grnsight 5.0.0 → 5.1.0

package/documents/developer_documents/testing_script_generator/edgeFeatures.json

@@ -1,178 +0,0 @@
-[
-    {
-        "id": "e1",
-        "title": "Dropdown Menu: Edge -> Enable Edge Coloring Based on Weight Value",
-        "text": "GRNsight should",
-        "options": {
-            "Check": "enable edge coloring and set the sidebar menu 'Enable Edge Coloring' to checked",
-            "Uncheck": "disable edge coloring and set the sidebar menu 'Enable Edge Coloring' to unchecked"
-        },
-        "included": false,
-        "availability": {
-            "NoGraphLoaded": true,
-            "WeightedGraphLoaded": true,
-            "UnWeightedGraphLoaded": true
-        }
-    },
-    {
-        "id": "e2",
-        "title": "Sidebar Menu: Enable Edge Coloring",
-        "text": "GRNsight should",
-        "options": {
-            "Check": "enable edge coloring and set the dropdown menu 'Enable Edge Coloring Based on Weight Value' to checked",
-            "Uncheck": "disable edge coloring and set the dropdown menu 'Enable Edge Coloring Based on Weight Value' to unchecked"
-        },
-        "included": false,
-        "availability": {
-            "NoGraphLoaded": true,
-            "WeightedGraphLoaded": true,
-            "UnWeightedGraphLoaded": true
-        }
-    },
-    {
-        "id": "e3",
-        "title": "Sidebar Menu: Hide/Show Edge Weights",
-        "text": "",
-        "options": {
-            "Select \"Show With Mouse Over\"": "A single edge weight should display when user mouses over a single edge.",
-            "Select \"Always Show Edge Weights\"": "All edge weights should always be visible.",
-            "Select \"Never Show Edge Weights\"": "No edge weights should be visible."
-        },
-        "included": false,
-        "availability": {
-            "NoGraphLoaded": false,
-            "WeightedGraphLoaded": true,
-            "UnWeightedGraphLoaded": false
-        }
-    },
-    {
-        "id": "e4",
-        "title": "Dropdown Menu: Edge -> Hide/Show Edge Weights",
-        "text": "",
-        "options": {
-            "Check \"Show With Mouse Over\"": "A single edge weight should display when user mouses over a single edge.",
-            "Check \"Always Show Edge Weights\"": "All edge weights should always be visible.",
-            "Check \"Never Show Edge Weights\"": "No edge weights should be visible."
-        },
-        "included": false,
-        "availability": {
-            "NoGraphLoaded": false,
-            "WeightedGraphLoaded": true,
-            "UnWeightedGraphLoaded": false
-        }
-    },
-    {
-        "id": "e5",
-        "title": "Sidebar Menu: Edge Weight Normalization Factor",
-        "text": "The graph should",
-        "options": {
-            "Enter a Number in the Box and Click \"Set Factor\" button": "reload with the new normalization factor applied to its edge weight thicknesses"
-        },
-        "included": false,
-        "availability": {
-            "NoGraphLoaded": false,
-            "WeightedGraphLoaded": true,
-            "UnWeightedGraphLoaded": false
-        }
-    },
-    {
-        "id": "e6",
-        "title": "Dropdown Menu: Edge -> Edge Weight Normalization Factor",
-        "text": "The graph should",
-        "options": {
-            "Enter a Number in the Box and Press Enter": "reload with the new normalization factor applied to its edge weight thicknesses"
-        },
-        "included": false,
-        "availability": {
-            "NoGraphLoaded": false,
-            "WeightedGraphLoaded": true,
-            "UnWeightedGraphLoaded": false
-        }
-    },
-    {
-        "id": "e7",
-        "title": "Sidebar Menu: Reset Factor Button",
-        "text": "The graph should",
-        "options": {
-            "Click": "reset to its default normalization factor and reload the graph"
-        },
-        "included": false,
-        "availability": {
-            "NoGraphLoaded": false,
-            "WeightedGraphLoaded": true,
-            "UnWeightedGraphLoaded": false
-        }
-    },
-    {
-        "id": "e8",
-        "title": "Dropdown Menu: Edge -> Reset Edge Weight Normalization",
-        "text": "The graph should",
-        "options": {
-            "Click": "reset to its default normalization factor and reload the graph"
-        },
-        "included": false,
-        "availability": {
-            "NoGraphLoaded": false,
-            "WeightedGraphLoaded": true,
-            "UnWeightedGraphLoaded": false
-        }
-    },
-    {
-        "id": "e9",
-        "title": "Sidebar Menu: Gray Threshold Slider",
-        "text": "The graph should reload, with",
-        "options": {
-            "Change the Grey Threshold Value": "edges that fall below the threshold value colored gray"
-        },
-        "included": false,
-        "availability": {
-            "NoGraphLoaded": false,
-            "WeightedGraphLoaded": true,
-            "UnWeightedGraphLoaded": false
-        }
-    },
-    {
-        "id": "e10",
-        "title": "Dropdown Menu: Edge -> Gray Threshold Input Box",
-        "text": "The graph should reload, with",
-        "options": {
-            "Change the Grey Threshold Value and Press Enter": "edges that fall below the threshold value colored gray"
-        },
-        "included": false,
-        "availability": {
-            "NoGraphLoaded": false,
-            "WeightedGraphLoaded": true,
-            "UnWeightedGraphLoaded": false
-        }
-    },
-    {
-        "id": "e11",
-        "title": "Sidebar Menu: Show Grey Edges as Dashed Checkbox",
-        "text": "The graph should",
-        "options": {
-            "Uncheck": "show gray lines as solid lines",
-            "Check": "show gray lines as dashed lines"
-        },
-        "included": false,
-        "availability": {
-            "NoGraphLoaded": false,
-            "WeightedGraphLoaded": true,
-            "UnWeightedGraphLoaded": false
-        }
-    },
-    {
-        "id": "e12",
-        "title": "Dropdown Menu: Edge -> Show Grey Edges as Dashed",
-        "text": "The graph should",
-        "options": {
-            "Uncheck": "show gray lines as solid lines",
-            "Check": "show gray lines as dashed lines"
-        },
-        "included": false,
-        "availability": {
-            "NoGraphLoaded": false,
-            "WeightedGraphLoaded": true,
-            "UnWeightedGraphLoaded": false
-        }
-    }
-]

package/documents/developer_documents/testing_script_generator/fileFeatures.json

@@ -1,100 +0,0 @@
-[
-    {
-        "id":"f1",
-        "title": "Dropdown Menu: Help",
-        "text": "GRNsight should",
-        "options": {
-            "Select \"Getting Started\"": "open the GRNsight documentation page",
-            "Select \"GRNsight Wiki\"": "open the GRNsight wiki page",
-            "Select \"About GRNsight\"": "open the About GRNsight page"
-        },
-        "included": false,
-        "availability": {
-            "NoGraphLoaded": true,
-            "WeightedGraphLoaded": true,
-            "UnWeightedGraphLoaded": true
-        }
-    },
-    {
-        "id":"f2",
-        "title": "Load Graph",
-        "text": "GRNsight should",
-        "options": {
-            "None": "have no graph in the viewport",
-            "Dropdown Menu: File -> Open File": "lay out a network graph from the Excel, SIF, or GraphML network if there are no errors in the file",
-            "Dropdown Menu: Demo -> Demo #1": "lay out an unweighted network graph from Demo #1",
-            "Dropdown Menu: Demo -> Demo #2": "lay out a weighted network graph from Demo #2",
-            "Dropdown Menu: Demo -> Demo #3": "lay out an unweighted network graph from Demo #3",
-            "Dropdown Menu: Demo -> Demo #4": "lay out a weighted network graph from Demo #4"
-        },
-        "included": false,
-        "availability": {
-            "NoGraphLoaded": true,
-            "WeightedGraphLoaded": true,
-            "UnWeightedGraphLoaded": true
-        }
-    },
-    {
-        "id":"f3",
-        "title": "Dropdown Menu: File -> Reload",
-        "text": "The graph should",
-        "options": {
-            "Select": "center, zoom to 100%, and reapply the force graph parameters"
-        },
-        "included": false,
-        "availability": {
-            "NoGraphLoaded": false,
-            "WeightedGraphLoaded": true,
-            "UnWeightedGraphLoaded": true
-        }
-    },
-    {
-        "id":"f4",
-        "title": "Dropdown Menu: File -> Export Data",
-        "text": "GRNsight should",
-        "options": {
-            "Select \"To Unweighted SIF\"": "export an unweighted SIF file from the graph currently loaded",
-            "Select \"To Weighted SIF\"": "export a weighted SIF file from the graph currently loaded",
-            "Select \"To Unweighted GraphML\"": "export an unweighted GraphML file from the graph currently loaded",
-            "Select \"To Weighted GraphML\"": "export a weighted GraphML file from the graph currently loaded",
-            "Select \"To Unweighted Excel\"": "export an unweighted Excel file from the graph currently loaded",
-            "Select \"To Weighted Excel\"": "export a weighted Excel file from the graph currently loaded"
-        },
-        "included": false,
-        "availability": {
-            "NoGraphLoaded": false,
-            "WeightedGraphLoaded": true,
-            "UnWeightedGraphLoaded": true
-        }
-    },
-    {
-        "id":"f5",
-        "title": "Dropdown Menu: File -> Export Image",
-        "text": "GRNsight should",
-        "options": {
-            "Select \"To PNG\"": "export a PNG image from the graph currently loaded",
-            "Select \"To SVG\"": "export a SVG image from the graph currently loaded",
-            "Select \"To PDF\"": "export a PDF file from the graph currently loaded"
-        },
-        "included": false,
-        "availability": {
-            "NoGraphLoaded": false,
-            "WeightedGraphLoaded": true,
-            "UnWeightedGraphLoaded": true
-        }
-    },
-    {
-        "id":"f6",
-        "title": "Dropdown Menu: File -> Print",
-        "text": "GRNsight should",
-        "options": {
-            "Select": "open the Print Dialogue Box"
-        },
-        "included": false,
-        "availability": {
-            "NoGraphLoaded": false,
-            "WeightedGraphLoaded": true,
-            "UnWeightedGraphLoaded": true
-        }
-    }
-]

package/documents/developer_documents/testing_script_generator/layoutFeatures.json

@@ -1,166 +0,0 @@
-[
-    {
-        "id":"l1",
-        "title": "Sidebar Menu: Grid Layout",
-        "text": "The graph should",
-        "options": {
-            "Keep at Default": "default to force graph layout",
-            "Click Grid Layout Button": "change to grid layout",
-            "Click Force Graph Layout Button": "change to force graph layout"
-        },
-        "included": true,
-        "availability": {
-            "NoGraphLoaded": true,
-            "WeightedGraphLoaded": true,
-            "UnWeightedGraphLoaded": true
-        }
-    },
-    {
-        "id":"l2",
-        "title": "Dropdown Menu: Layout -> Graph Options",
-        "text": "The graph should",
-        "options": {
-            "Keep at Default": "be in force graph layout by default",
-            "Grid Layout": "apply grid layout",
-            "Force Graph": "apply force graph layout"
-        },
-        "included": false,
-        "availability": {
-            "NoGraphLoaded": false,
-            "WeightedGraphLoaded": true,
-            "UnWeightedGraphLoaded": true
-        }
-    },
-    {
-        "id":"l3",
-        "title": "Dropdown Menu: Layout -> Lock Force Graph Parameters",
-        "text": "The Force Graph Parameter sliders should",
-        "options": {
-            "Check \"Lock Force Graph Parameters\"": "be disabled.",
-            "Uncheck \"Lock Force Graph Parameters\"": "be enabled."
-        },
-        "included": false,
-        "availability": {
-            "NoGraphLoaded": false,
-            "WeightedGraphLoaded": true,
-            "UnWeightedGraphLoaded": true
-        }
-    },
-    {
-        "id":"l4",
-        "title": "Dropdown Menu: Layout -> Reset Force Graph Parameters",
-        "text": "The force graph parameters should",
-        "options": {
-            "Click \"Reset Force Graph Parameters\"": "revert to the default values, if Lock Force Graph Parameters is unchecked"
-        },
-        "included": false,
-        "availability": {
-            "NoGraphLoaded": true,
-            "WeightedGraphLoaded": true,
-            "UnWeightedGraphLoaded": true
-        }
-    },
-    {
-        "id":"l5",
-        "title": "Dropdown Menu: Layout -> Undo Reset",
-        "text": "The force graph parameters should",
-        "options": {
-            "Click \"Undo Reset\"": "return to the values they had before the Undo Reset button (or menu item) was selected, if Undo Reset is enabled."
-        },
-        "included": false,
-        "availability": {
-            "NoGraphLoaded": true,
-            "WeightedGraphLoaded": true,
-            "UnWeightedGraphLoaded": true
-        }
-    },
-    {
-        "id":"l6",
-        "title": "Dropdown Menu: Layout -> Link Distance",
-        "text": "",
-        "options": {
-            "Input Value, then Press Enter": "The graph's edges should visibly change in length to the value entered if Lock Force Graph Parameters is unchecked"
-        },
-        "included": false,
-        "availability": {
-            "NoGraphLoaded": true,
-            "WeightedGraphLoaded": true,
-            "UnWeightedGraphLoaded": true
-        }
-    },
-    {
-        "id":"l7",
-        "title": "Dropdown Menu: Layout -> Charge",
-        "text": "",
-        "options": {
-            "Input Value, then Press Enter": "The graph's nodes should visibly change it's level of attraction to each other to the value entered if Lock Force Graph Parameters is unchecked"
-        },
-        "included": false,
-        "availability": {
-            "NoGraphLoaded": true,
-            "WeightedGraphLoaded": true,
-            "UnWeightedGraphLoaded": true
-        }
-    },
-    {
-        "id":"l8",
-        "title": "Sidebar Menu: Force Graph Parameter Sliders",
-        "text": "",
-        "options": {
-            "Keep at Default Values": "The graph should be laid out according to the default values of the force graph parameter sliders",
-            "Decrease Link Distance": "The graph's edges should visibly decrease in length if Lock Force Graph Parameters is unchecked",
-            "Increase Link Distance": "The graph's edges should visibly increase in length if Lock Force Graph Parameters is unchecked",
-            "Increase Charge": "The graph's nodes should visibly increase attraction to each other if Lock Force Graph Parameters is unchecked",
-            "Decrease Charge": "The graph's nodes should visibly decrease attraction to each other if Lock Force Graph Parameters is unchecked"
-        },
-        "included": false,
-        "availability": {
-            "NoGraphLoaded": true,
-            "WeightedGraphLoaded": true,
-            "UnWeightedGraphLoaded": true
-        }
-    },
-    {
-        "id":"l9",
-        "title": "Sidebar Menu: Lock Force Graph Parameters Checkbox",
-        "text": "The Force Graph Parameter sliders should",
-        "options": {
-            "Check": "be disabled.",
-            "Uncheck": "be enabled."
-        },
-        "included": false,
-        "availability": {
-            "NoGraphLoaded": true,
-            "WeightedGraphLoaded": true,
-            "UnWeightedGraphLoaded": true
-        }
-    },
-    {
-        "id":"l10",
-        "title": "Sidebar Menu: Reset Force Graph Parameters Button",
-        "text": "The Force Graph Parameter sliders should",
-        "options": {
-            "Click": "revert to the default values, if Lock Force Graph Parameters is unchecked."
-        },
-        "included": false,
-        "availability": {
-            "NoGraphLoaded": true,
-            "WeightedGraphLoaded": true,
-            "UnWeightedGraphLoaded": true
-        }
-    },
-    {
-        "id":"l11",
-        "title": "Sidebar Menu: Undo Reset Button",
-        "text": "The Force Graph Parameter sliders should",
-        "options": {
-            "Click": "return to the values they had before the Undo Reset button (or menu item) was selected, if the Undo Reset button is enabled."
-        },
-        "included": false,
-        "availability": {
-            "NoGraphLoaded": true,
-            "WeightedGraphLoaded": true,
-            "UnWeightedGraphLoaded": true
-        }
-    }
-]

package/documents/developer_documents/testing_script_generator/nodeFeatures.json

@@ -1,195 +0,0 @@
-[
-    {
-        "id":"n1",
-        "title": "Sidebar Menu: Top Dataset",
-        "text": "The top half of each node should be colored using data from",
-        "options": {
-            "Keep Default Selection": "the first expression dataset detected in the input workbook",
-            "Select Top Dataset from Dropdown List": "the selected dataset"
-        },
-        "included": false,
-        "conditional": "if expression data sheets are present in input workbook",
-        "availability": {
-            "NoGraphLoaded": false,
-            "WeightedGraphLoaded": true,
-            "UnWeightedGraphLoaded": true
-        }
-    },
-    {
-        "id":"n2",
-        "title": "Dropdown Menu: Node -> Select Top Dataset",
-        "text": "The top half of each node should be colored using data from",
-        "options": {
-            "Keep Default Selection": "the first expression dataset detected in the input workbook",
-            "Check New Top Dataset from Dropdown List": "the selected dataset"
-        },
-        "included": false,
-        "conditional": "if expression data sheets are present in input workbook",
-        "availability": {
-            "NoGraphLoaded": false,
-            "WeightedGraphLoaded": true,
-            "UnWeightedGraphLoaded": true
-        }
-    },
-    {
-        "id":"n3",
-        "title": "Sidebar Menu: Bottom Dataset",
-        "text": "The bottom half of each node should be colored using data from",
-        "options": {
-            "Keep Default Selection": "the same dataset as the top dataset",
-            "Select Bottom Dataset from Dropdown List": "the selected dataset"
-        },
-        "included": false,
-        "conditional": "if expression data sheets are present in input workbook",
-        "availability": {
-            "NoGraphLoaded": false,
-            "WeightedGraphLoaded": true,
-            "UnWeightedGraphLoaded": true
-        }
-    },
-    {
-        "id":"n4",
-        "title": "Dropdown Menu: Node -> Select Bottom Dataset",
-        "text": "The bottom half of each node should be colored using data from",
-        "options": {
-            "Keep Default Selection": "the same dataset as the top dataset",
-            "Check New Bottom Dataset from Dropdown List": "the selected dataset"
-        },
-        "included": false,
-        "conditional": "if expression data sheets are present in input workbook",
-        "availability": {
-            "NoGraphLoaded": false,
-            "WeightedGraphLoaded": true,
-            "UnWeightedGraphLoaded": true
-        }
-    },
-    {
-        "id":"n5",
-        "title": "Sidebar Menu: Log Fold Change Max Value",
-        "text": "The node coloring visualization's color intensity should",
-        "options": {
-            "Keep Default Value": "default to having a Log Fold Change Max Value of 3",
-            "Increase Log Fold Change Max Value": "decrease",
-            "Decrease Log Fold Change Max Value": "increase"
-        },
-        "included": false,
-        "conditional": "if expression data sheets are present in input workbook",
-        "availability": {
-            "NoGraphLoaded": false,
-            "WeightedGraphLoaded": true,
-            "UnWeightedGraphLoaded": true
-        }
-    },
-    {
-        "id":"n6",
-        "title": "Dropdown Menu: Node -> Log Fold Change Max Value",
-        "text": "The node coloring visualization's color intensity should",
-        "options": {
-            "Keep Default Value": "default to having a Log Fold Change Max Value of 3",
-            "Increase Log Fold Change Max Value": "decrease",
-            "Decrease Log Fold Change Max Value": "increase"
-        },
-        "included": false,
-        "conditional": "if expression data sheets are present in input workbook",
-        "availability": {
-            "NoGraphLoaded": false,
-            "WeightedGraphLoaded": true,
-            "UnWeightedGraphLoaded": true
-        }
-    },
-    {
-        "id":"n7",
-        "title": "Sidebar Menu: Average Replicates Values (Top Dataset)",
-        "text": "GRNsight should",
-        "options": {
-            "Check": "average replicate values for top dataset",
-            "Uncheck": "not average replicate values for top dataset"
-        },
-        "included": false,
-        "conditional": "if expression data sheets are present in input workbook",
-        "availability": {
-            "NoGraphLoaded": false,
-            "WeightedGraphLoaded": true,
-            "UnWeightedGraphLoaded": true
-        }
-    },
-    {
-        "id":"n8",
-        "title": "Dropdown Menu: Node -> Average Replicates Values (Top Dataset)",
-        "text": "GRNsight should",
-        "options": {
-            "Check": "average replicate values for top dataset",
-            "Uncheck": "not average replicate values for top dataset"
-        },
-        "included": false,
-        "conditional": "if expression data sheets are present in input workbook",
-        "availability": {
-            "NoGraphLoaded": false,
-            "WeightedGraphLoaded": true,
-            "UnWeightedGraphLoaded": true
-        }
-    },
-    {
-        "id":"n9",
-        "title": "Sidebar Menu: Average Replicates Values (Bottom Dataset)",
-        "text": "GRNsight should",
-        "options": {
-            "Check": "average replicate values for bottom dataset",
-            "Uncheck": "not average replicate values for bottom dataset"
-        },
-        "included": false,
-        "conditional": "if expression data sheets are present in input workbook",
-        "availability": {
-            "NoGraphLoaded": false,
-            "WeightedGraphLoaded": true,
-            "UnWeightedGraphLoaded": true
-        }
-    },
-    {
-        "id":"n10",
-        "title": "Dropdown Menu: Node -> Average Replicates Values (Bottom Dataset)",
-        "text": "GRNsight should",
-        "options": {
-            "Check": "average replicate values for bottom dataset",
-            "Uncheck": "not average replicate values for bottom dataset"
-        },
-        "included": false,
-        "conditional": "if expression data sheets are present in input workbook",
-        "availability": {
-            "NoGraphLoaded": false,
-            "WeightedGraphLoaded": true,
-            "UnWeightedGraphLoaded": true
-        }
-    },
-    {
-        "id":"n11",
-        "title": "Sidebar Menu: Node Coloring Toggle Button",
-        "text": "",
-        "options": {
-            "Click": "Node coloring should toggle between on and off, with default being on"
-        },
-        "included": false,
-        "conditional": "if expression data sheets are present in input workbook",
-        "availability": {
-            "NoGraphLoaded": false,
-            "WeightedGraphLoaded": true,
-            "UnWeightedGraphLoaded": true
-        }
-    },
-    {
-        "id":"n12",
-        "title": "Dropdown Menu: Node -> Enable Node Coloring",
-        "text": "",
-        "options": {
-            "Check": "Node coloring should become enabled, and Node Coloring Toggle Button text in sidebar menu should toggle on",
-            "Uncheck": "Node coloring should become disabled, and Node Coloring Toggle Button text in sidebar menu should toggle off"
-        },
-        "included": true,
-        "conditional": "if expression data sheets are present in input workbook",
-        "availability": {
-            "NoGraphLoaded": false,
-            "WeightedGraphLoaded": true,
-            "UnWeightedGraphLoaded": true
-        }
-    }
-]

package/documents/developer_documents/testing_script_generator/speciesFeatures.json

@@ -1,30 +0,0 @@
-[
-    {
-        "id":"s1",
-        "title": "Dropdown Menu: Species -> Current Species",
-        "text": "",
-        "options": {
-            "Select a species": "Opening gene information pages will use information of the selected species."
-        },
-        "included": false,
-        "availability": {
-            "NoGraphLoaded": true,
-            "WeightedGraphLoaded": true,
-            "UnWeightedGraphLoaded": true
-        }
-    },
-    {
-        "id":"s2",
-        "title": "Sidebar Menu: Species -> Current Species",
-        "text": "",
-        "options": {
-            "Select a species from a dropdown list": "Opening gene information pages will use information of the selected species."
-        },
-        "included": false,
-        "availability": {
-            "NoGraphLoaded": true,
-            "WeightedGraphLoaded": true,
-            "UnWeightedGraphLoaded": true
-        }
-    }
-]