pyegeria 5.3.6.2.4__py3-none-any.whl → 5.3.6.3__py3-none-any.whl

pyegeria/commands/cat/freddies-outbox/Terms-2025-03-06-13-20-30-Update-Form.md

@@ -1,78 +0,0 @@
-# Update Glossaries Form - created at 2025-03-06 13:20
-Glossaries found from the search string:  `All Glossaries`
-
-# Update Glossary
-
-## Glossary Name 
-Egeria-Markdown
-
-## Description
-Glossary to describe the vocabulary of Freddie - an Egeria Markdown language to support the exchange of metadata in a Markdown form.
-Freddie allows users to input metadata using any text entry system that supports the entry of standard Markdown characters and through post-processing
-commands, validates the Egeria content and allows the requests to be sent to Egeria. This is an update
-
-## Language
-English
-
-## Usage
-1) (optional) load an example or template for the type of object from Egeria.
-2) Create a new document (perhaps from the template) and edit it, adding in the content with the Freddie controlled Markdown language.
-3) Process the document to validate and display it before you submit it, Validation may annotate your document with recommendations and potential issues.
-4) Submit the document to Egeria using the Freddie_sings command.
-5) anything?
-
-## Qualified Name
-Glossary:Egeria-Markdown
-
-## GUID
-5d45b499-d0d5-4fad-bc23-763bc4073296
-
-
----
-
-# Update Glossary
-
-## Glossary Name 
-Teddy Bear Drop Foot Terminology
-
-## Description
-This glossary describes terminology invented for the fictitious study into Teddy Bear Drop Foot that is being used to demonstrate aspects of open governance without risk to real patient data. 
-
-## Language
-English
-
-## Usage
-Used with the Teddy Bear Drop Foot Demonstration Study.
-
-## Qualified Name
-Glossary:TeddyBearDropFootTerminology
-
-## GUID
-c103d0c9-7581-47e1-a684-6bbe0ecd596f
-
-
----
-
-# Update Glossary
-
-## Glossary Name 
-Sustainability Glossary
-
-## Description
-Terminology associated with Coco Pharmaceutical's sustainability initiative.
-
-## Language
-English
-
-## Usage
-For all Coco Pharmaceutical employees wishing to understand more about sustainability and the organization's efforts to improve its operations.
-
-## Qualified Name
-Glossary:Sustainability
-
-## GUID
-30bfe79e-adf2-4fda-b9c5-9c86ad6b0d6c
-
-
----
-

pyegeria/commands/cat/glossary_creation_experiment.ipynb

@@ -1,235 +0,0 @@
-{
- "cells": [
-  {
-   "cell_type": "markdown",
-   "id": "f211c1736f87555",
-   "metadata": {},
-   "source": [
-    "# This notebook contains experimental Freddie commands\n",
-    "## Lets see if this is parsed\n",
-    "meow"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "id": "3b321563-4977-496a-963b-9b9dd75de968",
-   "metadata": {},
-   "source": [
-    "# Create Glossary\n",
-    "## Glossary Name\n",
-    "\n",
-    "Egeria-Markdown\n",
-    "\n",
-    "## Language\n",
-    "English\n",
-    "\n",
-    "## Description\n",
-    "\n",
-    "Glossary to describe the vocabulary of Freddie - an Egeria Markdown language to support the exchange of metadata in a Markdown form.\n",
-    "Freddie allows users to input metadata using any text entry system that supports the entry of standard Markdown characters and through post-processing\n",
-    "commands, validates the Egeria content and allows the requests to be sent to Egeria.\n",
-    "\n",
-    "\n",
-    "## Usage\n",
-    "1) (optional) load an example or template for the type of object from Egeria.\n",
-    "2) Create a new document (perhaps from the template) and edit it, adding in the content with the Freddie controlled Markdown language.\n",
-    "3) Process the document to validate and display it before you submit it, Validation may annotate your document with recommendations and potential issues.\n",
-    "4) Submit the document to Egeria using the Freddie_sings command.\n",
-    "\n",
-    "## <Qualified Name>\n",
-    "\n",
-    "## <GUID>\n",
-    "\n"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "a7295df2-5afb-46ba-889a-94881d883678",
-   "metadata": {
-    "execution": {
-     "iopub.execute_input": "2025-02-27T15:23:58.820592Z",
-     "iopub.status.busy": "2025-02-27T15:23:58.820416Z",
-     "iopub.status.idle": "2025-02-27T15:24:00.802861Z",
-     "shell.execute_reply": "2025-02-27T15:24:00.802425Z",
-     "shell.execute_reply.started": "2025-02-27T15:23:58.820583Z"
-    }
-   },
-   "outputs": [],
-   "source": [
-    "%pip install jupyter-notebook-parser\n",
-    "%pip install marko"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "d02383df-f617-48f7-be54-e930b6275a7e",
-   "metadata": {
-    "execution": {
-     "iopub.execute_input": "2025-02-27T15:25:33.155175Z",
-     "iopub.status.busy": "2025-02-27T15:25:33.154695Z",
-     "iopub.status.idle": "2025-02-27T15:25:33.162801Z",
-     "shell.execute_reply": "2025-02-27T15:25:33.162362Z",
-     "shell.execute_reply.started": "2025-02-27T15:25:33.155158Z"
-    }
-   },
-   "outputs": [],
-   "source": [
-    "import json\n",
-    "import marko\n",
-    "from jupyter_notebook_parser import JupyterNotebookParser"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "b5560fcd-afe4-4133-8204-8f2535feb9b6",
-   "metadata": {
-    "execution": {
-     "iopub.execute_input": "2025-02-27T15:25:34.354443Z",
-     "iopub.status.busy": "2025-02-27T15:25:34.354300Z",
-     "iopub.status.idle": "2025-02-27T15:25:34.358702Z",
-     "shell.execute_reply": "2025-02-27T15:25:34.358236Z",
-     "shell.execute_reply.started": "2025-02-27T15:25:34.354435Z"
-    }
-   },
-   "outputs": [],
-   "source": [
-    "parsed = JupyterNotebookParser('glossary_creation_experiment.ipynb')\n",
-    "\n",
-    "parsed.get_all_cells()  # returns List[Dict], each Dict is a notebook cell\n",
-    "\n",
-    "cells = parsed.get_markdown_cells()  # returns List[Dict], each Dict is a markdown cel\n",
-    "indices = parsed.get_markdown_cell_indices()  # returns List[int], each is a markdown cell's index\n",
-    "cell_sources = parsed.get_markdown_cell_sources()  # returns List[str], each is a markdown cell's text\n",
-    "print(json.dumps(cell_sources, indent = 4))"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "79dffa96-7e2a-40e3-a0d7-ba363d87b70c",
-   "metadata": {
-    "execution": {
-     "iopub.execute_input": "2025-02-27T15:42:47.354237Z",
-     "iopub.status.busy": "2025-02-27T15:42:47.353238Z",
-     "iopub.status.idle": "2025-02-27T15:42:47.360634Z",
-     "shell.execute_reply": "2025-02-27T15:42:47.360090Z",
-     "shell.execute_reply.started": "2025-02-27T15:42:47.354193Z"
-    }
-   },
-   "outputs": [],
-   "source": [
-    "parsed_markdown = marko.parse(cell_sources[0])\n",
-    "print(type(parsed_markdown))"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "f3d66578-cf02-4e95-a102-f84fbe3aae95",
-   "metadata": {
-    "execution": {
-     "iopub.execute_input": "2025-02-27T15:44:51.000320Z",
-     "iopub.status.busy": "2025-02-27T15:44:51.000168Z",
-     "iopub.status.idle": "2025-02-27T15:44:51.007790Z",
-     "shell.execute_reply": "2025-02-27T15:44:51.007211Z",
-     "shell.execute_reply.started": "2025-02-27T15:44:51.000309Z"
-    }
-   },
-   "outputs": [],
-   "source": [
-    "parsed_source = marko.parse_source(cell_sources[0])"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "7cc1a99c-46b3-42c9-8b38-77fb721586a7",
-   "metadata": {
-    "execution": {
-     "iopub.execute_input": "2025-02-27T15:45:28.853162Z",
-     "iopub.status.busy": "2025-02-27T15:45:28.852948Z",
-     "iopub.status.idle": "2025-02-27T15:45:28.856556Z",
-     "shell.execute_reply": "2025-02-27T15:45:28.856159Z",
-     "shell.execute_reply.started": "2025-02-27T15:45:28.853153Z"
-    }
-   },
-   "outputs": [],
-   "source": [
-    "? marko"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "ca5f9660-1f56-4de9-8127-5e7e4a922b5f",
-   "metadata": {},
-   "outputs": [],
-   "source": []
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "e967897d83588f86",
-   "metadata": {},
-   "outputs": [],
-   "source": []
-  },
-  {
-   "cell_type": "markdown",
-   "id": "ed29f0e5d46a7c20",
-   "metadata": {},
-   "source": [
-    "# Create Glossary\n",
-    "## Glossary Name\n",
-    "\n",
-    "Another Test\n",
-    "\n",
-    "## Language\n",
-    "English\n",
-    "\n",
-    "## Description\n",
-    "\n",
-    "Another quick test\n",
-    "\n",
-    "## Usage\n",
-    "Alternate sundays\n",
-    "\n",
-    "## <Qualified Name>\n",
-    "\n",
-    "## <GUID>"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "e36a5074b9a94c1a",
-   "metadata": {},
-   "outputs": [],
-   "source": []
-  }
- ],
- "metadata": {
-  "kernelspec": {
-   "display_name": "Python 3 (ipykernel)",
-   "language": "python",
-   "name": "python3"
-  },
-  "language_info": {
-   "codemirror_mode": {
-    "name": "ipython",
-    "version": 3
-   },
-   "file_extension": ".py",
-   "mimetype": "text/x-python",
-   "name": "python",
-   "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython3",
-   "version": "3.12.9"
-  }
- },
- "nbformat": 4,
- "nbformat_minor": 5
-}

pyegeria/test_m.html

@@ -1,213 +0,0 @@
-
-    <!DOCTYPE html>
-    <html>
-        <head>
-          <style type="text/css">
-            #mySvgId {
-            width: 100%;
-            height: 600px;
-            overflow: scroll;
-            border: 2px solid #ccc;
-            position: relative;
-            margin-bottom: 10px;
-            }
-            svg {
-            cursor: grab;
-            }
-    
-          </style>
-        </head>
-    
-        <title>Component for Solution Blueprint - Clinical Trial Management Solution Blueprint </title>
-        <h3>Component for Solution Blueprint - Clinical Trial Management Solution Blueprint </h3>
-        GUID : c4f8d707-7c85-4125-b5fd-c3257a2ef2ef
-
-    
-        <body>
-        
-          <div id="graphDiv"></div>
-          <script src="https://bumbu.me/svg-pan-zoom/dist/svg-pan-zoom.min.js"></script>
-          <script type="module">
-            import mermaid from 'https://cdn.jsdelivr.net/npm/mermaid@11/dist/mermaid.esm.min.mjs';
-    
-            mermaid.initialize({startOnLoad: false});
-            await mermaid.run({
-              querySelector: '.mermaid',
-              postRenderCallback: (id) => {
-                const container = document.getElementById("diagram-container");
-                const svgElement = container.querySelector("svg");
-    
-                // Initialize Panzoom
-                const panzoomInstance = Panzoom(svgElement, {
-                  maxScale: 5,
-                  minScale: 0.5,
-                  step: 0.1,
-                });
-    
-                // Add mouse wheel zoom
-                container.addEventListener("wheel", (event) => {
-                  panzoomInstance.zoomWithWheel(event);
-                });
-              }
-            });
-    
-    
-            const drawDiagram = async function () {
-              const element = document.querySelector('#graphDiv');
-             const graphDefinition = `
-    flowchart TD
-%%{init: {"flowchart": {"htmlLabels": false}} }%%
-
-subgraph c4f8d707-7c85-4125-b5fd-c3257a2ef2ef [Components and Actors]
-fc2de77f-7320-48ea-8750-d434c6e870db@{ shape: text, label: "*Description*
-**A description of how a clinical trial is managed in Coco Pharmaceuticals.**"}
-37b8560d-84d4-434b-9b0d-105420fcc924@{ shape: subproc, label: "*Solution Component*
-**Certify Hospital**"}
-f37f3735-28a1-4e03-9ff5-3fe2f137f661@{ shape: trap-t, label: "*Solution Actor Role*
-**Clinical Trial Manager**"}
-f37f3735-28a1-4e03-9ff5-3fe2f137f661-->|"Certifier"|37b8560d-84d4-434b-9b0d-105420fcc924
-72a86eec-9734-4bc0-babb-4fec0aa7c9ff@{ shape: docs, label: "*Solution Component*
-**Assemble Treatment Assessment Report**"}
-48bc201e-3d4e-4beb-bdb2-0fd9d134f6d5@{ shape: rect, label: "*Solution Component*
-**Treatment Efficacy Evidence**"}
-48bc201e-3d4e-4beb-bdb2-0fd9d134f6d5-->|"Solution Linking Wire"|72a86eec-9734-4bc0-babb-4fec0aa7c9ff
-f37f3735-28a1-4e03-9ff5-3fe2f137f661-->|"Author"|72a86eec-9734-4bc0-babb-4fec0aa7c9ff
-b5c8da4c-f925-4cf1-8294-e43cd2c1a584@{ shape: rect, label: "*Solution Component*
-**Analyse Patient Data**"}
-b5c8da4c-f925-4cf1-8294-e43cd2c1a584-->|"Solution Linking Wire"|48bc201e-3d4e-4beb-bdb2-0fd9d134f6d5
-7f5dca65-50b4-4103-9ac7-3a406a09047a@{ shape: subproc, label: "*Solution Component*
-**Weekly Measurements Onboarding Pipeline**"}
-07705e15-efff-4f80-8992-f04ac85e0ef1@{ shape: rect, label: "*Solution Component*
-**Landing Folder Cataloguer**"}
-07705e15-efff-4f80-8992-f04ac85e0ef1-->|"Solution Linking Wire"|7f5dca65-50b4-4103-9ac7-3a406a09047a
-f37f3735-28a1-4e03-9ff5-3fe2f137f661-->|"Steward"|7f5dca65-50b4-4103-9ac7-3a406a09047a
-b0290339-c96c-4b05-904f-12fc98e54e14@{ shape: trap-t, label: "*Solution Actor Role*
-**Certified Data Engineer**"}
-b0290339-c96c-4b05-904f-12fc98e54e14-->|"Steward"|7f5dca65-50b4-4103-9ac7-3a406a09047a
-d48f579f-76d3-4c49-b1b4-575f5645a9d0@{ shape: lin-cyl, label: "*Solution Component*
-**Treatment Validation Sandbox**"}
-26c07ca4-3b8e-484b-812b-36c1ace4b275@{ shape: rect, label: "*Solution Component*
-**Populate Sandbox**"}
-26c07ca4-3b8e-484b-812b-36c1ace4b275-->|"Solution Linking Wire"|d48f579f-76d3-4c49-b1b4-575f5645a9d0
-ee2bb773-e630-4cf9-bdf1-7c2dd64fe4ec@{ shape: processes, label: "*Solution Component*
-**Hospital Processes**"}
-a8bd84ca-0aae-4534-b0e8-87e8659467a6@{ shape: trap-t, label: "*Solution Actor Role*
-**Clinical Trial Participating Hospital Coordinator**"}
-a8bd84ca-0aae-4534-b0e8-87e8659467a6-->|"Coordinator on behalf of hospital"|ee2bb773-e630-4cf9-bdf1-7c2dd64fe4ec
-30adaab5-8870-47a8-8ae9-facbf84cb05a@{ shape: trap-t, label: "*Solution Actor Role*
-**Clinical Trial Participating Hospital**"}
-30adaab5-8870-47a8-8ae9-facbf84cb05a-->|"Owner"|ee2bb773-e630-4cf9-bdf1-7c2dd64fe4ec
-d48f579f-76d3-4c49-b1b4-575f5645a9d0-->|"Solution Linking Wire"|b5c8da4c-f925-4cf1-8294-e43cd2c1a584
-ece17806-836c-4756-b3a2-2d12dde215f6@{ shape: trap-t, label: "*Solution Actor Role*
-**New Treatment Data Scientist**"}
-ece17806-836c-4756-b3a2-2d12dde215f6-->|"Data Analyser"|b5c8da4c-f925-4cf1-8294-e43cd2c1a584
-0c757e35-8a42-4d5f-b01b-c72a6cea65cc@{ shape: trap-t, label: "*Solution Actor Role*
-**New Treatment Researcher.**"}
-0c757e35-8a42-4d5f-b01b-c72a6cea65cc-->|"Results Interpreter"|b5c8da4c-f925-4cf1-8294-e43cd2c1a584
-e9c2f911-ffcb-40c6-aeee-8c4d43811576@{ shape: subproc, label: "*Solution Component*
-**Onboard Hospital**"}
-b0290339-c96c-4b05-904f-12fc98e54e14-->|"Initiator"|e9c2f911-ffcb-40c6-aeee-8c4d43811576
-849b0b42-f465-452b-813c-477d6398e082@{ shape: subproc, label: "*Solution Component*
-**Set up clinical trial**"}
-f37f3735-28a1-4e03-9ff5-3fe2f137f661-->|"Initiator"|849b0b42-f465-452b-813c-477d6398e082
-a5d4d638-6836-47e5-99d0-fdcde637e13f@{ shape: lin-cyl, label: "*Solution Component*
-**Weekly Measurements Data Lake Folder**"}
-7f5dca65-50b4-4103-9ac7-3a406a09047a-->|"Solution Linking Wire"|a5d4d638-6836-47e5-99d0-fdcde637e13f
-0bf2547c-937c-41b6-814f-6284849271a1@{ shape: odd, label: "*Solution Component*
-**Treatment Assessment Report Validation and Delivery**"}
-72a86eec-9734-4bc0-babb-4fec0aa7c9ff-->|"Solution Linking Wire"|0bf2547c-937c-41b6-814f-6284849271a1
-f6bc847b-868d-43cc-b767-41f5fe3e47d1@{ shape: trap-t, label: "*Solution Actor Role*
-**Clinical Trial Sponsor**"}
-f6bc847b-868d-43cc-b767-41f5fe3e47d1-->|"Reviewer"|0bf2547c-937c-41b6-814f-6284849271a1
-a5d4d638-6836-47e5-99d0-fdcde637e13f-->|"Solution Linking Wire"|26c07ca4-3b8e-484b-812b-36c1ace4b275
-fb32bef2-e79f-4893-b500-2e547f24d482@{ shape: subproc, label: "*Solution Component*
-**Set up Data Lake Folder**"}
-b0290339-c96c-4b05-904f-12fc98e54e14-->|"Initiator"|fb32bef2-e79f-4893-b500-2e547f24d482
-1c150d6e-30cf-481c-9afb-3b06c9c9e78f@{ shape: lin-cyl, label: "*Solution Component*
-**Hospital Landing Area Folder**"}
-ee2bb773-e630-4cf9-bdf1-7c2dd64fe4ec-->|"Solution Linking Wire"|1c150d6e-30cf-481c-9afb-3b06c9c9e78f
-1c150d6e-30cf-481c-9afb-3b06c9c9e78f-->|"Solution Linking Wire"|07705e15-efff-4f80-8992-f04ac85e0ef1
-11c7c850-c67c-41cc-9423-d74db47cbf3a@{ shape: subproc, label: "*Solution Component*
-**Nominate Hospital**"}
-f37f3735-28a1-4e03-9ff5-3fe2f137f661-->|"Initiator"|11c7c850-c67c-41cc-9423-d74db47cbf3a
-end
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-style 7f5dca65-50b4-4103-9ac7-3a406a09047a color:#FFFFFF, fill:#838cc7, stroke:#3079ab
-style ee2bb773-e630-4cf9-bdf1-7c2dd64fe4ec color:#FFFFFF, fill:#838cc7, stroke:#3079ab
-style 72a86eec-9734-4bc0-babb-4fec0aa7c9ff color:#FFFFFF, fill:#838cc7, stroke:#3079ab
-style b5c8da4c-f925-4cf1-8294-e43cd2c1a584 color:#FFFFFF, fill:#838cc7, stroke:#3079ab
-style f6bc847b-868d-43cc-b767-41f5fe3e47d1 color:#FFFFFF, fill:#AA00FF, stroke:#E1D5E7
-style d48f579f-76d3-4c49-b1b4-575f5645a9d0 color:#FFFFFF, fill:#838cc7, stroke:#3079ab
-style f37f3735-28a1-4e03-9ff5-3fe2f137f661 color:#FFFFFF, fill:#AA00FF, stroke:#E1D5E7
-style fb32bef2-e79f-4893-b500-2e547f24d482 color:#FFFFFF, fill:#838cc7, stroke:#3079ab`;
-              const {svg} = await mermaid.render('mySvgId', graphDefinition);
-              element.innerHTML = svg.replace(/( )*max-width:( 0-9\.)*px;/i, '');
-    
-              var doPan = false;
-              var eventsHandler;
-              var panZoom;
-              var mousepos;
-    
-              eventsHandler = {
-                haltEventListeners: ['mousedown', 'mousemove', 'mouseup']
-    
-                , mouseDownHandler: function (ev) {
-                  if (event.target.className == "[object SVGAnimatedString]") {
-                    doPan = true;
-                    mousepos = {x: ev.clientX, y: ev.clientY}
-                  }
-                  ;
-                }
-    
-                , mouseMoveHandler: function (ev) {
-                  if (doPan) {
-                    panZoom.panBy({x: ev.clientX - mousepos.x, y: ev.clientY - mousepos.y});
-                    mousepos = {x: ev.clientX, y: ev.clientY};
-                    window.getSelection().removeAllRanges();
-                  }
-                }
-    
-                , mouseUpHandler: function (ev) {
-                  doPan = false;
-                }
-    
-                , init: function (options) {
-                  options.svgElement.addEventListener('mousedown', this.mouseDownHandler, false);
-                  options.svgElement.addEventListener('mousemove', this.mouseMoveHandler, false);
-                  options.svgElement.addEventListener('mouseup', this.mouseUpHandler, false);
-                }
-    
-                , destroy: function (options) {
-                  options.svgElement.removeEventListener('mousedown', this.mouseDownHandler, false);
-                  options.svgElement.removeEventListener('mousemove', this.mouseMoveHandler, false);
-                  options.svgElement.removeEventListener('mouseup', this.mouseUpHandler, false);
-                }
-              }
-              panZoom = svgPanZoom('#mySvgId', {
-                zoomEnabled: true
-                , controlIconsEnabled: true
-                , fit: 1
-                , center: 1
-                , customEventsHandler: eventsHandler
-              })
-            };
-            await drawDiagram();
-          </script>
-        </body>    
-