Documentation

Summary

The OrderPortal system is a web-based portal that allows form-based submission of information from users to a facility. It was designed academic service facilities that handle discrete orders or project proposals, reports, etc, from its users (researchers). It has also been used as a system to gather reports from researchers and research units.

The OrderPortal system was originally created to satisfy the needs of the National Genomics Infrastructure (NGI) Sweden, which is a service facility for DNA sequencing and genotyping of samples provided by external researchers. The facility processes the samples according to the specifications in the order from the researcher. The available services are described in the forms for orders that the facility defines.

The OrderPortal system is not hardcoded for any specific area such as DNA sequencing. On the contrary, considerable effort has gone into making sure the design is as general as possible within the scope of the basic problem it is intended to solve.

Since the system is general in character, the installation of it requires specific configuration settings to suite your particular needs.

Features

  • Allow a user (researcher) to register an account, which is enabled by the facility staff.
  • Allows system administrators to create predefined forms with a specific set of input fields.
  • Allow the user to specify an order according to one of the predefined forms.
  • Allow input from the user of required project data, such as sample sheets.
  • Allow the user to submit the order to the facility.
  • The facility staff can review, accept or decline an order, depending on the configuration set up by system administrators.
  • Let the facility staff keep track of review and agreements.
  • Allow attaching files to an order.
  • Display project status reports.
  • Allow keeping track of Key Performance Indicators (KPIs), facilitating resource usage reports for the facility.

Basic concepts

  • Orders: The OrderPortal system is a portal for orders (requests, project proposals, etc) to a single facility from its users.

  • User: A user is a researcher external to the service facility, and may or may not be the Principal Investigator (PI) for one or more projects.

  • Order: An order is created, filled in and submitted by a user. The facility personnel (system administrators and/or staff) then handles the order, applying whatever workflow is defined by them. The order is moved along by changing its status.

  • Form: An order is created from a template which is called a form. The system administrators must set up and publish the forms for a user to be able to create an order. Each form defines the fields for data to be input by the user.

    The design of an order form is fairly general; there is nothing that is hardcoded for specific domains of science. The content of the order forms consists of a different fields for different types of input data, with optional constraints on the input data, and optional help text. The order forms are defined by the system administrators.

  • Report: A report is an HTML file or a document file (PDF, DOCX, etc) which can be attached to an order by the system administrators or staff. This can be used a means of delivering results to the user.

  • User account: A user account is defined within each OrderPortal instance. The email address of the user is the user account identifier. This means that if a user changes email address, a new account will have to be created.

  • Customization: The system administrators can (and should) customization the site logo, title, home page text blocks and the body of email messages sent by the system. Pages for showing information and documents are under control of the system administrators.

Facility

The term facility is used for the organisation providing the service specified by the order forms. A basic design principle is that one instance of the OrderPortal system handles one facility. All entities in the database back-end for the OrderPortal instance belong to one and only one facility.

There are three reasons for this design choice:

  1. Security between facilities. The existence and contents of a particular project in one facility must not be visible to the administrators or staff of another facility. This is a strict requirement for some facilities, and it is easier to implement if the database instance for each facility is separate from one another.

  2. The styling of an order portal is much easier to implement if each facility has its own OrderPortal instance.

  3. The introduction, or elimination, of a facility in the overall organisation becomes much easier if every instance of the system is independent of the other.

One drawback with this design choice is that it complicates the communication between, and linking of, different but related projects in different facilities.

Note that there is no entity called facility in the OrderPortal system. It is just a concept behind the design of the system.

The OrderPortal system is designed for only one facility, displaying up to about 8 different order forms. There is no hard limit to the number of simultaneously published forms, but the current design does not work well with more than about 8 forms.

If an organization has different facilities requiring different sets of forms, then it is probably a good idea to set up different instances of the OrderPortal system, with separate back-end database instances.

Users

A user is an account in the system. Almost all operation require that the user is logged in. The email address is the user account identifier.

There are three kinds (=roles) of users:

  1. User: An external scientist, who uses the portal to place one or more orders, and to follow the progress of their own orders. The "customer" of the facility.

  2. Staff: Facility staff, who may view all orders, but are not allowed to change very much.

  3. Admin: System administrators who are allowed to view and edit all aspects of the OrderPortal system that can be modified via the web interface. This includes processing orders, modifying the order fields, and handling user accounts. Often, the project coordinators of the facility are designated as system administrators, since they will be using the system to keep track of incoming orders (projects).

User accounts can be set as disabled, for example if the person leaves her position, or as a means of blocking invalid use. An account can be re-enabled. A user account cannot be deleted, since the logs and old orders contain a link to it.

An external scientist applies for a user account by providing the relevant information. Such an account is created with a status of pending. The system administrator reviews the pending user account and enables it if it appears legitimate. The user gets an email about the account having been enabled and with instructions on how to set the password for it.

Access privileges

The user can place orders as soon has she has logged in. By default, no other users except the admin and staff can view the orders.

A user is allowed to specify which other users will be able to access to her orders by creating a group to which the other users are invited. Access can also be granted by a user to other specific users for an individual order.

Order

An order is essentially a form with values. Its fields are defined by the order form (see below) it was created from.

An order belongs to one and only one user account.

An order has one and only on status at any time. When the order is created, it is in status Preparation, and while it is in that state, the user can edit it and save it. An order that is being prepared can be, but is usually not, inspected by the staff or system administrators.

An order usually contains at least some fields which require a value. An order lacking a required value can be saved, but it cannot be submitted. This allows the user to create and fill in an order partially and save it. Then, at a later data, she can return to the order to complete it and then submit it.

When all fields have been given valid values by the user, it becomes possible to submit it.

An order in status Submitted will be handled by the staff and system administrators.

Order status

The list of all possible order statuses.
Status Semantics
Preparation The order has been created and is being edited by the user.
Submitted The order has been submitted by the user for consideration.
Review The order is under review.
Queued The order has been queued.
Waiting The order is waiting for something else to happen.
Accepted The order has been checked and accepted.
Rejected The order has been rejected.
Processing The order is being processed in the lab.
Active The order is actively being worked on.
Analysis The order results are being analysed.
Onhold The order is on hold.
Halted The work on the order has been halted.
Aborted The work on the order has been permanently stopped.
Terminated The order has been terminated.
Cancelled The order has been cancelled.
Finished The work on the order has finished.
Completed The order has been completed.
Closed All work and other actions for the order have been performed.
Delivered The order results have been delivered.
Invoiced The order has been invoiced.
Archived The order has been archived.
Undefined The order has an undefined or unknown status.

Only the statuses Preparation and Submitted are enabled by default. All other statuses will have to be enabled to become available for use.

Statuses can be enabled only by the system administrators. Once enabled, a status cannot be disabled. The reason for this is that already existing orders may be in a specific status, or have a specific status recorded in its history, and removing such a status would introduce inconsistencies in the database. The description of the semantics of a status can be edited by the system administrators.

All orders will be in status Preparation when created.

Transitions between the statuses can be edited by the system administrators. The only transition enabled by default is the one from Preparation to Submitted.

Typically, enabling statuses and transitions should be done as part of the configuration and testing phase before the instance is launched into production. Obviously, this work needs to take into account the typical workflow of the facility.

Here are some general guidelines:

  • It is a good idea to keep the number of enabled statuses at a minimum. Since a status that has been enabled cannot be disabled, one should avoid cluttering the system with unnecessary statuses.
  • Transitions should be set to those that are sensible given the typical workflow.
  • Allowing too many transitions can lead to confusion and should be avoided.
  • However, setting up transitions can be done freely, since they can be removed later without any issue.
  • Since transitions can be added and removed at will by the system administrators, it is always in principle possible (if cumbersome) to 'rescue' an order which has been put in an incorrect status.

Attach files

Files such as agreements, specifications, images, etc, can be attached to an order. If the form has file input fields, these files will also be attached to the order.

Links to other web pages can be set for orders, allowing users to navigate to other relevant information systems. This feature can be disabled by modifying the order configuration.

Order tags

Tags (one-word labels) can be attached to orders, for searching purposes. This feature can be disabled by modifying the order configuration.

Order log

Each change of an order is logged, and the information "who, when, what" is stored. The log trace is written by the system automatically and cannot be edited by any user.

Form

The order form fields are fully configurable by the system administrators via the web interface. The field definitions are generic, and allow order forms to be designed for a wide variety of input data.

While an order form is being created and edited, it is upublished, and users cannot create orders from it. It is possible for the system administrators to test a form and create a dummy order for it. An order form can be used only when it has been enabled, which automatically publishes it on the home page of the OrderPortal system.

The input fields defined by an order form cannot be substantially changed after the form has been enabled. Basically only the help texts of the input fields can be edited. If an order form becomes outdated it can be disabled; this will remove it from view on the home page. Its orders, however, will still be accessible for processing. No new orders can be created from a disabled form. New order forms can be created by cloning from and older form; this is the most common way of updating an order form.

The reason for this is that if a form is changed by e.g. removing a field, or redefining it, then already created orders are in danger of becoming invalid. It was a design decision to stop this from happening by disallowing changing a form after it has been enabled.

Form fields

The fields of an order form, and by extension the orders created from it, are of different types, for input of text, number or other kinds of values. This is defined when a field is created within a form.

The order form allows hierarchical grouping of fields, with dynamic display according to simple rules. This allows for cases where a top-level selection of e.g. a specific technology determines which further input fields are required to be filled in.

The system administrators design the forms by setting up the fields which determine what the user must fill in for an order. The system administrators can clone a form in order to make a new variant of it. Old forms can be disabled, and new forms enabled, as needed.

Once a form has been enabled, its fields cannot be changed, except for editing the help texts. When an order is created, its fields definitions are copied from the form. Once an order has been created, its fields and selected options are effectively frozen, and remain fixed. Only the values of the fields may be changed, not the definition of them.

This is a major design limitation of the OrderPortal system, which must be kept in mind when planning and implementing the content of the forms. The following routine has been used with good results:

  1. For a new form, create and edit the input fields that it defines for an order.
  2. Set the version marker for the form, using some reasonable convention, such as a version number, or a date.
  3. Enable it.
  4. When an update of the form is required, make a clone of it.
  5. Edit the fields of the clone to make the changes.
  6. Set a new version marker, keeping the title of the new form unchanged compared to the old. To the users it will look like just an updated form, not a new one.
  7. Enable the new form.
  8. Disable the old form.

Adding a field in a new form requires deciding on the following parameters:

  • Field identifier.
  • Field data type.
  • Is a field value required?
  • Field description.
  • Value options, if relevant.
  • Hierarchy and order, including conditional visibility.
  • Visibility to the user; some fields may be visible only to the staff.

A field may be conditional, meaning that it is displayed only of some other field has been assigned a specific value. This is useful for orders where the relevant fields depend on some high-level choice, such a type of technology to use for a project.

Field types

The order form field types are:

  • String: One single line of text, such as a name or a title.
  • Email: One single email address.
  • Int: A number that is a whole integer.
  • Float: A number that may contain fractions.
  • Boolean: A selection between Yes and No.
  • Url: One single URL (link address).
  • Select: A choice of one among a set of text given values.
  • Multiselect: A choice among a set of text given values, allowing multiple selected values.
  • Text: A multiline text which may use Markdown formatting.
  • Date: One single date, using ISO format (YYY-MM-DD).
  • Table: A basic table allowing several columns.
  • File: An uploaded file which is attached to the order.
  • *Group: A group of a set of other fields. Does not contain a value.

Report

An order may have any number of reports attached to it by the system administrators or staff. If the report is an HTML file it will be shown in-line, otherwise it will be downloadable by the user.

The report feature is intended as a means to deliver results in the form of written reports to the user. There is a very simple review system, which allows requesting other staff to review a report before publishing it.

Info pages

There is a very basic information page subsystem, intended to allow displaying information about the orders and/or the facility to the user or the general public. It is not a full-fledged wiki. The system administrators can edit these pages via the web interface.

This feature can be disabled by the system administrators in the display configuration page.

Documents

There is a simple feature to store documents (files), such as PDFs or XLSX files in a general system-wide manner for any user to access. This can be used to provide the users with templates or information documents.

This feature can be disabled by the system administrators in the display configuration page.

Interfaces

There are three main interfaces to the system, the web, the API (Application Programming Interface) and the CLI (Command-Line Interface).

The web interface behaves slightly differently depending on the role of the user account logged in.

Web

The web interace is the standard interface for accessing and using OrderPortal.

Depending on the role of the user account, the privileges in the web interface differ. In principle, the ordinary user can view and edit only her own orders. Staff can view most things, while admin can perform all view and edit operations that are available in the web interface.

API

The Application Programming Interface (API) allows other systems to interact with the order portal. It is based on RESTful principles using JSON and linked data to allow other systems to access and/or modify various data entities in the portal.

The API is currently fairly limited.

The web pages having a link JSON which leads to the JSON format representation of the entity in the page.

The account to be used for API interactions must have its API key set. That key provides authentication for programmatic access to the API. Set it by checking the box Set new API key in the edit page of your account. The user identified by the API key has the same privileges in the API as in the web interface.

The JSON for the entities may contain links to other entities or actions. The design is inspired by (but not identical to) the proposed standard Hypertext Application Language (HAL). See Mike Kelly's original proposal at http://stateless.co/hal_specification.html and the (defunct) IETF proposal at https://tools.ietf.org/html/draft-kelly-json-hal-08. The most important difference is that the key links, rather than _links, is used.

There are a number of sample scripts showing various interactions with the API. Note that the example script uses the third-party module requests (see here) which is much nicer to work with than the standard Python urllib module.

API Get order data

An example script that gets all data about an order in JSON format is provided here: get_order.py.

The data obtained is the same as one gets by clicking the JSON link in the upper right corner of the order's web page.

One should note that the order can always be identified by its IUID. If the site has enabled identifiers (which typically look something like XYZ00102), then it is possible to use that identifier instead of the IUID for this particular case. For some cases, the IUID must be used in the URL. The IUID is the safest bet, so if you have it readily at hand, use it.

API Create order

An order can be created by POST of JSON data containing the IUID of the relevant form, and optionally a title. The returned data will contain the full representation of the newly created order, which will contain no data for the fields.

It is not possible to set any initial values of the fields using this call. You will have to set the field values using a separate edit (see API Edit order.

For an example order create script, see create_order.py.

API Edit order

An order can be edited by POST of JSON data containing the fields to change. In principle, the data to send should look like a subset of the full JSON representation of an order.

Fields that are not included in the data are not touched. Only fields present in the form for the order can be set, and only when the current user is allowed to do so. Attempts to set other fields will be silently ignored.

In addition to the fields, the title, tags and history of an order can also be set via the API.

NOTE: setting history explicitly should be done with care, so as to avoid fake data in the history. The point of the history is to show when status changes happened without having to go through the entire log of the order.

For an example order edit script, see edit_order.py.

API Set order status

The API can be used to set the status of an order. The allowed status transitions are the same as in the web interface, and depend on the current status of the order and the role of the account.

The allowed transitions and their URLs are provided in the JSON data for the order in the form of a dictionary with the target states as key and as value another dictionary with the key href and the corresponding URL as value. One must use the HTTP method POST for these URLs, since they change the order.

See the example script submit_order.py for the code used to submit an order. Similar code is used for other status transitions.

API Add order report

A report for an order can be added by doing a PUT to the order report URI with the report content file as request body.

The content type (MIME type) of the data is recorded with the report. If it is text/html or text/plain, the content will be display in-line in the user's browser. Otherwise the content will be downloaded as a file to the user's browser when the report button is clicked.

For an example add report script, see add_report.py.

CLI

The Command Line Interface (CLI) allows system various maintenance operations, such as backup, account creation and such. It is executed on the command line of the machine which hosts the OrderPortal instance. This means that only users with accounts of sufficient privilege on this machine can use it.

Backup

Backups of the CouchDB database can easily be produced using the CLI:

$ sudo -u nginx PYTHONPATH=/var/www/apps/xyz/OrderPortal python3 cli.py dump

This creates a tar.gz file with today's date in the file name. There are command options for setting the name of the file, or the directory in which it is written. See the --help option of the CLI.

Instructions

Creating order form

A system administrator will have to prepare a form for the end-user to be able to prepare an order.

Like so:

  • Go to the forms list page.
  • Click the button "Create form".
  • Fill in the title and description. These can be edited later.
  • Click "Save".

Now add fields. A "group" field is a container for other fields, and does not contain a value of its own. The other types of fields are fairly self-explanatory.

  • Click "Create field".
  • Choose group. If no groups have been created, only the top level is available. This choice cannot be edited later.
  • The identifier must be like a common programming language identifier: Begin with an alphabetical character, and then any number of alphanumerical and underscore characters. No blanks. It must be unique within the form. It cannot be edited later.
  • The label is what is shown for the user. If none, then the identifer will be shown, somewhat prettified. Can be edited later.
  • The field can be made read-only for user, or invisible to the user. Can be edited later.
  • The description is the help text visible to the user. Can be edited later.
  • Click "Save."
  • The field will be added below the others in its group. The placement in the group can be edited later.
  • If you make a mistake (giving wrong identifier, placing in wrong group, etc) you will probably have to delete the field and try again. Currently, only the label, access, placement and description can be edited later.
  • Conditional visibility is specified when editing a field. Currently, only a single value in another select field can be tested against.

After having added some fields, it is possible to test what an order for it will look like: Click "Testing". This will allow only the system administrators to create and edit a test order for the form.

Once done with testing, click "Pending" to allow editing of the form again. Any orders created while "Testing" will automatically be deleted.

Clicking "Enable" will enable the form for users to create orders. This cannot be undone! So be sure that the form is OK before you do this.

Installation

The current installation procedure is described in README for the GitHub repo.

Software design

The implementation of Anubis is based on the following design decisions:

  • The back-end is written in Python using tornado.
    • The back-end generates HTML for display using the tornado template system.
    • The front-end uses Bootstrap.
  • The back-end uses the No-SQL database CouchDB.
    • Each entity instance is stored in one document in the CouchDB database.
    • The entities are in most cases identified internally by a IUID (Instance-unique identifier) which is a UUID4 value.
    • The entities contain pointers to each other using the IUIDs.
    • The CouchDB indexes ("designs") are vital for the computational efficiency of the system.
  • There is a command-line interface (CLI) tool for certain operations, such as creating and loading dumps.

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OrderPortal 11.1.1