Merge branch 'develop' into develop

.github/workflows/testing-all-oses.yml

@@ -29,13 +29,13 @@ jobs:
           sed -e "s/.*://" > requirements.tmp.txt
         cat requirements.d/development.txt >> requirements.tmp.txt
         echo "pytest-randomly" >> requirements.tmp.txt
-        sed -e '/^$/d' -e '/^#.*$/d' requirements.tmp.txt > requirements.txt
+        sed -e '/^$/d' -e '/^#.*$/d' -e 's/\s*# \[not win\]$//' requirements.tmp.txt > requirements.txt
         rm requirements.tmp.txt
         cat requirements.txt
     - name: Get current year and calendar week
       id: year-and-week
       run: echo "year-and-week=$(date +%Y-%V)" >> "$GITHUB_OUTPUT"
-    - uses: mamba-org/setup-micromamba@v1
+    - uses: mamba-org/setup-micromamba@v2
       with:
         environment-file: requirements.txt
         environment-name: ci
@@ -44,8 +44,4 @@ jobs:
         cache-environment-key: environment-${{ steps.year-and-week.outputs.year-and-week }}
     - name: Run tests
       timeout-minutes: 40
-      # The ignored files can somehow cause the test suite to timeout.
-      # I have no idea yet on why this happens and how to fix it.
-      # Even a module level skip is not enough, they need to be completely ignored.
-      # TODO: fix those tests and drop the ignores
       run: micromamba run -n ci env QT_QPA_PLATFORM=offscreen pytest -v -n logical --durations=20 --cov=mslib tests

CHANGES.rst

@@ -1,6 +1,14 @@
 Changelog
 =========
 
+Version 9.3.0
+~~~~~~~~~~~~~
+Bug fix release and minor enhancements:
+We removed unused modules from the mscolab saml2 setup.
+
+All changes:
+https://github.com/Open-MSS/MSS/milestone/108?closed=1
+
 Version 9.2.0
 ~~~~~~~~~~~~~
 

CONTRIBUTING.md

@@ -1,17 +1,8 @@
 # Contributing
 
-When contributing to this repository, please first discuss the change you wish to make via issue,
-email, or any other method with the owners of this repository before making a change.
+We'd love for your contribution to the Mission Support System (MSS) to help make it better!
+We want contributing to MSS to be fun and educational for everyone.
+All kind of contributions are welcome, including issue descriptions and new documents,
+as well as updates and improvements and more.
 
-Please note we have a code of conduct, please follow it in all your interactions with the project.
-
-## Pull Request Process
-
-1. Ensure any install or build dependencies are removed before the end of the layer when doing a
-   build.
-2. Update the README.md with details of changes to the interface, this includes new environment
-   variables, exposed ports, useful file locations and container parameters.
-3. Increase the version numbers in any examples files and the README.md to the new version that this
-   Pull Request would represent. The versioning scheme we use is [SemVer](http://semver.org/).
-4. You may merge the Pull Request in once you have the sign-off of two other developers, or if you
-   do not have permission to do that, you may request the second reviewer to merge it for you.
+Our **[contributing](https://open-mss.github.io/contributing/)** guidelines provide instructions on how to get involved.

README.md

@@ -114,3 +114,11 @@ in the same directory as this README file.
    When using this software, please be so kind and acknowledge its use by
    citing the above mentioned reference documentation in publications,
    presentations, reports, etc. that you create. Thank you very much.
+
+Acknowledgements
+----------------
+
+We are very grateful for your continuing support for MSS!
+
+See our [Contributors page](https://mss.readthedocs.io/en/stable/authors.html) for a list of authors. See also our info on [funding](
+https://mss.readthedocs.io/en/stable/funding.html).

docs/development.rst

@@ -533,8 +533,27 @@ Publish on Conda Forge
 Google Summer of Code(TM)
 -------------------------
 
-MSS takes part in Google Summer of Code
-as a sub-organization of Python Software Foundation(PSF).
+MSS takes part in `Google Summer of Code <https://summerofcode.withgoogle.com/>`_
+as a `sub-organization of Python Software Foundation (PSF) <https://python-gsoc.org/>`_.
+
+
+GSoC'24 Projects
+................
+
+- `Aryan Gupta: (MSS) msui: Improve MSUI : GSoC 2024 <https://github.com/Open-MSS/MSS/wiki/Aryan-Gupta:-(MSS)-msui:-Improve-MSUI-:-GSOC2024>`_
+- `Preetam Sundar Das: MISSION SUPPORT SYSTEM(MSS): GUI FOR AUTOMATED PLOTTING : GSOC 2024 <https://github.com/Open-MSS/MSS/wiki/Preetam-Sundar-Das:-MISSION-SUPPORT-SYSTEM(MSS):-GUI-FOR-AUTOMATED-PLOTTING-:-GSOC2024>`_
+- `Rohit Prasad: Mission Support System: Improve multiple flightpath docking widget : GSOC 2024 <https://github.com/Open-MSS/MSS/wiki/Rohit-Prasad:-Mission-Support-System:-Improve-multiple-flightpath-docking-widget-:-GSOC2024>`_
+
+
+GSoC'23 Projects
+................
+
+- `Shubh Gaur: Mission Support System(MSS) : UI-improvements : GSOC 2023 <https://github.com/Open-MSS/MSS/wiki/UI%E2%80%90improvements-GSOC-2023>`_
+
+- `Nilupul Manodya: Mission Support System : Implement a SAML 2.0 service provider (SP) into mscolab : GSOC 2023 <https://github.com/Open-MSS/MSS/wiki/Implement-a-SAML-2.0-service-provider-(SP)-into-mscolab-:-GSOC-2023>`_
+
+
+
 
 GSoC'22 Projects
 ................

docs/funding.rst

@@ -0,0 +1,112 @@
+Funding and Support
+===================
+
+The Mission Support System (MSS) kindly acknowledges funding and support from the following sources:
+
+Conda-Forge
+-----------
+
+.. figure:: https://conda-forge.org/img/logo.png
+   :alt: Logo conda-forge
+   :target: https://conda-forge.org/
+   :width: 300
+
+.. raw:: html
+
+   <div style="height:20px;"></div>
+
+We kindly acknowledge support by the open-source `conda-forge community <https://conda-forge.org/docs/>`_
+
+
+Google Summer of Code
+---------------------
+
+.. figure:: https://libertem.github.io/images/GSoC-icon-192.png
+   :alt: Logo Google Summer of Code
+   :target: https://summerofcode.withgoogle.com/
+   :width: 300
+
+.. raw:: html
+
+   <div style="height:20px;"></div>
+
+We kindly acknowledge funding from `Google Summer of Code 2019, 2020, 2021, 2022, 2023 and 2024 <https://summerofcode.withgoogle.com/>`_ under the `umbrella of the Python Software Foundation <https://python-gsoc.org/>`_.
+
+
+
+DFG, German Research Foundation – UN 311/3-1
+--------------------------------------------
+
+.. figure:: https://www.dfg.de/resource/image/196784/16x9/858/483/500dfa2178773cc68721440c14d86911/B385802C0C046A4BD6F0138CDC3478F0/logo-negativ-267.png
+   :alt: Logo DFG, German Research Foundation
+   :target: https://www.dfg.de/en
+   :width: 300
+
+.. raw:: html
+
+   <div style="height:20px;"></div>
+
+Atmospheric research with HALO is supported by the Priority Programme SPP 1294 of the Deutsche Forschungsgemeinschaft (DFG).
+In 2021 we were funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) – UN 311/3-1.
+
+
+
+COVERALLS
+---------
+
+.. figure:: https://s3.amazonaws.com/assets.coveralls.io/assets/coveralls_logo-blue_wshad.png
+   :alt: Logo Coveralls
+   :target: https://coveralls.io/
+   :width: 300
+
+.. raw:: html
+
+   <div style="height:20px;"></div>
+
+We kindly acknowledge support by the COVERALLS company for `open source projects <https://coveralls.io/sign-up>`_.
+
+
+
+Dockerhub
+---------
+
+.. figure:: https://www.docker.com/wp-content/uploads/2023/08/logo-guide-logos-1.svg
+   :alt: Logo Dockerhub
+   :target: https://www.docker.com
+   :width: 300
+
+.. raw:: html
+
+   <div style="height:20px;"></div>
+
+We kindly acknowledge support by the docker company for adding our `application <https://hub.docker.com/u/openmss>`_ to the `Docker-Sponsored Open Source Program <https://www.docker.com/community/open-source/application/>`_.
+
+
+GitHub
+------
+
+.. figure:: https://github.githubassets.com/assets/GitHub-Mark-ea2971cee799.png
+   :alt: Logo GitHub
+   :target: https://github.com/
+   :width: 300
+
+.. raw:: html
+
+   <div style="height:20px;"></div>
+
+We kindly acknowledge support by GitHub for `open-source projects <https://github.com/open-source>`_.
+
+
+
+Forschungszentrum Jülich, `Stratosphere (ICE-4) <https://www.fz-juelich.de/en/ice/ice-4>`_
+------------------------------------------------------------------------------------------
+
+.. figure:: https://www.fz-juelich.de/en/ibg/ibg-1/images/research_groups/general/fz-juelich-logo/@@images/7ca073aa-be02-4577-a1f4-49cf2462a13e.jpeg
+   :target: https://www.fz-juelich.de/er-c/EN/Home/home_node.html
+   :width: 300
+
+.. raw:: html
+
+   <div style="height:20px;"></div>
+
+Forschungszentrum Jülich is supporting MSS with funding for personnel, access to its infrastructure and administrative support.

docs/index.rst

@@ -40,6 +40,7 @@ Topics
    authors
    tutorial
    gallery/index
+   funding
 
 
 Indices and tables

mslib/mscolab/models.py

@@ -216,5 +216,7 @@ def __init__(self, op_id, u_id, commit_hash, version_name=None, comment=None):
         self.op_id = int(op_id)
         self.u_id = int(u_id)
         self.commit_hash = str(commit_hash)
-        self.version_name = str(version_name)
-        self.comment = str(comment)
+        if version_name is not None:
+            self.version_name = str(version_name)
+        if comment is not None:
+            self.comment = str(comment)

mslib/msui/flighttrack.py

@@ -40,7 +40,8 @@
 
 import fs
 import xml.dom.minidom
-import xml.parsers.expat
+import defusedxml.minidom
+from defusedxml import DefusedXmlException
 
 from PyQt5 import QtGui, QtCore, QtWidgets
 
@@ -56,7 +57,8 @@
 from mslib.msui.performance_settings import DEFAULT_PERFORMANCE
 
 from mslib.utils import writexml, LOGGER
-xml.dom.minidom.Element.writexml = writexml
+xml.dom.minidom.Element.writexml = writexml  # nosec, we take care of writing correct XML
+
 # Constants for identifying the table columns when the WaypointsTableModel is
 # used with a QTableWidget.
 LOCATION, LAT, LON, FLIGHTLEVEL, PRESSURE = list(range(5))
@@ -98,8 +100,8 @@ def seconds_to_string(seconds):
 
 def load_from_xml_data(xml_content, name="Flight track"):
     try:
-        doc = xml.dom.minidom.parseString(xml_content)
-    except xml.parsers.expat.ExpatError as ex:
+        doc = defusedxml.minidom.parseString(xml_content)
+    except DefusedXmlException as ex:
         raise SyntaxError(str(ex))
 
     ft_el = doc.getElementsByTagName("FlightTrack")[0]
@@ -632,7 +634,7 @@ def save_to_ftml(self, filename=None):
         file_dir.close()
 
     def get_xml_doc(self):
-        doc = xml.dom.minidom.Document()
+        doc = xml.dom.minidom.Document()  # nosec, we take care of writing correct XML
         ft_el = doc.createElement("FlightTrack")
         ft_el.setAttribute("version", __version__)
         doc.appendChild(ft_el)

mslib/msui/kmloverlay_dockwidget.py

@@ -602,8 +602,13 @@ def merge_file(self):
                     for index in checked_files:  # index is the indices of checked files
                         _dirname, _name = os.path.split(self.listWidget.item(index).text())
                         _fs = fs.open_fs(_dirname)
+                        # Create a secure XML Parser
+                        secure_parser = et.XMLParser(resolve_entities=False, no_network=True)
+                        # resolve_entities False, prevents entity expansion
+                        # no_network, prevents automatically loading remote documents
+                        # https://gist.github.com/jack-om/f2c762f399e6ee652f05320921ece4c9
                         with _fs.open(_name, 'r') as kmlf:
-                            tree = et.parse(kmlf)  # parse kml file
+                            tree = et.parse(kmlf, parser=secure_parser)  # nosec, parse using the secured parser
                             root = tree.getroot()  # get the root of the file
                             self.remove_ns(root)  # removes <kml> and </kml>
                             element.append(copy.deepcopy(root[0]))

mslib/msui/mpl_map.py

@@ -151,8 +151,8 @@ def __init__(self, identifier=None, CRS=None, BBOX_UNITS=None, OPERATION_NAME=No
         # Print project name and CRS identifier into figure.
         if not hasattr(self, "_info_text"):
             self._info_text = self.ax.figure.text(0, 0, "")
-            self._infos = [None] * 4
-        self.update_info_text(name=self.operation_name, crs=self.crs)
+            self._infos = [None] * 3
+        self.update_info_text(crs=self.crs)
 
         if self.appearance["draw_graticule"]:
             pass
@@ -170,15 +170,13 @@ def __init__(self, identifier=None, CRS=None, BBOX_UNITS=None, OPERATION_NAME=No
             self.airspaces = None
             self.airspacetext = None
 
-    def update_info_text(self, openaip=None, ourairports=None, name=None, crs=None):
+    def update_info_text(self, openaip=None, ourairports=None, crs=None):
         if openaip is not None:
             self._infos[0] = openaip
         if ourairports is not None:
             self._infos[1] = ourairports
-        if name is not None:
-            self._infos[2] = name
         if crs is not None:
-            self._infos[3] = crs
+            self._infos[2] = crs
         self._info_text.set_text(
             "\n".join([_i for _i in self._infos if _i]))  # both None and ""
 

mslib/msui/mpl_qtwidget.py

@@ -113,6 +113,7 @@ def __init__(self, fig=None, ax=None, settings_tag=None, settings=None):
 
     def draw_metadata(self, title="", init_time=None, valid_time=None,
                       level=None, style=None):
+
         if style:
             title += f" ({style})"
         if level:
@@ -733,7 +734,9 @@ def draw_legend(self, img):
             raise NotImplementedError
 
     def draw_image(self, xmls, colors=None, scales=None):
+        title = self.fig._suptitle.get_text()
         self.clear_figure()
+        self.fig.suptitle(title, x=0.95, ha='right')
         offset = 40
         self.ax.patch.set_visible(False)
 

mslib/msui/mscolab_version_history.py

@@ -30,10 +30,10 @@
 
 import requests
 from urllib.parse import urljoin, urlencode
+from PyQt5 import QtCore, QtWidgets, QtGui
 
 from mslib.utils.verify_user_token import verify_user_token
 from mslib.msui.flighttrack import WaypointsTableModel
-from PyQt5 import QtCore, QtWidgets, QtGui
 from mslib.msui.qt5 import ui_mscolab_version_history as ui
 from mslib.utils.qt import show_popup
 from mslib.utils.config import config_loader
@@ -71,7 +71,7 @@ def __init__(self, token, op_id, user, operation_name, conn, parent=None,
         self.mscolab_server_url = mscolab_server_url
 
         # Event handlers
-        self.refreshBtn.clicked.connect(self.handle_refresh)
+        self.conn.signal_reload.connect(self.handle_refresh)
         self.checkoutBtn.clicked.connect(self.handle_undo)
         self.nameVersionBtn.clicked.connect(self.handle_named_version)
         self.deleteVersionNameBtn.clicked.connect(self.handle_delete_version_name)
@@ -134,7 +134,7 @@ def load_all_changes(self):
                 "op_id": self.op_id
             }
             named_version_only = False
-            if self.versionFilterCB.currentIndex() == 0:
+            if self.versionFilterCB.currentIndex() == 1:
                 named_version_only = True
             query_string = urlencode({"named_version": named_version_only})
             url_path = f'get_all_changes?{query_string}'