. """
-		
+		""" Do whatever this checker is supposed to do. """
+
 		# use env.tmpdir() to get the sandbox folder
-		# env.sources() contains the uploades files ala [(unicode_name, unicode_content)...] - all these files will exist in the sandbox folder
+		# env.sources() contains the uploaded files ala [(unicode_name, unicode_content)...] - all these files will exist in the sandbox folder
 		# env.user() returns the author of the solution
 
-		# to pass information to a checker which runs at a later time save it in env, but make sure the checkers will be executet in the right order.
+		# to pass information to a checker which runs at a later time save it in env, but make sure the checkers will be executed in the right order.
 
-		# if you need to to create or copy files use the methods from utilities.file_operations - these will alter the owner and rights of the files apropriately
-		# if you need to run external programs/scripts use execute(...) - this will enshure that it will be executed with a user with restricted rights - if so configured
+		# if you need to to create or copy files use the methods from utilities.file_operations - these will alter the owner and rights of the files appropriately
+		# if you need to run external programs/scripts use execute(...) - this will ensure that it will be executed with a user with restricted rights - if so configured
 
 		# Create a result
-		result = CheckerResult(checker=self)			
+		result = CheckerResult(checker=self)
 		# Set the massage for the user and if this checker has passed then return it.
 		result.set_log(self.configuration_field)
 		result.set_passed(True)
@@ -54,7 +54,7 @@ class ExampleCheckerInline(CheckerInline):
 	model = ExampleChecker
 
 
-# A more advanced example: By overwriting the form of the checkerinline the initial values of the inherited atributes can be overritten.
+# A more advanced example: By overwriting the form of the checkerinline the initial values of the inherited attributes can be overwritten.
 # An other example would be to validate the inputfields in the form. (See Django documentation)
 #class ExampleForm(AlwaysChangedModelForm):
 	#def __init__(self, **args):

src/checker/basemodels.py

@@ -252,7 +252,7 @@ def is_critical(self):
     def set_log(self, log,timed_out=False,truncated=False,oom_ed=False):
         """ Sets the log of the Checker run. timed_out and truncated indicated if appropriate error messages shall be appended  """
         if timed_out:
-            log = '<div class="error">Timeout occured!</div>' + log
+            log = '<div class="error">Timeout occurred!</div>' + log
         if truncated:
             log = '<div class="error">Output too long, truncated</div>' + log
         if oom_ed:
@@ -420,8 +420,10 @@ def run_checks(solution, env, run_all):
             else:
                 # make non passed result
                 # this as well as the dependency check should propably go into checker class
+                # TODO: Move code to checker class ?
                 result = checker.create_result(env)
-                result.set_log("Checker konnte nicht ausgeführt werden, da benötigte Checker nicht bestanden wurden.")
+                #result.set_log("Checker konnte nicht ausgeführt werden, da benötigte Checker nicht bestanden wurden.")
+                result.set_log("Checker failed to run because required checkers failed.")
                 result.set_passed(False)
 
             elapsed_time = time.time() - start_time