What's New - Pipette Release Notes

Last Updated: Oct 31, 2016 12:11AM PDT

Summary: These release notes cover new features, improvements, and resolved issues for Pipette Analysis. Most of the updates are intended for end users, unless otherwise noted.

Updates

v2.10.1 (23-Oct-2016)

Category Subcategory Description
Charting Resolved Issue (Minor) Fix issue causing a page reload when removing a chart when the title is being edited.
Sketcher Resolved Issue (Minor)

Write abbreviation s groups to RXN file, rather than just the explicit chemistry.

Render bond reacting center status for reaction bonds if it is present on the input data.

Render valence for atoms if it is present on the input data.

Render ring bond count for atoms if it is present on the input data.

Render query hydrogen count for atoms if it is present on the input data.

Render query substitution count for atoms if it is present on the input data.

Render radicals for atoms if it is present on the input data.

Improve rendering of partial haptic bonds read from non-Pipette mol files.

Support atom mapping for reactions.

For Developers:

Category Subcategory Description
Sketcher Resolved Issue (Major) Fix loading of abbreviations on Linux.

v2.10.0 (08-Oct-2016)

Category Subcategory Description
Charting Resolved Issue

Added an Export button to the grid, to allow the data to be sent to Excel with the correct columns.

Added a histogram to numeric filters to aid with filtering.
Sketcher Resolved Issue

Allow pass-through of molfile features in pasted structures that cannot yet be edited in Pipette. This includes radicals, query substitution count, query hydrogen count, valence, and ring bond count.

Allow the user to pick from a set of functional group abbreviations, such as COOMe, that are available on the Pipeline Pilot server. These groups can the expanded or collapsed as required.

For Developers:

Category Subcategory Description
Charting Improvement User context passed on the URL is passed to the Create and Remove Template Services to ensure any custom folder lookup service has access to it.

v2.91 (30-Aug-2016)

Category Subcategory Description
Charting Improvement Significantly improved performance of table scrolling and grouping in Internet Explorer.
Sketcher Resolved Issue (Minor) Improve display of reaction cleared screen.

For Developers:

Category Subcategory Description
Charting Improvement Some double character combinations such as __ || and ;; are special in the charting URL fragment as they delimit dashboards. If these are present in property names, they are escaped with a \ before being written to the URL fragment (hash).

v2.90 (16-Aug-2016)

Category Subcategory Description
Charting Improvements

Calculate the number of points in the dataset correctly for datasets with very sparse data. This avoids switching over to server-side mode unless needed.

Improve performance of various dialogs when many hundreds of properties are available.

Increase the number of columns allowed on the grid from 16 to 500.

Display intuitive message when card view is too narrow to show cards.
Charting Resolved Issues (Minor) Property names containing the characters correctly read and write the chart definition on the page URL.
Sketcher Improvements

Switch Add Fragment and Remove Fragment buttons, so the Remove Fragment button does not appear under the mouse when adding multiple fragments.

Do not show the Remove Fragment button for a single empty R group fragment, as it is not needed.

Do not show the join atoms change when they are already joined.

Allow the periodic table to be closed by pressing the Esc key.

Improve the display of the periodic table.

Support reading V3000 RXN files.
Sketcher Resolved Issues (Minor)

Improve format for writing repeat units to mol files, so it can be ready by a wider range of tools.

Ensure error message is shown when dropping a second .mol file that contains unsupported features.
Pipelining Improvement Update the repeat unit star atom appearance to match the standard Biovia depiction.

For Developers:

Category Subcategory Description
Charting Improvements postMessage calls are queued until the app is ready to handle them. This means applications launching the charting can be more aggressive at passing in config and other settings.

When embedded on another page, ensure charting sets the # containing the chart configuration on the frame, not the main page.

Avoid flicker when launching the charting in fullscreen mode when embedded in another application.
Pipelining Improvement Added a _userContext URL parameter to Charting and Pipelining. The value of this is passed on to the services that list the services, outputs and templates. If a custom protocol provides these items, the user context can filter the results.
Sketcher Improvement Check if the Sketcher Pipeline Pilot component is allowed to break out of the iframe before attempting it. This may not be allowed if the parent window is running on a different domain.

2.8.0 (20-Jun-2016)

Category Subcategory Description
Sketcher Resolved Issue Fix rendering of structures with * atoms, but bonds from it are incorrectly defined as single bonds, not coordination bonds.
Sketcher Improvements Ensure pasting in a structure and dropping in a .mol file behave consistently and perform a 2D layout.
Do not show an unsupported feature message due to abbreviation groups that are expanded by default.
Ensure structures pasted in with stereo bonds are cleaned the first 2D layout is performed.

For Developers:

Category Subcategory Description
Charting Improvements To restore the selection from a previous session, the selection message can be passed back into Pipette Charting.
Pipette Charting fires a filter event whenever users add, remove or change filters on the filters tab.
Selection message can be passed back into Pipette Charting to restore selection from a previous session.
Filter message can be passed back into Pipette Charting to restore filters from a previous session.
Added support for highlighting new table data using highlightProperty metadata.
Added support for hiding properties in Pipette Charting using hidden metadata.
Sketcher Resolved Issue Make Sketcher API consistent whenever users clear the current compound. In all uses of the API, this now sends back an empty string.
Improvement Do not display an unsupported feature message due to repeat unit brackets with an explicit position in the .mol file.

v2.7.0 (March 6 2016)

Category Subcategory Description
Analysis Resolved Issue (Minor) Categorical chart data is now exported correctly when the category is numeric, but stored as a string in the raw data set.
Improvements Implemented better placement of histogram tooltips on tall bars that are close to the top edge of the browser.
When creating a table without defining the columns, the order of the data properties on the first data record is now used.
Sketcher Resolved Issue (Minor) Fixed an issue that caused an error when a reaction is dropped into the Sketcher.
Improvements When getting files locally, the crossorigin script tag attribute is not set.
Added prototype support for reading simple helm strings.
By default, the Sketcher JavaScript, CSS, and images are retrieved from the package, and not from the Content Delivery Network.

v2.60 (February 29 2016)

Category Subcategory Description
Analysis Improvements Changed default display for charting when launched from the new Pro Client.
    Analyze service use protocol no longer generates an error log file if users have never run a service.
Sketcher Improvements Added service to get HELM monomers.
    Changed the depiction of r group attachment points in images to the zigzag representation.

For Developers:

Category Subcategory Description
Sketcher Improvement Added an editable package global to allow the sketcher to run without a connection to Amazon.

v2.5.2 (Nov 18 2015)

Category Subcategory Description
Charting Resolved Issue (Trivial) The 3D scatter plot is no longer colored by non-categorical strings.
Sketcher Improvements Show homopolymer labels in lowercase.
Allow rotate and flip in iPhone sketcher.

v2.5.1 (Nov 16 2015)

Category Subcategory Description
Charting Resolved Issue (Trivial) Ensure charts are rendered correctly when paging through them very quickly in the single page view.
Ensure the table re-renders correctly when charts are added to the dashboard.
Hosting Improvement Improve startup performance by using pre-compressed libraries.
Sketcher Improvement Do not load organization names in Get Details for Sketcher
Enhance details captured for startup performance.

For Developers:

Category Subcategory Description
Sketcher New Feature Allow the help link to be hidden in the Sketcher by using the nohelplink body class.

v2.5.0 (Nov 08 2015)

Category Subcategory Description
Charting Resolved Issue Fix issue with Chrome dialog remaining open when changing a table restricted to a selection, to a chart.
Pipelining Improvement Improved service list keyboard paging when mouse hovers a list item.
Sketcher Improvement Create Pipette version of Depict SMILES example.

For Developers:

Category Subcategory Description
Pipelining Improvement Removed component whitelisting functionality added in 2.4.0.
Sketcher Improvement Add new postMessage('save') functionality that saves the Sketcher's current structure to the user's folder on the Pipeline Pilot server for 24 hours. This can be used to render preview images in situations where cross-domain issues prevented the preview service being called in older versions. This is documented fully in the Sketcher Integration Guide.
SMILES strings can be sent to the sketcher via the API (they were previously supported through Ctrl+V paste).

v2.4.3 (Nov 05 2015)

Category Subcategory Description
Charting Resolved Issue (Minor) Ensure chain and ring query bonds are written correctly in all cases.
Ensure table columns can be reordered correctly in Microsoft Internet Explorer 10.
Improvement If the color range is a log scale, clearly indicate on the color range bar.
Pipelining Improvement Ensure Required Parameters dialog is displayed when the service from the service list is selected with the keyboard.
Sketcher Resolved Issue (Trivial) Avoid flagging of single Chiral Center and Enantiomers.
Resolved Issue (Major) If relative stereochemistry is present, write out abs groups in v3000 .mol file.
Improvement Make coordination bond heads arrows closed.

 

v2.4.2 (Oct 30 2015)

Category Subcategory Description
Charting Resolved Issue (Minor) When more than 1,000 data points are filtered, ensure that axis sizes are reduced, if needed.
Improvement Support a custom title for each chart. This is saved to both the URL and template.
Improve number formatting in boxplot tooltips.
Allow the xy plot x-axis to be categorical.
When the Charting application is in maximized mode, a full-screen Chart button is included.
When table or card view is restricted to the selection and no selection is available, a message (No Data Selected) is displayed. Previously, all data was shown.

v2.4.1 (Sept 25 2015)

Category Subcategory Description
Charting Resolved Issue (Trivial) Boxplot tooltips are now available after boxplot configuration is changed.
Resolved Issue (Major) Avoid switch from stacked to single categorical histogram causing incorrect rendering.
Improvements A mean indicator was added to boxplots and their tooltips.
When the x-axis is a single property broken down into several categorical values, the boxplot y-axis is labeled.
Improved radar plot rendering, by removing labels when the radar chart is very small, (such as trellised and on a dashboard).
Support was added to log scales for platemap well colors and heatmap cell colors.
Long column headings now wrap in the charting table view.
Box plot coloring was enhanced.
Sketcher Improvement Sketcher footer now includes a help link.

v2.4.0 (Sept 16 2015)

Category Subcategory Description
Charting Resolved Issue (Major) When it locked to a selection, tables no longer snap back to the first row.
Resolved Issues (Minor) Fixed reordering of columns in the table by drag and drop.
Radar plots can now display up to 1,000 records on each page, not just for the full dataset.
Resolved Issue (Trivial) After the charting dataset is filtered, an internal __pipette_type property is no longer shown in some lists of properties.
Improvement Unnecessary decimal numbers are no longer displayed on the histogram y-scale.
Boxplots now have useful tooltips that display the values for the distribution.
Toggling the Restrict to Selection button on tables and cards no longer clears the selection.
Improved the appearance of boxplots that contain data that is close to 0, but is not negative.
The Chart Picker dialog now displays chart name in a tooltip.
Improved clarity of shading for platemap wells with no data.
A new icon was introduced for Surface Plot with Outliers.
To enhance clarity, axis names for platemaps was renamed to Well Color and Border Color.
Alternative Charts button was removed to simplify chart setup.
Support log x-scale on server-side histograms (this was already supported on client-side histograms).
Pipelining Improvements Remove has priority when a property is both renamed and removed in the Rename dialog.
Unicode characters in service names, parameters, and data are now rendered correctly.
Whitelist more service help HTML tags, including tables.

For Developers:

Category Subcategory Description
Charting Improvement Upgraded to latest D3 charting libraries.
Added a flag to prevent Pipette log files from being overwritten when the package is reinstalled. This will only work with recent builds of Pipeline Pilot.
Pipelining Improvement Components can now be published as service without wrapping them in a Pipeline Pilot Protocol. The components or component folders need to be listed in a file specified in the ComponentWhitelist package global.

2.3.8 (24-Aug-2015)

Category Subcategory Description
Charting Resolved Issue (Trivial) Prevent 3D scatter plot display option for trellising.
Pipelining Resolved Issue (Trivial) Prevent tooltips from remaining when a data store is removed.
Resolved Issue (Major) Workaround popup blockers prevent reports from being displayed, if they show a form for user input before the report is rendered.

For Developers:

Category Subcategory Description
Pipelining Resolved Issue (Major) Workaround popup blockers prevent reports from being displayed, if they show a form for user input before the report is rendered.

2.3.7 (03-Aug-2015)

Category Subcategory Description
Charting New Feature Added support for paging of charts using non-categorical properties. Applies to heat maps, plate maps, box plots, radar plots, and xy plots.
Resolved Issue (Trivial) Ensure brushing on trellised histograms always works correctly on the y axis.
Improvements
  • Update non-trellised plate map empty well depiction to match the prettier depiction on trellised plate maps.
  • Allow plate map border to be colored with a fifth property. This is useful for highlighting positive or negative controls.
  • Allow histograms to be paged using non-categorical properties.
  • Keep the number of bins the same in trellised and non-trellised histograms.
  • Improve histogram selection performance.
  • Do not show decimal places on the color range bar, if the color property is an integer.
  • Label trellised histograms with both the property on the x axis and the trellis value.

2.3.6 (16-July-2015)

Category Subcategory Description
Charting New Features

Added support for log x axes on histograms.

Card view can be set to show just the selected data using the Restrict button in the chart header.

Enable moving of dashboard charts using keyboard arrow keys.

Show distribution of numeric property values in the Property Info popup.

Improvements
  • Added support for trellised line plots when several properties are broken down by a categorical property.
  • Added support for coloring radar plot lines using a categorical property.
  • Added support for trellised histogram plots when a categorical property is provided to color by.
  • To show that data is continuous, removed whitespace between bars in numeric histograms.
  • To optimize display of trellised charts, improved trellis layout rules.
  • Added support for trellised radar plots when a categorical property is provided to color by.
  • Added support for trellised box plots when several properties are broken down by a categorical property.
  • For easier selection, grouped the different plots in the Configure Chart dialog.
  • Stacked histograms are colored with different colors.


For easier plot type selection, the following icons were combined:

  • Histogram and stacked histogram plot
  • Trellised and non-trellised icons for plate maps, heat maps, and XY plots
  • Standard and min / max radar plot
  • Box plot
  • Line plot
  • Word Cloud plot

2.3.5 (1-July-2015)

Category Subcategory Description
Charting New Feature To support exploring trends in data, multiple values can be displayed on each well in plate maps.
Improvements
  • Change table behavior so a single click adds or removes the row to / from the current selection.
  • Add tooltips for Fullscreen, Remove, and Lock to Selection buttons on plots.
  • Ensure table selection is not cleared when sorting on column values.
  • The left and right arrow keys can be used to navigate the records in the current Pipette Pipelining step.
  • Increased the width of labels in the Service Settings dialog to enhance reading online.
  • Improved wording in the Filter dialog to ensure that currently selected data is clearly described.
Resolved Issue (Minor) Spaces in list box values are now correctly handled for custom Pipeline Pilot service setting forms.
For Developers:
Category Subcategory Description
Charting New Feature Selection events are fired, enabling applications launching Pipette Charting to monitor and respond to the current user selected data.

2.3.4 (8-Jun-2015)

Category Subcategory Description
Pipelining Improvement Long filenames, without spaces, underscores, or camel case, wrap correctly in the data pool.

Pipelining

Resolved Issues (Minor)

  • Array parameters are no longer displayed in the Filters dialog.
  • Protocol form parameterization for services displays correctly in Pipeline Pilot 9.5.

2.3.3 (31-May-2015)

Category Subcategory Description
Sketcher Resolved Issue (Minor) Multiple compounds with R groupings are serialized correctly.

2.3.2 (21-May-2015)

Category Subcategory Description
Sketcher Improvement Parameter metadata on Pipette Sketcher component is now hidden.

2.3.1 (13-May-2015)

Category Subcategory Description
Charting Resolved Issues (Major) The newest version of the Chrome web browser stopped working with certain histograms. A workaround was added to correct this problem.
Resolved Issues (Minor) Column sorting in table clearing the selection on the table, but not on other charts, is prevented for consistency.
Sketcher Resolved Issue (Trivial) Move Fragment Right keyboard shortcut icon now works correctly.

Resolved Issues (Minor)

  • Undo on R grouping always acts correctly.
  • Empty fragments are not allowed to have repeat units defined.

2.3.0 (10-May-2015)

Category Subcategory Description
Charting Improvement Table column width is preserved when columns are reordered in the table.

Resolved Issues (Minor)

  • Chart configuration remains consistent when properties are filtered out.
  • Only XY Trellis chart selections are displayed for the current category being selected.

Sketcher

New Features

  • Repeat unit support added both at the fragment level and inline within structures.
  • Improved control over R group numbering, including the ability to have multiple R groups with the same number.
  • Fragments can be assigned to R groupings in Markush structures. These groupings are automatically added when there is a numbered R group in the structure.

Improvements

  • Pipette Sketcher component now supports changing the size from the default 200x200 pixels.
  • Add a Show Properties from Pipette Sketcher example to match the JDraw and standalone sketcher versions.

Resolved Issues (Minor)

  • The correct Delete Atom button is displayed when an atom is removed from a ring and after the Undo button is used.
  • Pipette Sketcher component cannot have its OK button clicked before server-side compound layouts are complete.
For Developers:
Category Subcategory Description
Sketcher Resolved Issue (Minor) Pipette Sketcher API function getMolFile can now accept a callback that is called once any server-side layouts are done. This callback approach should be used in preference to the mol file returned by getMolFile.
Pipelining Improvement Pipette server-side logs are written in their own subfolder.

2.2.3 (13-Apr-2015)

Category Subcategory Description

Charting

Improvements

  • Added intuitive tooltips to the property types on the Property Info dialog.
  • A legend for the color ranges on XY plots is displayed when appropriate.
  • Chart loading performance is improved.
  • Increased the number of columns allowed on the table to 16.

Sketcher

Improvements

  • Positioning of auto-positioned attachment points is improved.
  • Pasted text is shown when it cannot be processed as a valid chemistry format.

2.2.2 (6-Apr-2015)

Category Subcategory Description
Charting New Feature A new Charting Data Summary box shows the current data source, number of records, and number of properties. It also allows property types to be previewed.

Improvements

  • Moved the ability to lock the table display to the selection into the header.
  • Table columns can now be reordered using drag and drop.
  • List picker interface was enhanced for better usage.
  • Switched chart table to the new library to allow improved future functionality.

Pipelining

Improvement

Style and size of Settings dialog is improved.

2.2.1 (22-Mar-2015)

Category Subcategory Description

Pipelining

Improvements

  • Dialogs can no longer drop below a minimum useful size.
  • Moved Add Service dialog to the improved new style.
  • Moved Rename dialog to the improved new style.

Sketcher

Improvement

Removed repeat unit functionality until Pipeline Pilot support is resolved.

2.2.0 (19-Mar-2015)

Category Subcategory Description
Charting Improvement Simple repeat units on compounds is supported.
Resolved Issue (Minor) Table header is correctly aligned when the table is sized at full screen.

Pipelining

Improvements

  • A Structure Exists filter can now be defined.
  • Added support for Pipeline Pilot 9.5.

Sketcher

New Feature

Supports bond creation with two atom selection across fragments

Improvements

  • A hydrogen bond is created by default when an H atom is attached to multiple atoms.
  • Modal sketcher windows are resized when Pipelining is resized.
  • Improved appearance of coordination bonds.
  • Definition and rendering of attachment points in structures is supported.
  • V3000 .mol files that contain multiple CTABs are supported.
Resoled Issue (Minor) Fixed problem where multiple structure pastes in Internet Explorer previously caused a security issue.
For Developers:
Category Subcategory Description
Charting Resolved Issue (Minor) Increased wait time for generating an output report by 15 seconds.

2.1.4 (9-February-2015)

Category Subcategory Description
Sketcher New Feature A new feature allows bonds to be defined with the chain or ring query flag.

Improvements

  • Improves odd-sized ring rendering with haptic bonds in some situations.
  • Allows hydrogen bonds to be defined.
  • Improves rendering of aromatic bonds in fused rings.
  • Improves double-bond intersection appearance in various use cases.
  • Allows atom-atom coordination bonds to be defined.
Pipelining Improvement Preprocesses and fixes bad JSON generated by Pipeline Pilot for small numbers in scientific notation.

2.1.3 (2-February-2015)

Category Subcategory Description
Charting Resolved Issue (Major) Pipette Charting no longer shows an error message at loading when certain types of single-valued integer properties are passed to it.
Sketcher New Feature Flagging of AND and OR stereocenters is now supported.

2.1.2 (26-January-2015)

Category Subcategory Description

Sketcher

Improvements

  • Add the keyboard shortcut "D" to duplicate a selected fragment in the Pipette Sketcher.
  • Improved double-bond positioning in some structures with many single-bond connected rings.
Sketcher Resolved Issue (Minor) The sketcher is better at flagging features used in .mol files that are not currently supported.
Pipelining New Feature Opening compounds in Pipette Sketcher from Pipelining now opens a window on the current tab, not a new browser tab.

Pipelining

Improvements

  • New style dialogs now resize and center when the browser is resized.
  • The Pipelining Filter dialog is less cluttered, easier to use, and supports new features, such as substructure filtering and display of histograms for numeric properties.

Pipelining

Resolved Issues (Minor)

  • To ensure the Input Data Store property always remains categorical, data store names are trimmed when they are used as input data store tags.
  • To avoid sending data to outputs before a tag update is applied, preview data is cleared as soon as the user starts typing in the Tag field.

2.1.1 (7-January-2015)

Category Subcategory Description

Charting

Improvements

  • Hover indicator shows on axes if the property on the axis can be changed by clicking.
  • Improved behavior when a chart template that does not fully align to the current data is applied. Even if all properties are not available, the chart can be valid.
  • To improve usability, the template and output buttons are not highlighted default.

Resolved Issues (Trivial)

  • Trellis XY plots now always have at least two x-axis labels visible.
  • x-axis labels no longer slightly overlap in small charts.
Pipelining Improvement Added an explanation of service and template icons for the help text.
For Developers:
Category Subcategory Description
Pipelining Improvement More support is available for Pipeline Pilot Reporting component configurations in protocol-based service settings dialogs. This includes improved support for radio buttons, checkboxes, and multi-select list boxes.

2.1.0 (2-January-2015)

Category Subcategory Description

Charting

Improvements

  • Rather than displaying an error message as was done previously, users are now prevented from saving empty charting templates.
  • It is now possible to page between charts in full-screen single-chart view.
  • Area selections on XY plots can be converted into filters.
  • Individual charts can be made to go full-screen by clicking the button in the top-right of the chart on the chart selection bar.
  • 3D scatter plots are now supported with Microsoft Internet Explorer 11. Users should ensure they have the latest IE 11 Windows updates to avoid rendering issues.

Charting

Resolved Issues (Minor)

  • Categorical properties containing values with commas "," are now filtered correctly.
  • Charting no longer avoids a different filter to the one the user selected, sometimes being added to the end of the filter chain.

Pipelining

Improvements

  • Added support for a new settings field type that allows selection of a saved Pipette Analysis datastore.
  • ScienceCloud users can see the template scope "Everyone" as "Everyone – Your Organization Inc". The underlying behavior of "Everyone" has always been just for your organization, but the label now more accurately reflects this.
  • Pipelining data displayed in steps can be linked to external images or systems.
  • The service list can also be sorted alphabetically, in addition to the traditional "smart sort" that uses your previous activities to predict the services you could use next.
  • Allow Pipeline Pilot based reporting forms to be used to define input dialogs for services.
  • Data can be sorted using date properties.
  • Services can be filtered using tags defined by the administrator.
  • The settings dialog layout is improved when the setting names are long and only broken with underscores "_".
For Developers:
Category Subcategory Description

Pipelining

Improvements

  • The parameter type for selecting a Pipette Analysis datastore is PipetteDataStoreType. It submits the user-scoped cache ID of the store selected.
  • There are two types of property links that are supported – images and links. Currently, both links behave the same, but this is likely to change in the future. To have a property link display in the interface, add metadata to the data record property with the "image" or "link" key.
  • Services are automatically tagged with the XMLDB folder names below the Pipette root(s). Multiple levels of folders will result in multiple tags.
  • Pipeline Pilot Reporting based service input dialogs are defined in the usual way, with the Protocol Form parameter. They behave slightly differently from Web Port, due to needing to reload field values, etc. This may mean protocol forms with complex JavaScript or non-standard controls may not submit or reload correctly. In addition, some items on the form, such as the Submit button, might be changed or removed to ensure clean integration with the Pipette interface. If you feel it is reasonable to support a form that is not working, provide ScienceCloud Support with an example so we can follow up.

 


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