Merge branch 'main' of https://github.com/SPARC-FAIR-Codeathon/2024-t…

…eam-2
SPARC-FAIR-Codeathon · Aug 13, 2024 · 158b819 · 158b819
2 parents e7a4ff4 + ea040d3
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diff --git a/tutorials/tutorial_1_annotate_tools-workflow/example_create_sds.py b/tutorials/tutorial_1_annotate_tools-workflow/example_create_sds.py
@@ -0,0 +1,13 @@
+import sparc_flow
+
+new_tool = sparc_flow.Tool()
+
+# name of your tool
+new_tool.set_tool_name("tool_extract_indep_var_sds_test")
+
+# directory of where your tool was saved
+new_tool.set_tool_dir(".")
+
+# creates sds dataset in the first file path argument, whilst duplicating the contents of the
+# second file path argument in dataset > primary > tools
+new_tool.create_sds("../resources/tutorial_1_resources/mock_dataset", ".")
diff --git a/...tools-workflow/input_extract_dep_var.yaml → ...tools-workflow/input_extract_dep_var.yaml b/...tools-workflow/input_extract_dep_var.yaml → ...tools-workflow/input_extract_dep_var.yaml
@@ -1,4 +1,4 @@
 xFile:
   class: File
-  path: './outputs/time.txt'
+  path: './resources/time.txt'
 outputFile: 'voltage.txt'
diff --git a/...ols-workflow/input_extract_indep_var.yaml → ...ols-workflow/input_extract_indep_var.yaml b/...ols-workflow/input_extract_indep_var.yaml → ...ols-workflow/input_extract_indep_var.yaml
diff --git a/...nnotate_tools-workflow/resources/time.txt → ...nnotate_tools-workflow/resources/time.txt b/...nnotate_tools-workflow/resources/time.txt → ...nnotate_tools-workflow/resources/time.txt
diff --git a/...tate_tools-workflow/resources/voltage.txt → ...tate_tools-workflow/resources/voltage.txt b/...tate_tools-workflow/resources/voltage.txt → ...tate_tools-workflow/resources/voltage.txt
diff --git a/tutorials/tutorial_1_annotate_tools-workflow/tool_extract_dep_var_sds.cwl b/tutorials/tutorial_1_annotate_tools-workflow/tool_extract_dep_var_sds.cwl
@@ -0,0 +1,23 @@
+cwlVersion: v1.2
+class: CommandLineTool
+baseCommand: [python, ../tool_extract_dep_var_sds.py]
+inputs:
+  x_file:
+      type: File
+      inputBinding:
+          position: 1
+<<<<<<< HEAD:tutorials/tutorial_1_annotate_tools-workflow/tool_extract_dep_var_sds.cwl
+          prefix: --xFile
+  outputFile:
+    type: string
+    inputBinding:
+      position: 2
+      prefix: --outputFile
+=======
+          prefix: --x_file
+
+>>>>>>> 628e10f00e2ef94ec25584c0dd9f96d542a1b0fd:tutorials/tutorial_5_assemble_workflow/resources/tools/tool_extract_dep_var_sds.cwl
+outputs:
+  y_file:
+      type: File
+
diff --git a/...ools-workflow/tool_extract_dep_var_sds.py → ...ools-workflow/tool_extract_dep_var_sds.py b/...ools-workflow/tool_extract_dep_var_sds.py → ...ools-workflow/tool_extract_dep_var_sds.py
@@ -1,8 +1,8 @@
 """
 Created on 11/08/2024 (NZT time)
 
-This tool uses obtain dependent variable measurements from a SDS dataset at the
-corresponding independent variable measurements from tool_extract_indep_var_sds.py
+This tool extracts the dependent variable measurements from a SDS dataset at the
+corresponding independent variable measurements from tool_extract_indep_var_sds.py.
 
 Author: Max Dang Vu
 Organisation: Auckland Bioengineering Institute
@@ -18,11 +18,12 @@ def extract_dependent_variable_sds(xFile, outputFile):
     """
     This function extracts an array of the dependent variable measurements from a SDS dataset
     at the specified independent variable measurements from tool_extract_indep_var_sds.py.
+    The dependent variable measurements are also saved to a .txt file.
 
     :param xFile: independent variable quantity measurements from dataset extracted from a .txt file
     :type xFile: directory
-    :param outputFile: file path for saving dependent variable measurements from dataset
-    :type yFile: string
+    :param outputFile: Output filename for .txt file
+    :type outputFile: str
     """
 
     #   Load file
@@ -184,6 +185,7 @@ def extract_dependent_variable_sds(xFile, outputFile):
           -7.328525557563466932e-07,
           -8.203079358028723468e-07]]
 
+    #   Save dependent variable measurement to .txt files
     parent_dir = os.path.dirname(outputFile)
     os.makedirs(parent_dir, exist_ok=True)
     np.savetxt(outputFile, np.array(y).T, delimiter=',')

diff --git a/...s-workflow/tool_extract_indep_var_sds.cwl → ...s-workflow/tool_extract_indep_var_sds.cwl b/...s-workflow/tool_extract_indep_var_sds.cwl → ...s-workflow/tool_extract_indep_var_sds.cwl
diff --git a/...ls-workflow/tool_extract_indep_var_sds.py → ...ls-workflow/tool_extract_indep_var_sds.py b/...ls-workflow/tool_extract_indep_var_sds.py → ...ls-workflow/tool_extract_indep_var_sds.py
diff --git a/tutorials/tutorial_1_annotate_tools-workflow/tutorial_1_annotating_tools_models.ipynb b/tutorials/tutorial_1_annotate_tools-workflow/tutorial_1_annotating_tools_models.ipynb
diff --git a/...utorial_creating_knowledge_graph/.gitkeep → ...orial_2_creating_knowledge_graph/.gitkeep b/...utorial_creating_knowledge_graph/.gitkeep → ...orial_2_creating_knowledge_graph/.gitkeep
diff --git a/...tutorial_2_creating_knowledge_graph.ipynb → ...tutorial_2_creating_knowledge_graph.ipynb b/...tutorial_2_creating_knowledge_graph.ipynb → ...tutorial_2_creating_knowledge_graph.ipynb
diff --git a/...al_assemble_workflow/assemble_workflow.py → ..._5_assemble_workflow/assemble_workflow.py b/...al_assemble_workflow/assemble_workflow.py → ..._5_assemble_workflow/assemble_workflow.py
diff --git a/...emble_workflow/resources/kg_example_1.owl → ...emble_workflow/resources/kg_example_1.owl b/...emble_workflow/resources/kg_example_1.owl → ...emble_workflow/resources/kg_example_1.owl
diff --git a/...emble_workflow/resources/kg_example_2.owl → ...emble_workflow/resources/kg_example_2.owl b/...emble_workflow/resources/kg_example_2.owl → ...emble_workflow/resources/kg_example_2.owl
diff --git a/...ources/tools/tool_extract_dep_var_sds.cwl → ...ources/tools/tool_extract_dep_var_sds.cwl b/...ources/tools/tool_extract_dep_var_sds.cwl → ...ources/tools/tool_extract_dep_var_sds.cwl
diff --git a/...urces/tools/tool_extract_dep_var_sds.json → ...urces/tools/tool_extract_dep_var_sds.json b/...urces/tools/tool_extract_dep_var_sds.json → ...urces/tools/tool_extract_dep_var_sds.json
diff --git a/...rces/tools/tool_extract_indep_var_sds.cwl → ...rces/tools/tool_extract_indep_var_sds.cwl b/...rces/tools/tool_extract_indep_var_sds.cwl → ...rces/tools/tool_extract_indep_var_sds.cwl
diff --git a/...ces/tools/tool_extract_indep_var_sds.json → ...ces/tools/tool_extract_indep_var_sds.json b/...ces/tools/tool_extract_indep_var_sds.json → ...ces/tools/tool_extract_indep_var_sds.json
diff --git a/...rkflow/tutorial_5_assemble_workflow.ipynb → ...rkflow/tutorial_5_assemble_workflow.ipynb b/...rkflow/tutorial_5_assemble_workflow.ipynb → ...rkflow/tutorial_5_assemble_workflow.ipynb
diff --git a/...un_workflow/tutorial_6_run_workflow.ipynb → ...un_workflow/tutorial_6_run_workflow.ipynb b/...un_workflow/tutorial_6_run_workflow.ipynb → ...un_workflow/tutorial_6_run_workflow.ipynb
diff --git a/tutorials/tutorial_annotate_tools-workflow/tool_extract_dep_var_sds.cwl b/tutorials/tutorial_annotate_tools-workflow/tool_extract_dep_var_sds.cwl