ose-app 0.2.5__py3-none-any.whl

ose_app/static/main.css

@@ -0,0 +1 @@
+:root{--bs-callout-link: 10, 88, 202;--bs-callout-code-color: #ab296a}.callout-success{--bd-callout-color: var(--bs-success-text-emphasis);--bd-callout-bg: var(--bs-success-bg-subtle);--bd-callout-border: var(--bs-success-border-subtle)}.callout-danger{--bd-callout-color: var(--bs-danger-text-emphasis);--bd-callout-bg: var(--bs-danger-bg-subtle);--bd-callout-border: var(--bs-danger-border-subtle)}.callout-warning{--bd-callout-color: var(--bs-warning-text-emphasis);--bd-callout-bg: var(--bs-warning-bg-subtle);--bd-callout-border: var(--bs-warning-border-subtle)}.callout-info{--bd-callout-color: var(--bs-info-text-emphasis);--bd-callout-bg: var(--bs-info-bg-subtle);--bd-callout-border: var(--bs-info-border-subtle)}.callout{--bs-link-color-rgb: var(--bs-callout-link);--bs-code-color: var(--bs-callout-code-color);padding:1.25rem;margin-top:1.25rem;margin-bottom:1.25rem;color:var(--bd-callout-color, inherit);background-color:var(--bd-callout-bg, var(--bs-gray-100));border-left:.25rem solid var(--bd-callout-border, var(--bs-gray-300))}.banner{text-align:center;background:#ff0;background:repeating-linear-gradient(-45deg, #666600, #666600, 20px, black 20px, black 40px);color:#fff}.modal-dialog .release-file-settings{display:grid;grid-template-columns:auto 1fr auto;grid-gap:8px 16px}.modal-dialog .release-file-settings h4{grid-column:1/3}.modal-dialog .release-file-settings label{grid-column:1}.modal-dialog .release-file-settings input,.modal-dialog .release-file-settings textarea{grid-column:2}.modal-dialog .release-file-settings span{grid-column:3}.breadcrumb-item.active{font-weight:bold}.loader{width:40px;aspect-ratio:1;position:relative}.loader:before,.loader:after{content:"";position:absolute;top:0;left:0;margin:-8px 0 0 -8px;width:16px;aspect-ratio:1;background:#3fb8af;animation:l2-1 2s infinite,l2-2 1s infinite}.loader:after{background:#ff3d7f;animation-delay:-1s,0s}@keyframes l2-1{0%{top:0;left:0}25%{top:100%;left:0}50%{top:100%;left:100%}75%{top:0;left:100%}100%{top:0;left:0}}@keyframes l2-2{40%,50%{transform:rotate(0.25turn) scale(0.5)}100%{transform:rotate(0.5turn) scale(1)}}:root{--ose-curation-status-discussed: moccasin;--ose-curation-status-proposed: #FFFFFF;--ose-curation-status-to_be_discussed: #eee8aa;--ose-curation-status-in_discussion: #fffacd;--ose-curation-status-published: #7fffd4;--ose-curation-status-obsolete: #2f4f4f;--ose-curation-status-external: #D3D3D3;--ose-curation-status-pre_proposed: #ebfad0}

ose_app/static/main.css.map

@@ -0,0 +1,7 @@
+{
+"version": 3,
+"mappings": "AACA,KAAM;EACJ,iBAAiB,CAAC,YAAY;EAC9B,uBAAuB,CAAC,QAAQ;;AAGlC,gBAAiB;EACf,kBAAkB,CAAC,gCAAgC;EACnD,eAAe,CAAC,4BAA4B;EAC5C,mBAAmB,CAAC,gCAAgC;;AAGtD,eAAgB;EACd,kBAAkB,CAAC,+BAA+B;EAClD,eAAe,CAAC,2BAA2B;EAC3C,mBAAmB,CAAC,+BAA+B;;AAGrD,gBAAiB;EACf,kBAAkB,CAAC,gCAAgC;EACnD,eAAe,CAAC,4BAA4B;EAC5C,mBAAmB,CAAC,gCAAgC;;AAGtD,aAAc;EACZ,kBAAkB,CAAC,6BAA6B;EAChD,eAAe,CAAC,yBAAyB;EACzC,mBAAmB,CAAC,6BAA6B;;AAGnD,QAAS;EACP,mBAAmB,CAAC,uBAAuB;EAC3C,eAAe,CAAC,6BAA6B;EAC7C,OAAO,EAAE,OAAO;EAChB,UAAU,EAAE,OAAO;EACnB,aAAa,EAAE,OAAO;EACtB,KAAK,EAAE,gCAAgC;EACvC,gBAAgB,EAAE,wCAAwC;EAC1D,WAAW,EAAE,0DAA0D;;AAGzE,OAAQ;EACN,UAAU,EAAE,MAAM;EAClB,UAAU,EAAE,MAAM;EAClB,UAAU,EAAE,iFAAuG;EACnH,KAAK,EAAE,KAAK;;AAId,oCAAqC;EACnC,OAAO,EAAE,IAAI;EACb,qBAAqB,EAAE,aAAa;EACpC,QAAQ,EAAE,QAAQ;EAElB,uCAAG;IACD,WAAW,EAAE,GACf;EAEA,0CAAM;IACJ,WAAW,EAAE,CAAC;EAGhB,yFAAgB;IACd,WAAW,EAAE,CAAC;EAGhB,yCAAK;IACH,WAAW,EAAE,CAAC;;AAOlB,uBAAwB;EACtB,WAAW,EAAE,IAAI;;AAGnB,sCAAsC;AACtC,OAAQ;EACN,KAAK,EAAE,IAAI;EACX,YAAY,EAAE,CAAC;EACf,QAAQ,EAAE,QAAQ;;AAGpB;aACc;EACZ,OAAO,EAAE,EAAE;EACX,QAAQ,EAAE,QAAQ;EAClB,GAAG,EAAE,CAAC;EACN,IAAI,EAAE,CAAC;EACP,MAAM,EAAE,aAAa;EACrB,KAAK,EAAE,IAAI;EACX,YAAY,EAAE,CAAC;EACf,UAAU,EAAE,OAAO;EACnB,SAAS,EAAE,kCACK;;AAGlB,aAAc;EACZ,UAAU,EAAE,OAAO;EACnB,eAAe,EAAE,OAAO;;AAG1B,eAqBC;EApBC,EAAG;IACD,GAAG,EAAE,CAAC;IACN,IAAI,EAAE,CAAC;EAET,GAAI;IACF,GAAG,EAAE,IAAI;IACT,IAAI,EAAE,CAAC;EAET,GAAI;IACF,GAAG,EAAE,IAAI;IACT,IAAI,EAAE,IAAI;EAEZ,GAAI;IACF,GAAG,EAAE,CAAC;IACN,IAAI,EAAE,IAAI;EAEZ,IAAK;IACH,GAAG,EAAE,CAAC;IACN,IAAI,EAAE,CAAC;AAIX,eAOC;EANC,QAAS;IACP,SAAS,EAAE,2BACb;EACA,IAAK;IACH,SAAS,EAAE,wBACb",
+"sources": ["main.scss"],
+"names": [],
+"file": "main.css"
+}

ose_app/static/main.scss

@@ -0,0 +1,147 @@
+@use "sass:color";
+
+:root {
+  --bs-callout-link: 10, 88, 202;
+  --bs-callout-code-color: #ab296a;
+}
+
+.callout-success {
+  --bd-callout-color: var(--bs-success-text-emphasis);
+  --bd-callout-bg: var(--bs-success-bg-subtle);
+  --bd-callout-border: var(--bs-success-border-subtle);
+}
+
+.callout-danger {
+  --bd-callout-color: var(--bs-danger-text-emphasis);
+  --bd-callout-bg: var(--bs-danger-bg-subtle);
+  --bd-callout-border: var(--bs-danger-border-subtle);
+}
+
+.callout-warning {
+  --bd-callout-color: var(--bs-warning-text-emphasis);
+  --bd-callout-bg: var(--bs-warning-bg-subtle);
+  --bd-callout-border: var(--bs-warning-border-subtle);
+}
+
+.callout-info {
+  --bd-callout-color: var(--bs-info-text-emphasis);
+  --bd-callout-bg: var(--bs-info-bg-subtle);
+  --bd-callout-border: var(--bs-info-border-subtle);
+}
+
+.callout {
+  --bs-link-color-rgb: var(--bs-callout-link);
+  --bs-code-color: var(--bs-callout-code-color);
+  padding: 1.25rem;
+  margin-top: 1.25rem;
+  margin-bottom: 1.25rem;
+  color: var(--bd-callout-color, inherit);
+  background-color: var(--bd-callout-bg, var(--bs-gray-100));
+  border-left: 0.25rem solid var(--bd-callout-border, var(--bs-gray-300));
+}
+
+.banner {
+  text-align: center;
+  background: yellow;
+  background: repeating-linear-gradient(-45deg, color.adjust(yellow, $lightness: -30%), color.adjust(yellow, $lightness: -30%), 20px, black 20px, black 40px);
+  color: white
+}
+
+//.release {
+.modal-dialog .release-file-settings {
+  display: grid;
+  grid-template-columns: auto 1fr auto;
+  grid-gap: 8px 16px;
+
+  h4 {
+    grid-column: 1/3
+  }
+
+  label {
+    grid-column: 1;
+  }
+
+  input, textarea {
+    grid-column: 2;
+  }
+
+  span {
+    grid-column: 3;
+  }
+}
+
+//}
+
+
+.breadcrumb-item.active {
+  font-weight: bold;
+}
+
+/* HTML: <div class="loader"></div> */
+.loader {
+  width: 40px;
+  aspect-ratio: 1;
+  position: relative;
+}
+
+.loader:before,
+.loader:after {
+  content: "";
+  position: absolute;
+  top: 0;
+  left: 0;
+  margin: -8px 0 0 -8px;
+  width: 16px;
+  aspect-ratio: 1;
+  background: #3FB8AF;
+  animation: l2-1 2s infinite,
+  l2-2 1s infinite;
+}
+
+.loader:after {
+  background: #FF3D7F;
+  animation-delay: -1s, 0s;
+}
+
+@keyframes l2-1 {
+  0% {
+    top: 0;
+    left: 0
+  }
+  25% {
+    top: 100%;
+    left: 0
+  }
+  50% {
+    top: 100%;
+    left: 100%
+  }
+  75% {
+    top: 0;
+    left: 100%
+  }
+  100% {
+    top: 0;
+    left: 0
+  }
+}
+
+@keyframes l2-2 {
+  40%, 50% {
+    transform: rotate(0.25turn) scale(0.5)
+  }
+  100% {
+    transform: rotate(0.5turn) scale(1)
+  }
+}
+
+:root {
+  --ose-curation-status-discussed: moccasin;
+  --ose-curation-status-proposed: #FFFFFF;
+  --ose-curation-status-to_be_discussed: #eee8aa;
+  --ose-curation-status-in_discussion: #fffacd;
+  --ose-curation-status-published: #7fffd4;
+  --ose-curation-status-obsolete: #2f4f4f;
+  --ose-curation-status-external: #D3D3D3;
+  --ose-curation-status-pre_proposed: #ebfad0;
+}

ose_app/static/mindmup-editabletable.js

@@ -0,0 +1,131 @@
+/*global $, window*/
+$.fn.editableTableWidget = function (options) {
+	'use strict';
+	return $(this).each(function () {
+		var buildDefaultOptions = function () {
+				var opts = $.extend({}, $.fn.editableTableWidget.defaultOptions);
+				opts.editor = opts.editor.clone();
+				return opts;
+			},
+			activeOptions = $.extend(buildDefaultOptions(), options),
+			ARROW_LEFT = 37, ARROW_UP = 38, ARROW_RIGHT = 39, ARROW_DOWN = 40, ENTER = 13, ESC = 27, TAB = 9,
+			element = $(this),
+			editor = activeOptions.editor.css('position', 'absolute').hide().appendTo(element.parent()),
+			active,
+			showEditor = function (select) {
+				active = element.find('td:focus');
+				if (active.length) {
+					editor.val(active.text())
+						.removeClass('error')
+						.show()
+						.offset(active.offset())
+						.css(active.css(activeOptions.cloneProperties))
+						.width(active.width())
+						.height(active.height())
+						.focus();
+					if (select) {
+						editor.select();
+					}
+				}
+			},
+			setActiveText = function () {
+				var text = editor.val(),
+					evt = $.Event('change'),
+					originalContent;
+				if (active.text() === text || editor.hasClass('error')) {
+					return true;
+				}
+				originalContent = active.html();
+				active.text(text).trigger(evt, text);
+				if (evt.result === false) {
+					active.html(originalContent);
+				}
+			},
+			movement = function (element, keycode) {
+				if (keycode === ARROW_RIGHT) {
+					return element.next('td');
+				} else if (keycode === ARROW_LEFT) {
+					return element.prev('td');
+				} else if (keycode === ARROW_UP) {
+					return element.parent().prev().children().eq(element.index());
+				} else if (keycode === ARROW_DOWN) {
+					return element.parent().next().children().eq(element.index());
+				}
+				return [];
+			};
+		editor.blur(function () {
+			setActiveText();
+			editor.hide();
+		}).keydown(function (e) {
+			if (e.which === ENTER) {
+				setActiveText();
+				editor.hide();
+				active.focus();
+				e.preventDefault();
+				e.stopPropagation();
+			} else if (e.which === ESC) {
+				editor.val(active.text());
+				e.preventDefault();
+				e.stopPropagation();
+				editor.hide();
+				active.focus();
+			} else if (e.which === TAB) {
+				active.focus();
+			} else if (this.selectionEnd - this.selectionStart === this.value.length) {
+				var possibleMove = movement(active, e.which);
+				if (possibleMove.length > 0) {
+					possibleMove.focus();
+					e.preventDefault();
+					e.stopPropagation();
+				}
+			}
+		})
+		.on('input paste', function () {
+			var evt = $.Event('validate');
+			active.trigger(evt, editor.val());
+			if (evt.result === false) {
+				editor.addClass('error');
+			} else {
+				editor.removeClass('error');
+			}
+		});
+		element.on('click keypress dblclick', showEditor)
+		.css('cursor', 'pointer')
+		.keydown(function (e) {
+			var prevent = true,
+				possibleMove = movement($(e.target), e.which);
+			if (possibleMove.length > 0) {
+				possibleMove.focus();
+			} else if (e.which === ENTER) {
+				showEditor(false);
+			} else if (e.which === 17 || e.which === 91 || e.which === 93) {
+				showEditor(true);
+				prevent = false;
+			} else {
+				prevent = false;
+			}
+			if (prevent) {
+				e.stopPropagation();
+				e.preventDefault();
+			}
+		});
+
+		element.find('td').prop('tabindex', 1);
+
+		$(window).on('resize', function () {
+			if (editor.is(':visible')) {
+				editor.offset(active.offset())
+				.width(active.width())
+				.height(active.height());
+			}
+		});
+	});
+
+};
+$.fn.editableTableWidget.defaultOptions = {
+	cloneProperties: ['padding', 'padding-top', 'padding-bottom', 'padding-left', 'padding-right',
+					  'text-align', 'font', 'font-size', 'font-family', 'font-weight',
+					  'border', 'border-top', 'border-bottom', 'border-left', 'border-right'],
+	editor: $('<input>')
+};
+

ose_app/static/schema/release_script.json

@@ -0,0 +1,215 @@
+{
+  "$schema": "http://json-schema.org/draft-06/schema#",
+  "definitions": {
+    "release-step-name": {
+      "type": "string",
+      "enum": [
+        "GITHUB_PUBLISH",
+        "HUMAN_VERIFICATION",
+        "IMPORT_EXTERNAL",
+        "BUILD",
+        "MERGE",
+        "PREPARATION",
+        "VALIDATION",
+        "BCIO_SEARCH",
+        "ADDICTO_VOCAB",
+        "HIERARCHICAL_SPREADSHEETS"
+      ]
+    },
+    "file": {
+      "type": "object",
+      "properties": {
+        "sources": {
+          "oneOf": [
+            {
+              "type": "string",
+              "minLength": 1
+            },
+            {
+              "type": "array",
+              "items": {
+                "oneOf": [
+                  {
+                    "type": "string",
+                    "minLength": 1
+                  },
+                  {
+                    "type": "object",
+                    "properties": {
+                      "file": {
+                        "type": "string"
+                      },
+                      "type": {
+                        "type": "string",
+                        "enum": [
+                          "classes",
+                          "individuals",
+                          "relations",
+                          "owl"
+                        ]
+                      }
+                    },
+                    "required": [
+                      "file",
+                      "type"
+                    ]
+                  }
+                ]
+              }
+            }
+          ]
+        },
+        "target": {
+          "anyOf": [
+            {
+              "type": "object",
+              "properties": {
+                "file": {
+                  "type": "string",
+                  "minLength": 1
+                },
+                "iri": {
+                  "type": "string",
+                  "minLength": 1
+                },
+                "ontology_annotations": {
+                  "type": "object",
+                  "properties": {},
+                  "additionalProperties": {
+                    "type": "string",
+                    "minLength": 1
+                  }
+                }
+              },
+              "required": [
+                "file",
+                "iri"
+              ]
+            },
+            {
+              "type": "string"
+            }
+          ]
+        },
+        "needs": {
+          "type": "array",
+          "minLength": 0,
+          "items": {
+            "type": "string",
+            "minLength": 1
+          }
+        },
+        "renameTermFile": {
+          "anyOf": [
+            {
+              "type": "string",
+              "description": "Path to a csv file containing at least two columns ID and NEW LABEL",
+              "minLength": 1
+            },
+            {
+              "type": "null"
+            }
+          ]
+        },
+        "addParentsFile": {
+          "anyOf": [
+            {
+              "type": "string",
+              "description": "Path to a csv file containing at least two columns ID and NEW PARENT ID",
+              "minLength": 1
+            },
+            {
+              "type": "null"
+            }
+          ]
+        }
+      },
+      "required": [
+        "sources",
+        "target"
+      ]
+    }
+  },
+  "description": "Release script schema",
+  "type": "object",
+  "properties": {
+    "$schema": {
+      "type": "string"
+    },
+    "external": {
+      "$ref": "#/definitions/file"
+    },
+    "files": {
+      "type": "object",
+      "properties": {
+      },
+      "additionalProperties": {
+        "$ref": "#/definitions/file"
+      },
+      "propertyNames": {
+        "pattern": "^[A-Za-z_][A-Za-z0-9_]*$"
+      }
+    },
+    "iri_prefix": {
+      "type": "string",
+      "minLength": 1
+    },
+    "prefixes": {
+      "type": "object",
+      "additionalProperties": {
+        "type": "string",
+        "minLength": 1
+      },
+      "properties": {}
+    },
+    "short_repository_name": {
+      "type": "string",
+      "minLength": 1
+    },
+    "full_repository_name": {
+      "type": "string",
+      "minLength": 1
+    },
+    "steps": {
+      "type": "array",
+      "minLength": 1,
+      "default": [
+        "PREPARATION",
+        "VALIDATION",
+        "IMPORT_EXTERNAL",
+        "BUILD",
+        "MERGE",
+        "HUMAN_VERIFICATION",
+        "GITHUB_PUBLISH"
+      ],
+      "items": {
+        "anyOf": [
+          {
+            "$ref": "#/definitions/release-step-name"
+          },
+          {
+            "type": "object",
+            "properties": {
+              "name": {
+                "$ref": "#/definitions/release-step-name"
+              },
+              "args": {
+                "type": "object",
+                "additionalProperties": true
+              }
+            }
+          }
+        ]
+      }
+    }
+  },
+  "required": [
+    "external",
+    "files",
+    "iri_prefix",
+    "short_repository_name",
+    "full_repository_name",
+    "steps"
+  ],
+  "additionalProperties": false
+}

ose_app/static/schema/req_body_edit.json

@@ -0,0 +1,35 @@
+{
+  "$schema": "http://json-schema.org/draft-04/schema#",
+  "type": "object",
+  "properties": {
+    "id": {
+      "type": "string",
+      "minLength": 1,
+      "pattern": "^[A-Za-z0-9_]+:[0-9]+$"
+    },
+    "term": {
+      "type": "object",
+      "properties": {
+        "id": {
+          "type": "string",
+          "minLength": 1,
+          "pattern": "^[A-Za-z0-9_]+:[0-9]+$"
+        },
+        "label": {
+          "type": "string",
+          "minLength": 1
+        },
+        "parent": {
+          "type": "string",
+          "minLength": 1
+        }
+      },
+      "additionalProperties": false
+    }
+  },
+  "required": [
+    "id",
+    "term"
+  ],
+  "additionalProperties": false
+}

ose_app/static/schema/req_body_guess_parent.json

@@ -0,0 +1,38 @@
+{
+  "$schema": "http://json-schema.org/draft-04/schema#",
+  "type": "object",
+  "properties": {
+    "term": {
+      "type": "object",
+      "properties": {
+        "id": {
+          "type": "string",
+          "minLength": 1
+        },
+        "label": {
+          "type": "string",
+          "minLength": 1
+        }
+      },
+      "required": [ "id", "label" ]
+    },
+    "origin_ontology": {
+      "type": "string",
+      "minLength": 1
+    },
+    "parent": {
+      "type": "object",
+      "properties": {
+        "id": {
+          "type": "string",
+          "minLength": 1
+        },
+        "label": {
+          "type": "string",
+          "minLength": 1
+        }
+      }
+    }
+  },
+  "required": [ "term", "parent" ]
+}

ose_app/static/schema/req_body_import.json

@@ -0,0 +1,47 @@
+{
+  "$schema": "http://json-schema.org/draft-04/schema#",
+  "type": "object",
+  "properties": {
+    "ontologyId": {
+      "type": "string",
+      "minLength": 2
+    },
+    "purl": {
+      "type": "string",
+      "minLength": 1
+    },
+    "rootId": {
+      "type": "string",
+      "minLength": 1
+    },
+    "intermediates": {
+      "type": "string",
+      "minLength": 1
+    },
+    "prefix": {
+      "type": "string",
+      "minLength": 1
+    },
+    "terms": {
+      "type": "array",
+      "items": {
+        "type": "object",
+        "properties": {
+          "id": {
+            "type": "string",
+            "minLength": 1
+          },
+          "label": {
+            "type": "string",
+            "minLength": 1
+          }
+        }
+      },
+      "minLength": 1
+    }
+  },
+  "required": [
+    "terms",
+    "ontologyId"
+  ]
+}

ose_app/static/schema/req_body_release_start.json

@@ -0,0 +1,9 @@
+{
+  "$schema": "http://json-schema.org/draft-04/schema#",
+  "type": "object",
+  "properties": {
+    "release_script": {
+      "$ref": "release_script.json"
+    }
+  }
+}

ose_app/static/schema/req_body_visualise.json

@@ -0,0 +1,18 @@
+{
+    "$schema": "http://json-schema.org/draft-04/schema#",
+    "type": "object",
+    "properties": {
+        "rows": {
+            "type": "array",
+            "items": {
+                "type": "array",
+                "items": { "type": ["string", "null", "number", "boolean"] }
+            }
+        },
+        "header": {
+            "type": "array",
+            "items": { "type": "string" }
+        }
+    },
+    "additionalProperties": false
+}