@teselagen/ove 0.0.13 → 0.0.15

package/src/redux/primerLengthsToHide.js

@@ -0,0 +1,27 @@
+import createMergedDefaultStateReducer from "./utils/createMergedDefaultStateReducer";
+import createAction from "./utils/createMetaAction";
+
+// ------------------------------------
+// Actions
+// ------------------------------------
+export const updatePrimerLengthsToHide = createAction(
+  "updatePrimerLengthsToHide"
+);
+export const togglePrimerLengthsToHide = createAction(
+  "togglePrimerLengthsToHide"
+);
+
+// ------------------------------------
+// Reducer
+// ------------------------------------
+export default createMergedDefaultStateReducer(
+  {
+    [updatePrimerLengthsToHide]: (state, payload) => {
+      return { ...state, ...payload };
+    },
+    [togglePrimerLengthsToHide]: (state) => {
+      return { ...state, enabled: !state["enabled"] };
+    }
+  },
+  { enabled: false, min: 0, max: 40 }
+);

package/src/redux/propertiesTool.js

@@ -0,0 +1,40 @@
+import createAction from "./utils/createMetaAction";
+import createMergedDefaultStateReducer from "./utils/createMergedDefaultStateReducer";
+
+// ------------------------------------
+// Actions
+// ------------------------------------
+// export const propertiesViewToggle = createAction(
+//   "TOGGLE_PROPERTIES_VIEW",
+//   () => {}
+// ); //NOTE!!:: second argument sanitizes actions so no payload is passed
+// export const propertiesViewOpen = createAction(
+//   "Open_PROPERTIES_VIEW",
+//   () => {}
+// ); //NOTE!!:: second argument sanitizes actions so no payload is passed
+export const propertiesViewTabUpdate = createAction("propertiesViewTabUpdate"); //NOTE!!:: second argument sanitizes actions so no payload is passed
+
+// ------------------------------------
+// Reducer
+// ------------------------------------
+export default createMergedDefaultStateReducer(
+  {
+    [propertiesViewTabUpdate]: (
+      state,
+      tabId,
+      selectedAnnotationOrAnnotationId
+    ) => {
+      return {
+        ...state,
+        selectedAnnotationId: selectedAnnotationOrAnnotationId
+          ? selectedAnnotationOrAnnotationId.id ||
+            selectedAnnotationOrAnnotationId
+          : undefined,
+        tabId
+      };
+    }
+  },
+  {
+    tabId: "general"
+  }
+);

package/src/redux/readOnly.js

@@ -0,0 +1,28 @@
+//./caretPosition.js
+import { createReducer } from "redux-act";
+import createAction from "./utils/createMetaAction";
+import { noop } from "lodash";
+
+// ------------------------------------
+// Actions
+// ------------------------------------
+export const toggleReadOnlyMode = createAction(
+  "TOGGLE_READ_ONLY_MODE",
+  noop
+); //NOTE!!:: second argument sanitizes actions so no payload is passed
+export const updateReadOnlyMode = createAction("UPDATE_READ_ONLY_MODE");
+
+// ------------------------------------
+// Reducer
+// ------------------------------------
+export default createReducer(
+  {
+    [updateReadOnlyMode]: (state, payload) => {
+      return payload;
+    },
+    [toggleReadOnlyMode]: state => {
+      return !state;
+    }
+  },
+  true
+);

package/src/redux/replacementLayers.js

@@ -0,0 +1,36 @@
+//./selectionLayer.js
+import { createReducer } from "redux-act";
+import createAction from "./utils/createMetaAction";
+import omit from "lodash/omit";
+
+// ------------------------------------
+// Actions
+// ------------------------------------
+export const replacementLayerClear = createAction("replacementLayerClear");
+export const replacementLayerUpdate = createAction("REPLACEMENT_LAYER_UPDATE");
+export const replacementLayerDelete = createAction("REPLACEMENT_LAYER_DELETE");
+
+// ------------------------------------
+// Reducer
+// ------------------------------------
+export default createReducer(
+  {
+    [replacementLayerClear]: () => {
+      return {};
+    },
+    [replacementLayerUpdate]: (state, payload) => {
+      return {
+        ...state,
+        [payload.id]: {
+          color: "darkolivegreen",
+          id: payload.id,
+          ...payload.range
+        }
+      };
+    },
+    [replacementLayerDelete]: (state, payload) => {
+      return omit(state, payload.id);
+    }
+  },
+  {}
+);

package/src/redux/restrictionEnzymes.js

@@ -0,0 +1,52 @@
+import { combineReducers } from "redux";
+import { createReducer } from "redux-act";
+import createAction from "./utils/createMetaAction";
+import specialCutsiteFilterOptions from "../constants/specialCutsiteFilterOptions";
+// ------------------------------------
+// Actions
+// ------------------------------------
+export const filteredRestrictionEnzymesUpdate = createAction(
+  "FILTERED_RESTRICTION_ENZYMES_UPDATE"
+);
+export const isEnzymeFilterAndUpdate = createAction("IS_ENZYME_FILTER_AND");
+export const filteredRestrictionEnzymesReset = createAction(
+  "FILTERED_RESTRICTION_ENZYMES_RESET"
+);
+export const filteredRestrictionEnzymesAdd = createAction(
+  "FILTERED_RESTRICTION_ENZYMES_ADD"
+);
+// ------------------------------------
+// Reducer
+// ------------------------------------
+const defaultInitialState = [specialCutsiteFilterOptions.single];
+// let initialState = defaultInitialState;
+// const localDefault = window.localStorage.getItem("tgInitialCutsiteFilter");
+
+// if (localDefault) {
+//   try {
+//     initialState = JSON.parse(localDefault);
+//     if (!Array.isArray(initialState)) throw new Error("Must be an array");
+//   } catch (e) {
+//     initialState = defaultInitialState;
+//   }
+// }
+
+export default combineReducers({
+  //filteredRestrictionEnzymes refer to the enzymes actively included in the react-select filter component
+  isEnzymeFilterAnd: createReducer(
+    {
+      [isEnzymeFilterAndUpdate]: (state, payload) => payload
+    },
+    false
+  ),
+  filteredRestrictionEnzymes: createReducer(
+    {
+      [filteredRestrictionEnzymesReset]: () => defaultInitialState,
+      [filteredRestrictionEnzymesUpdate]: (state, payload) => payload,
+      [filteredRestrictionEnzymesAdd]: function (state, payload) {
+        return [...state, payload];
+      }
+    },
+    defaultInitialState
+  )
+});

package/src/redux/selectedAnnotations.js

@@ -0,0 +1,89 @@
+import { showContextMenu } from "@teselagen/ui";
+import without from "lodash/without";
+import { createReducer } from "redux-act";
+import createAction from "./utils/createMetaAction";
+
+// ------------------------------------
+// Actions
+// ------------------------------------
+export const annotationSelect = createAction("VE_ANNOTATION_SELECT");
+export const updateSelectedAnnotation = createAction(
+  "VE_ANNOTATION_UPDATE_SELECTED"
+);
+export const annotationDeselect = createAction("VE_ANNOTATION_DESELECT");
+export const annotationDeselectAll = createAction("VE_ANNOTATION_DESELECT_ALL");
+
+export function replacementLayerRightClicked({ event, annotation }, meta) {
+  event.preventDefault();
+  event.stopPropagation();
+  return function (dispatch /* getState */) {
+    const items = [
+      {
+        text: "Remove Edit",
+        onClick: function () {
+          dispatch({
+            type: "REPLACEMENT_LAYER_DELETE",
+            meta,
+            payload: { ...annotation }
+          });
+        }
+      }
+    ];
+
+    showContextMenu(items, undefined, event);
+  };
+}
+
+// ------------------------------------
+// Reducer
+// ------------------------------------
+const startingState = {
+  idMap: {},
+  idStack: []
+};
+export default createReducer(
+  {
+    [annotationSelect]: (state, payload) => {
+      if (!payload.id) throw new Error("Annotation must have an id!");
+      const newState = {
+        idMap: {
+          ...state.idMap,
+          [payload.id]: payload
+        },
+        idStack: [...state.idStack, payload.id]
+      };
+      return newState;
+    },
+    [annotationDeselect]: (state, payload) => {
+      const id = payload.id || payload;
+      const idMap = { ...state.idMap };
+      delete idMap[id];
+      const idStack = without(state.idStack, id);
+      return {
+        idMap,
+        idStack
+      };
+    },
+    [updateSelectedAnnotation]: (state, payload) => {
+      const id = payload.id;
+      const idMap = { ...state.idMap };
+      if (!idMap[id]) {
+        return state;
+      }
+      return {
+        idMap: {
+          ...idMap,
+          [id]: {
+            ...idMap[id],
+            ...payload
+          }
+        },
+        idStack: state.idStack
+      };
+    },
+    [annotationDeselectAll]: () => {
+      return startingState;
+    }
+  },
+  startingState
+);

package/src/redux/selectedPartTags.js

@@ -0,0 +1,21 @@
+import { createReducer } from "redux-act";
+import createAction from "./utils/createMetaAction";
+
+// ------------------------------------
+// Actions
+// ------------------------------------
+
+export const updateSelectedPartTags = createAction("UPDATE_SELECTED_PART_TAGS");
+
+// ------------------------------------
+// Reducer
+// ------------------------------------
+
+export default createReducer(
+  {
+    [updateSelectedPartTags]: (state, payload) => {
+      return { ...state, parts: payload };
+    }
+  },
+  {}
+);

package/src/redux/selectionLayer.js

@@ -0,0 +1,46 @@
+//./selectionLayer.js
+import { createReducer } from "redux-act";
+import createAction from "./utils/createMetaAction";
+
+// ------------------------------------
+// Actions
+// ------------------------------------
+export const selectionLayerClear = createAction("SELECTION_LAYER_CLEAR");
+export const selectionLayerUpdate = createAction("SELECTION_LAYER_UPDATE");
+
+// ------------------------------------
+// Reducer
+// ------------------------------------
+export default createReducer(
+  {
+    CARET_POSITION_UPDATE: () => {
+      //clear the selection layer if the caret is updated!
+      return {
+        start: -1,
+        end: -1
+      };
+    },
+    [selectionLayerClear]: () => {
+      return {
+        start: -1,
+        end: -1
+      };
+    },
+    [selectionLayerUpdate]: (state, newSelectionLayer) => {
+      if (
+        !newSelectionLayer ||
+        !(newSelectionLayer.start >= 0 && newSelectionLayer.end >= 0)
+      ) {
+        console.error(
+          "we should never be here! selectionLayerUpdate must always be called with a valid selection layer"
+        );
+        return state
+      }
+      return newSelectionLayer;
+    }
+  },
+  {
+    start: -1,
+    end: -1
+  }
+);

package/src/redux/sequenceData/circular.js

@@ -0,0 +1,19 @@
+import { createReducer } from "redux-act";
+import createAction from "../utils/createMetaAction";
+
+// ------------------------------------
+// Actions
+// ------------------------------------
+export const _updateCircular = createAction("UPDATE_CIRCULAR");
+
+// ------------------------------------
+// Reducer
+// ------------------------------------
+export default createReducer(
+  {
+    [_updateCircular]: (state, payload) => {
+      return payload;
+    }
+  },
+  true
+);

package/src/redux/sequenceData/description.js

@@ -0,0 +1,21 @@
+import { createReducer } from "redux-act";
+import createAction from "../utils/createMetaAction";
+
+// ------------------------------------
+// Actions
+// ------------------------------------
+export const sequenceDescriptionUpdate = createAction(
+  "sequenceDescriptionUpdate"
+);
+
+// ------------------------------------
+// Reducer
+// ------------------------------------
+export default createReducer(
+  {
+    [sequenceDescriptionUpdate]: (state, payload) => {
+      return payload;
+    }
+  },
+  ""
+);

package/src/redux/sequenceData/features.js

@@ -0,0 +1,19 @@
+import { createReducer } from "redux-act";
+import createAction from "../utils/createMetaAction";
+import upsertDeleteActionGenerator from "./upsertDeleteActionGenerator";
+
+// ------------------------------------
+// Actions
+// ------------------------------------
+export const upsertFeature = createAction("UPSERT_FEATURE");
+export const deleteFeature = createAction("DELETE_FEATURE");
+
+// ------------------------------------
+// Reducer
+// ------------------------------------
+export default createReducer(
+  {
+    ...upsertDeleteActionGenerator(upsertFeature, deleteFeature),
+  },
+  {}
+);

package/src/redux/sequenceData/index.js

@@ -0,0 +1,81 @@
+import deepEqual from "deep-equal";
+import { tidyUpSequenceData } from "@teselagen/sequence-utils";
+import uuid from "shortid";
+
+import createAction from "../utils/createMetaAction";
+import features from "./features";
+import parts from "./parts";
+import name from "./name";
+import description from "./description";
+import primers from "./primers";
+import sequence from "./sequence";
+import circular from "./circular";
+import materiallyAvailable from "./materiallyAvailable";
+import translations from "./translations";
+import combineReducersDontIgnoreKeys from "../../utils/combineReducersDontIgnoreKeys";
+// import cleanSequenceData from "../../utils/cleanSequenceData";
+
+import { createReducer } from "redux-act";
+// export * from './sharedActionCreators';
+export * from "./primers";
+export * from "./features";
+export * from "./parts";
+export * from "./name";
+export * from "./description";
+// export * from './sequence';
+export * from "./circular";
+export * from "./materiallyAvailable";
+export * from "./translations";
+
+// ------------------------------------
+// Actions
+// ------------------------------------
+
+const _updateSequenceData = createAction("SEQUENCE_DATA_UPDATE");
+export const updateSequenceData = function (seqData, ...rest) {
+  //tnrtodo: currently we're not using that type variable for anything
+  return _updateSequenceData(
+    tidyUpSequenceData(seqData, { annotationsAsObjects: true }),
+    ...rest
+  );
+};
+
+// ------------------------------------
+// Reducer
+// ------------------------------------
+
+const coreReducer = combineReducersDontIgnoreKeys({
+  primers,
+  features,
+  parts,
+  sequence,
+  translations,
+  size: (state = {}) => state,
+  circular,
+  materiallyAvailable,
+  name,
+  description,
+  fromFileUpload: createReducer({}, false)
+});
+
+export default function (state, action) {
+  let stateToPass = state;
+  if (action.type === "SEQUENCE_DATA_UPDATE") {
+    stateToPass = action.payload;
+  }
+  //tnr: do a clone deep here in order to make sure we are using a totally new object for undo/redo tracking
+  // stateToPass = cloneDeep(stateToPass);
+
+  const newState = coreReducer(stateToPass, action);
+  if (deepEqual(newState, state)) {
+    return state;
+  } else {
+    //tnr: do a clone deep here in order to make sure we are using a totally new object for undo/redo tracking
+    // mm: we don't need this if we are not mutating the newState, which we shouldn't be doing.
+    return {
+      // ...cloneDeep(newState),
+      ...newState,
+      stateTrackingId: newState.stateTrackingId ? uuid() : "initialLoadId"
+    };
+  }
+}

package/src/redux/sequenceData/lineageLines.js

@@ -0,0 +1,11 @@
+import { createReducer } from "redux-act";
+
+// ------------------------------------
+// Actions
+// ------------------------------------
+// export const caretPositionClear = createAction('caretPositionClear')
+
+// ------------------------------------
+// Reducer
+// ------------------------------------
+export default createReducer({}, []);

package/src/redux/sequenceData/materiallyAvailable.js

@@ -0,0 +1,19 @@
+import { createReducer } from "redux-act";
+import createAction from "../utils/createMetaAction";
+
+// ------------------------------------
+// Actions
+// ------------------------------------
+export const updateAvailability = createAction("updateAvailability");
+
+// ------------------------------------
+// Reducer
+// ------------------------------------
+export default createReducer(
+  {
+    [updateAvailability]: (state, payload) => {
+      return payload;
+    }
+  },
+  true
+);

package/src/redux/sequenceData/name.js

@@ -0,0 +1,19 @@
+import { createReducer } from "redux-act";
+import createAction from "../utils/createMetaAction";
+
+// ------------------------------------
+// Actions
+// ------------------------------------
+export const sequenceNameUpdate = createAction("sequenceNameUpdate");
+
+// ------------------------------------
+// Reducer
+// ------------------------------------
+export default createReducer(
+  {
+    [sequenceNameUpdate]: (state, payload) => {
+      return payload;
+    }
+  },
+  "Untitled Sequence"
+);

package/src/redux/sequenceData/parts.js

@@ -0,0 +1,19 @@
+import { createReducer } from "redux-act";
+import createAction from "../utils/createMetaAction";
+import upsertDeleteActionGenerator from "./upsertDeleteActionGenerator";
+
+// ------------------------------------
+// Actions
+// ------------------------------------
+export const upsertPart = createAction("UPSERT_PART");
+export const deletePart = createAction("DELETE_PART");
+
+// ------------------------------------
+// Reducer
+// ------------------------------------
+export default createReducer(
+  {
+    ...upsertDeleteActionGenerator(upsertPart, deletePart)
+  },
+  {}
+);

package/src/redux/sequenceData/primers.js

@@ -0,0 +1,19 @@
+import { createReducer } from "redux-act";
+import createAction from "../utils/createMetaAction";
+import upsertDeleteActionGenerator from "./upsertDeleteActionGenerator";
+
+// ------------------------------------
+// Actions
+// ------------------------------------
+export const upsertPrimer = createAction("UPSERT_PRIMER");
+export const deletePrimer = createAction("DELETE_PRIMER");
+
+// ------------------------------------
+// Reducer
+// ------------------------------------
+export default createReducer(
+  {
+    ...upsertDeleteActionGenerator(upsertPrimer, deletePrimer)
+  },
+  {}
+);

package/src/redux/sequenceData/sequence.js

@@ -0,0 +1,12 @@
+import { createReducer } from "redux-act";
+import createAction from "../utils/createMetaAction";
+
+// ------------------------------------
+// Actions
+// ------------------------------------
+export const addBps = createAction("addBps");
+
+// ------------------------------------
+// Reducer
+// ------------------------------------
+export default createReducer({}, "");

package/src/redux/sequenceData/translations.js

@@ -0,0 +1,20 @@
+import { createReducer } from "redux-act";
+import createAction from "../utils/createMetaAction";
+import upsertDeleteActionGenerator from "./upsertDeleteActionGenerator";
+
+// ------------------------------------
+// Actions
+// ------------------------------------
+export const _upsertTranslation = createAction("UPSERT_TRANSLATION");
+export const deleteTranslation = createAction("DELETE_TRANSLATION");
+
+const defaultValue = {};
+// ------------------------------------
+// Reducer
+// ------------------------------------
+export default createReducer(
+  {
+    ...upsertDeleteActionGenerator(_upsertTranslation, deleteTranslation)
+  },
+  defaultValue
+);

package/src/redux/sequenceData/upsertDeleteActionGenerator.js

@@ -0,0 +1,31 @@
+import omit from "lodash/omit";
+import uuid from "shortid";
+
+// ------------------------------------
+// Reducer
+// ------------------------------------
+export default function upsertDeleteActionGenerator(
+  upsertAction,
+  deleteAction
+) {
+  return {
+    [upsertAction]: (state, payload) => {
+      const idToUse = payload.id || uuid();
+      return {
+        ...state,
+        [idToUse]: { ...(state[idToUse] || {}), ...payload, id: idToUse }
+      };
+    },
+    [deleteAction]: (state, payload) => {
+      let ids;
+      if (Array.isArray(payload)) {
+        ids = payload.map((val) => {
+          return val.id || val;
+        });
+      } else {
+        ids = [payload.id || payload];
+      }
+      return omit(state, ids);
+    }
+  };
+}