Skip to content

Commit

Permalink
Merge pull request #1221 from briehl/PTV-682-pangenome-widget
Browse files Browse the repository at this point in the history 
PTV-682 - temp fix to Pangenome viewer
  • Loading branch information
@briehl
briehl committed Dec 16, 2017
2 parents 2935f95 + 9f670e3 commit 16a0cf4
Show file tree
Hide file tree
Showing 3 changed files with 24 additions and 48 deletions.
4 changes: 1 addition & 3 deletions kbase-extension/static/kbase/js/kbaseNarrative.js
View file
Original file line number Diff line number Diff line change
Expand Up @@ -837,16 +837,14 @@ define([
nearIdx = 0;
if (cell) {
nearIdx = Jupyter.notebook.find_cell_index(cell);
$(cell.element).off('dblclick');
$(cell.element).off('keydown');
}
var objInfo = {};
// If a string, expect a ref, and fetch the info.
if (typeof obj === 'string') {
objInfo = this.sidePanel.$dataWidget.getDataObjectByRef(obj, true);
}
// If an array, expect it to be an array of the info, and convert it.
else if (obj instanceof Array) {
else if (Array.isArray(obj)) {
objInfo = ServiceUtils.objectInfoToObject(obj);
}
// If not an array or a string, it's our object already.
Expand Down
6 changes: 5 additions & 1 deletion kbase-extension/static/kbase/js/widgets/function_output/kbasePanGenome.js
View file
Original file line number Diff line number Diff line change
Expand Up @@ -36,7 +36,11 @@ define([

init: function(options) {
this._super(options);
this.objRef = this.options.ws + '/' + this.options.name;
if (this.options.name.indexOf('/') > -1) {
this.objRef = this.options.name;
} else {
this.objRef = this.options.ws + '/' + this.options.name;
}
if (!ApiUtil.checkObjectRef(this.objRef)) {
this.$elem.append(Display.createError('Bad object.', 'PanGenome Object Unavailable.'));
this.isError = true;
Expand Down
62 changes: 18 additions & 44 deletions kbase-extension/static/kbase/js/widgets/narrative_core/kbaseNarrativeWorkspace.js
View file
Original file line number Diff line number Diff line change
Expand Up @@ -130,10 +130,10 @@ define([
// This property is only set in accordance with the Jupyter.notebook.writable property.
// It is set here, at the outset, and also in a listener for the
// 'updateReadOnlyMode.Narrative' jquery event, which, as far as I can tell
// is not issued anywhere in the system. The effect of this would be to
// is not issued anywhere in the system. The effect of this would be to
// cause a narrative to flip from edit->view or view->edit while a user is
// engaged with the narrative. This seems like a jarring experience, and would
// certainly need some ui mechanism like a dialog to explain what is happening
// engaged with the narrative. This seems like a jarring experience, and would
// certainly need some ui mechanism like a dialog to explain what is happening
// to the user.
// So, effectively, this is a constant.
this.narrativeIsReadOnly = !Jupyter.notebook.writable;
Expand All @@ -147,21 +147,21 @@ define([

// The "inReadOnlyMode" is the user-configurable setting for this.
// TODO: it should be renamed to something else. It is confusing to have
// the permanent "not writable == narrativeIsReadOnly == readonly" setting,
// which reflects the (during this runtime session) permanent state of the
// the permanent "not writable == narrativeIsReadOnly == readonly" setting,
// which reflects the (during this runtime session) permanent state of the
// narrative.
// this.inReadOnlyMode = false;

// isViewMode is really a cheap way of representing edit mode.
// If false, the mode is 'edit', if true the mode is 'view'.
// If there were more than two modes, we would need to store this as
// If there were more than two modes, we would need to store this as
// another type of value -- string or number.
// this.isViewMode = false;
// uiMode is one of 'edit', view'.
// A string enum, because although we have two ui states now,
// edit, which basically follows read-write
// A string enum, because although we have two ui states now,
// edit, which basically follows read-write
// view, which shadows read-only
// we may have additional modes (as has been discussed) -
// we may have additional modes (as has been discussed) -
this.uiMode = this.narrativeIsReadOnly ? 'view' : 'edit';
Jupyter.narrative.uiMode = this.uiMode;

Expand Down Expand Up @@ -764,11 +764,11 @@ define([
// within these enter... calls above.

// In true read-only (non-writable) mode, the view-mode toggle button
// is not available. Interestingly, this function can only be called
// is not available. Interestingly, this function can only be called
// from the toggle button itself..., so I've disabled that logic and it
// should just be removed...
// If this narrative became read-only after the toggle button was rendered,
// then simply disabling the class-switching is not enough, the entire
// then simply disabling the class-switching is not enough, the entire
// mechanism should be disabled (and the button hidden as well.)
// if (!this.narrativeIsReadOnly) {
var icon = $('#kb-view-mode span');
Expand All @@ -779,7 +779,7 @@ define([

// Warning, do not look for the code for this ... it will burn your
// eyes out to their bare sockets.
// Note also, there is code in this module which supposdly does the same thing
// Note also, there is code in this module which supposdly does the same thing
// (see readOnlyMode, readWriteMode), but doesn't seem to work.
Jupyter.CellToolbar.rebuild_all();
this.runtime.bus().emit('read-only-changed', {
Expand Down Expand Up @@ -972,10 +972,10 @@ define([
* This is called during initialization and by the view-mode toggle.
* Note that this is for the view-only ui mode, and thus the narrative
* itself may be writable (read-write). This crossover of terminology is
* a bit confusing to follow, and thus I've attempted to introduct the
* ui view/edit mode as orthgonal to narrative
* a bit confusing to follow, and thus I've attempted to introduct the
* ui view/edit mode as orthgonal to narrative
* permission (read-only/read-write/read-write-share).
*
*
* TODO: probably a better design to set the read / view only flags
* and thsn simply render everything that is interested in this.
* Otherwise, we just have to propogate the state that _will_ be true when
Expand Down Expand Up @@ -1039,7 +1039,7 @@ define([

/**
* Set narrative from read-only mode to read-write mode
* This is only called in the context of an editable Narrative
* This is only called in the context of an editable Narrative
* in which the user is togging between view/edit mode in order
* to evaluate how the narrative appears on view-only mode.
*
Expand Down Expand Up @@ -1979,9 +1979,8 @@ define([
},


createViewerCell: function (cellIndex, data, widget) {
createViewerCell: function (cellIndex, data) {
var placement = data.placement || 'below';
var cell;
var cellData = {
type: 'data',
objectInfo: data.info
Expand All @@ -1991,31 +1990,6 @@ define([
} else {
Jupyter.notebook.insert_cell_below('code', cellIndex, cellData);
}
// var title = (data.info && data.info.name) ? data.info.name : 'Data Viewer';
// var type = 'viewer';
// $(cell.element).trigger('toggleCodeArea.cell');


// var meta = {
// 'kbase': {
// 'attributes': {
// 'status': 'new',
// 'title': title
// },
// 'type': 'output',
// 'subtype': 'data'
// }
// };
// cell.metadata = meta;
// cell.execute();
// $([Jupyter.events]).trigger('inserted.Cell', {
// cell: cell,
// kbase: {
// type: 'data'
// },
// objectInfo: data.info
// });

},

/**
Expand Down Expand Up @@ -2539,4 +2513,4 @@ define([
return color;
}
});
});
});

0 comments on commit 16a0cf4

Please sign in to comment.