ispyb / exi Goto Github PK

Extended User Interface for ISPyB based on ISPyB's API

JavaScript 56.45% CSS 30.42% HTML 9.35% Ruby 0.02% PHP 0.20% Python 0.10% ActionScript 0.01% Makefile 0.01% Jupyter Notebook 0.49% Shell 0.01% Dockerfile 0.01% SCSS 2.95%

exi's Introduction

ISPyB Project

Installing
Database creation and update
Database schema

Installing

Clone the ISPyB repository:

git clone https://github.com/ispyb/ISPyB.git

ISPyB needs the third-party libraries provided in the dependencies directory. These don't exist in a public repository, so install them to the local Maven repository so that Maven can find them:
```
cd dependencies && mvn initialize
```

Build ISPyB using Maven:

mvn clean install

By default, ISPyB builds for the GENERIC site and the development environment. These can be changed with the ispyb.site and ispyb.env system properties. For example, to build for the ESRF site and the test environment:

mvn -Dispyb.site=ESRF -Dispyb.env=test clean install

If the build succeeds, a summary message will be printed like this:

[INFO] Reactor Summary:
[INFO]
[INFO] ispyb-parent ...................................... SUCCESS [0.251s]
[INFO] ispyb-ejb3 ........................................ SUCCESS [10.243s]
[INFO] ispyb-ws .......................................... SUCCESS [1.751s]
[INFO] ispyb-ui .......................................... SUCCESS [7.212s]
[INFO] ispyb-ear ......................................... SUCCESS [5.048s]
[INFO] ispyb-bcr ......................................... SUCCESS [2.217s]
[INFO] ispyb-bcr-ear ..................................... SUCCESS [1.806s]

Database creation and update

Run the following creation scripts from the ispyb-ejb module (note that this requires the pxadmin database user to exist and have full permissions):

ispyb-ejb/db/scripts/pyconfig.sql: This corresponds to the menu options and contains both structure and data.
ispyb-ejb/db/scripts/pydb.sql: This corresponds to the ISPyB metadata and contains only the database structure.
ispyb-ejb/db/scripts/schemastatus.sql: This corresponds to the SchemaStatus table and contains both structure and data. The entries indicate which update scripts have been run.
ispyb-ejb/db/scripts/ispybAutoprocAttachment.sql: This corresponds to the type and names of different autoPROC attachments.

The creation scripts are normally updated for each tag, but if you are using the master branch, you may have to run the update scripts in ispyb-ejb/db/scripts/ahead.

Check the entries in the SchemaStatus table to know which scripts to execute. The scripts already run for the current tag are in ispyb-ejb/db/scripts/passed.

Creating an update script

The first line must be:

insert into SchemaStatus (scriptName, schemaStatus) values ('2017_06_06_blabla.sql','ONGOING');

Then comes the actual updates of the script:

-- SQL statements here

And the last line must be:

update SchemaStatus set schemaStatus = 'DONE' where scriptName = '2017_06_06_blabla.sql';

The last line updates the SchemaStatus table to mark the script as having been run.

Database schema

A patch or commit that changes the database schema must be accompanied by a corresponding change to the schema file to keep it up to date. This file can be edited using MySQL Workbench (a free tool from MySQL).

exi's People

Contributors

Stargazers

Watchers

Forkers

antolinos milanprica ivarskarpics sergiogf93 olofsvensson delageniere davydedurpel clemenbor martinsavko hormiai76 dsanchez-cells hzb-mx baokangwen

exi's Issues

Display 1D curves in linear scale

Possibility to add a option box that allows to display the curve in lin-lin

Session panel for managers

Sessions should be better arranged in the main panel. It is also needed the possibility to look for a date, proposal code and number but also by title of the proposal

Display machine status on EXI

We could add something to display the machine status:

<!DOCTYPE html>
<html>
<style>
.tooltip {
    position: relative;
    display: inline-block;
    border-bottom: 1px dotted black;
}

.tooltip .tooltiptext {
    visibility: hidden;
   
    color: #fff;
    text-align: center;
    border-radius: 6px;
    padding: 5px 0;

    /* Position the tooltip */
    position: absolute;
    z-index: 1;
}

.tooltip:hover .tooltiptext {
    visibility: visible;
}
</style>
<body style="text-align:center;">

<p>Move the mouse over the text below:</p>

<div class="tooltip">Hover over me
  <span class="tooltiptext">
  <img src='http://www.esrf.fr/esrf_status/gifs/img1.png'>
  <img src='http://www.esrf.fr/esrf_status/gifs/img2.png'>
  <img src='http://www.esrf.fr/esrf_status/gifs/img3.png'>
  </span>
</div>


</body>
</html>

Typo error on datacollection group grid

Workflow and wavelength contain typo errors

Editable dataCollection comment

There is the need to allow the edition of comments in the dataCollectionGrid.

A webService may be needed.

New tab for Molecular Replacement

Molecular replacement is filling the phasing tables and we need a new tab at level of data collection group summary to display the results.
These results are the phasing results filtered by method = MR

Biosaxs Results with lazy loading

BioSAXS sample changer results should use lazy loading for the images.

PuckWidgetContainer

In the constructor of PuckWidgetContainer class args.puckType should not be integer but string to make easier to understand.
As well as args.x and args.y, if they are the margin then they should be called margin

Dewars from shipment whithout a session attached

It seems like the method with the url:

this.get('/{token}/proposal/{proposal}/dewar/list');

Doesn't return the dewars that belong to a shipment without a beamline attached.

Would it be possible to alse return these kind of dewars?

ISA parameter to be displayed in the results

Autoproc files are not well displayed vertically

Refactorize autoprocessing parameters as a widget

This needs to be refactorized in a widge to keep the menu short and clean:
`MXManagerMenu.prototype.getManagerMenu = function() {
var _this = this;
function onItemCheck(item, checked) {
if (item.text == "Autoproc Scaling Statistics") {
var scatteringForm = new ScatteringForm({width : 650, height : 560});

		var window = Ext.create('Ext.window.Window', {
			title: "Plot autoprocessing values for last week",
			height : 560,
			width : 650,
			modal : true,
			layout : 'fit',
			items : [ scatteringForm.getPanel() ],
			buttons : [ {
					text : 'Plot',
					handler : function() {
						scatteringForm.plot();
					}
				}, {
					text : 'Cancel',
					handler : function() {
						window.close();
					}
				} ]
		}).show();

		var keys = ["ISA", "rPimWithinIPlusIMinus","anomalousMultiplicity","multiplicity","resolutionLimitLow","ccHalf",
		"strategySubWedgeOrigId","completeness","rMerge","anomalous","meanIOverSigI","ccAno","autoProcScalingId",
		"nTotalObservations","sigAno","rMeasWithinIPlusIMinus","anomalousCompleteness","resolutionLimitHigh",
		"fractionalPartialBias","rMeasAllIPlusIMinus","nTotalUniqueObservations","rPimAllIPlusIMinus"];

		var scatteringData = {title : "AutoprocIntegrator", keys : keys};

		scatteringForm.load(scatteringData);
	}
}

return Ext.create('Ext.menu.Menu', {
	items : [
				{
					text : 'Statistics',
					icon : '../images/icon/ic_insert_chart_black_36dp.png',
					menu : {       
							items: [
								{
									text: 'Autoproc Scaling Statistics',
									icon : '../images/icon/ic_insert_chart_black_36dp.png',
									handler: onItemCheck,
									disabled : false
								}
							]
						}
				}
		] 
});`

Lab contact's WebService needs to store and get the Lab name and the Lab address

Right now we can edit the Lab name and the Lab address for a given Lab contact but it's not persisted:

We need to save this values so that they can be shown, just like at the current version of ispyb:

Problem when updating status of a shipment because of whitespace

When status is "At ESRF"

[org.jboss.resteasy.plugins.server.servlet.ServletContainerDispatcher](default task-112) Failed to parse request.: java.lang.IllegalArgumentException: Illegal character in path at index 122: https://wwws.esrf.fr/ispyb/ispyb-ws/rest/96c44b0399e49f96c126de48b9eaae88fbc09ec8/proposal/mx415/shipping/301616/status/at ESRF/update

Lab contact creation

We need to be able to create new shipping addresses.

We try to do this by sending a json through the following method with the labContactId set to null:

EXI.getDataAdapter().proposal.labcontacts.saveLabContact

This does not creates an id for the created Lab contact though.

Manager Menu

There is the need to create a manager menu class.

SaveContainer

The method EXI.getDataAdapter({).proposal.shipping.saveContainer receives a json as a parameter with the container information but the containerType value is not updated.

Industrials users can not log in

Role of industrial users is: Industrial
EXI does not about Industrial only Users and Managers (+ localcontacts)

EXI should behave with an industrial as if it was an user

Display file name in the online results tab for BioSAXS

Filename is missing for earch data collection. It should appear somehow here:

Value might be Subtraction_sampleAverageFilePath

Allow beamline reset when unloading the sample changer in Prepare Experiment

When the button "Unload all" is clicked, the beamline should be set to null for each container:

It would be necessary that the method:

EXI.getDataAdapter().proposal.dewar.updateSampleLocation([containerId], [beamline], [sampleChangerLocation]);

Could receive an empty string or a null value at the beamline parameter to achieve this.

Make images clickable to redirect either MX or SAXS

Session grid: Hide title of the proposal and show PI

Best autoprocessing results doesn't display correctly

Overall and outer displays always the same result

Statistics does not work because eonasdan-bootstrap-datetimepicker is not minified

Problem with auto-processing graphs

There's something wrong with the graphs of auto-processing results - there are graphs even when there are no results:

Prepare Experiment menu but not proposal selected

A warning should be displayed when user (or manager) click on prepare experiment but no proposal has been selected.

New Feature: Added YUIDoc for online documentation

YUIDoc is a Node.js application that generates API documentation from comments in source, using a syntax similar to tools like Javadoc and Doxyge

Format data collection group list on data collection grid

Sort autoprocessing

Group autoprocessing results by anomalous and non anoumaluos and sort by:

Space group
Lower rMerge

Add image quality indicators plot to data collection "Summary" view

Today the "Summary" view of data collections in ISPyB looks like this:

I propose to add a small thumbnail image of the image quality indicators plot:

Filter sessions by beamline

New feature

Make a filter per beamline in the session grid. First approach based on checkbox

Improvements of data collection tab

I have a patch ready that makes the following improvements to the data collection tab:

Swap of prefix and run number:
Add image template to directory popup:

Font for displaying path to big

The font used for displaying the path in the data collection tab should be made smaller:

Data collection tab: problem when both comment and results

If there's a long comment the results are not visible in the data collection tab:

When session expires EXI keeps refreshing the page

Compact autoprocessing results

It should be great if it may be compacted the auoprocessing results in one line instead of big blocks

Improvements of "Data Collections" tab

The current design of this tab:

New suggested design:

Shipping fields needs to be updated when a shipment is sent to ESRF

The method EXI.getDataAdapter().proposal.shipping.saveShipment
with the URL: /{token}/proposal/{proposal}/shipping/save'

Needs to update shippingStatus, deliveryAgentDeliveryDate, deliveryAgentShippingDate, and for each dewar in dewarVOs trackingNumberToSynchrotron.

Refactorize labcontacts from Shipping Router

Enable animated gifs for crystal snapshots

The MXPress workflows will be modified to produce animated gifs of the sample snapshots:

I'll submit a patch which enables the view of this animated gif also on the data collection summary table by hovering the mouse over the snapshot:

Color code on pipeline results of MX

Result of completeness between:
90-100 green/blue
50-<90 yellow
<50 red

Add project structure for documentation taking advantage of grunt-project-structure plugin

https://www.npmjs.com/package/grunt-project-structure

MTZ files on DataCollection group grid

Display and download MTZ files, all of them or at least ones from the best autoprocessing result

Data collection tab not fully visible for last sample in summary list

One cannot sometimes see all data collections for the last sample in the summary list:

There's a workaround: resize the browser window, or open and then close the developers tools, makes the last data collections appear:

Needed values for the sessions at the welcome page

The session grid interface is being changed into something like this:

We need to display the workflowCount, the autoprocResultsCount and the phasingResultsCount for each sessions.

It would be nice if these parameters were returned by the following urls:

this.get('/{token}/proposal/{0}/session/list'.format([proposal]));
this.get('/{token}/proposal/session/beamlineoperator/{0}/list'.format([beamlineOperator]));
this.get('/{token}/proposal/{0}/session/date/{1}/{2}/list'.format([proposal, startDate, endDate]));
this.get('/{token}/proposal/session/date/{0}/{1}/list'.format([startDate, endDate]));

Stats about number of users that logs in EXI

It would be great if we could have a table where we can see the number of users currently connected and also the number of users that use EXI
I can imagine a plot like this where it is displayed the number of unique connections and the number of total connections to EXI.