Merge pull request #60 from keara-soloway/chapbook-demo

add: new Writer and galaxy tool for Chapbook demo
CHESSComputing · Jun 28, 2023 · d90f34d · d90f34d
2 parents ee1df7d + 743573b
commit d90f34d
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diff --git a/CHAP/common/__init__.py b/CHAP/common/__init__.py
@@ -28,6 +28,7 @@
 )
 from CHAP.common.writer import (
     ExtractArchiveWriter,
+    MatplotlibFigureWriter,
     NexusWriter,
     YAMLWriter,
     TXTWriter,

diff --git a/CHAP/common/writer.py b/CHAP/common/writer.py
@@ -37,6 +37,37 @@ def write(self, data, filename):
         return data
 
 
+class MatplotlibFigureWriter(Writer):
+    """Writer for saving matplotlib figures to image files."""
+    def write(self, data, filename, savefig_kw={}, force_overwrite=False):
+        """Write the matplotlib.fgure.Figure contained in `data` to
+        the filename provided.
+
+        :param data: input containing a matplotlib figure
+        :type data: CHAP.pipeline.PipelineData
+        :param filename: name of the file to write to.
+        :param savefig_kw: keyword args to pass to
+            matplotlib.figure.Figure.savefig, defaults to {}
+        :type savefig_kw: dict, optional
+        :param force_overwrite: flag to allow data in `filename` to be
+            overwritten, if it already exists.
+        :return: the original input data
+        """
+
+        if os.path.isfile(filename) and not force_overwrite:
+            raise FileExistsError(f'{filename} already exists')
+
+        figure = self.unwrap_pipelinedata(data)
+
+        from matplotlib.figure import Figure
+        if not isinstance(figure, Figure):
+            raise TypeError('Cannot write object of type'
+                            f'{type(figure)} as a matplotlib Figure.')
+
+        figure.savefig(filename, **savefig_kw)
+        return figure
+
+
 class NexusWriter(Writer):
     """Writer for NeXus files from `NXobject`-s"""
     def write(self, data, filename, force_overwrite=False):

diff --git a/galaxy-tools/chapbook_demo/chapbook_demo.xml b/galaxy-tools/chapbook_demo/chapbook_demo.xml
@@ -0,0 +1,45 @@
+<tool id="CHAP_chapbook_demo" name="CHAPbook" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" python_template_version="@PYTHON_TEMPLATE_VERSION@" profile="@PROFILE@">
+  <macros>
+    <import>../macros.xml</import>
+  </macros>
+  <requirements>
+    <expand macro="chap-requirement" />
+    <requirement type="package" version="1.0.1">nexusformat</requirement>
+    <requirement type="package" version="2023.3.0">pyfai</requirement>
+    <requirement type="package" version="1.10.7">pydantic</requirement>
+  </requirements>
+  <command detect_errors="exit_code"><![CDATA[
+      pip --exists-action i install certif-pyspec==1.5.3 &&
+      cd '$indir' &&
+      CHAP --config '$config'
+]]></command>
+  <environment_variables>
+    <environment_variable name="PYTHONPATH">/home/chess_chapaas/chess/chap/</environment_variable>
+  </environment_variables>
+  <inputs>
+      <param type="data" name="config" format="yaml" label="Pipeline Configuration File" />
+      <param type="text" name="indir" label="Input Directory" />
+  </inputs>
+  <outputs>
+      <data name="data" format="nex" label="Reduced data"/>
+      <data name="plot" format="png" label="Plot"/>
+  </outputs>
+  <tests>
+      <test>
+          <param name="config" value="config.yaml"/>
+	  <param name="indir" value="/tmp/"/>
+      </test>
+  </tests>
+  <help><![CDATA[
+      CHESS Analysis Pipeline (CHAP):
+
+      To run it on command line you'll use:
+      CHAP --config CONFIG
+
+      To run it within galaxy you'll only need to upload your
+      required configuration pipeline and necessary data.
+  ]]></help>
+  <citations>
+    <expand macro="chap-citation" />
+  </citations>
+</tool>