Alacat site map

This page lists all available URLs (including AJAX and debugging pages).

Entities

Title	URL	Documentation
View text	/<results>/text/<subject>	Online viewer for ‵Qmenu‵. Online viewer for `Qmenu`. No form is supplied to select the results set or entity, these parameters must be supplied by the caller.
View Qbrick	/<results>/qbricks/<subject>	Online viewer for ‵Qbrick‵. Online viewer for `Qbrick`. No form is supplied to select the results set or entity, these parameters must be supplied by the caller.
View Qconcat	/<results>/qconcats/<subject>	Online viewer for ‵Qconcat‵. Online viewer for `Qconcat`. No form is supplied to select the results set or entity, these parameters must be supplied by the caller.
View Column	/<results>/columns/<subject>	Online viewer for ‵Column‵. Online viewer for `Column`. No form is supplied to select the results set or entity, these parameters must be supplied by the caller.
View Qbrick	/<results>/qpeptides/<subject>	Online viewer for ‵LinkedPeptide‵. Online viewer for `LinkedPeptide`. No form is supplied to select the results set or entity, these parameters must be supplied by the caller.
View Peptide	/<results>/peptides/<subject>	Online viewer for ‵Peptide‵. Online viewer for `Peptide`. No form is supplied to select the results set or entity, these parameters must be supplied by the caller.
View Qblock	/<results>/qblocks/<subject>	Online viewer for ‵Qblock‵. Online viewer for `Qblock`. No form is supplied to select the results set or entity, these parameters must be supplied by the caller.
View Qmenu	/<results>/qmenus/<subject>	Online viewer for ‵Qmenu‵. Online viewer for `Qmenu`. No form is supplied to select the results set or entity, these parameters must be supplied by the caller.
View Handler	/<results>/handlers/<subject>	Online viewer for ‵Handler‵. Online viewer for `Handler`. No form is supplied to select the results set or entity, these parameters must be supplied by the caller.
View Protein	/<results>/proteins/<subject>	Online viewer for ‵Protein‵. Online viewer for `Protein`. No form is supplied to select the results set or entity, these parameters must be supplied by the caller.

Help

Title	URL	Documentation
Alacat site map	/alacat/sitemap	This page lists all available URLs (including AJAX and debugging pages).
Exit	/alacat/help/exit	Returns to the server root.
Report a bug	/alacat/bug	Allows the user to report a bug. Allows the user to report a bug. The bug is recorded as for any other exception trace.
Alacat about	/alacat/about	Displays the application credits.

New

	Title	URL	Documentation
	Alacat main	/alacat/	Main Alacat query submission screen.
	Consequence	/alacat/consequence	Makes Alacat look like Consequence.

Results

Title	URL	Documentation
Alacat model details	/<results>/model	Shows the code necessary to define the pipeline parameters. Shows the code necessary to define the pipeline parameters. No form is supplied to select the result set, this parameter must be supplied by the caller.
Scores table	/<results>/tables/<table>	Shows the full table of scores. Shows the full table of scores. No form is supplied to select the results set or scores table, these parameters must be supplied by the caller.
Final report	/<results>/report	The final selection, presented as a table. The final selection, presented as a table. Most of the columns are obvious, the main ones of interest are "choice" and "warnings". Qmenu, Qconcat, Qblock, Qbrick, Protein, Peptide The selected entity. You can click through to see detailed information and compare to other entities. NLink, CLink, NNat, CNat The linkers. Link is the suggested qconcat linker. Nat is the native linker in the protein. Choice "Choice" is a list of three values (for the peptide, the qbrick and the qconcat), showing who thinks they are a good idea: the user (u), the system (s) or system-equivalent (e). In the final choice, "u" will always override "s", so we have these possibilities: "u" is an entity that is in the input, but the software wouldn't have chosen by itself. "su" is an entity that is in the input, and the software would also have chosen. "eu" is an entity that is in the input, and the software wouldn't have have chosen, but that it thinks is an equally good choice. "s" is where the input didn't contain a suggestion, so the system has chosen by itself. Warnings "warnings" are the reasons the software doesn't like this peptide, qbrick, or qconcat. These are the scores for the output columns, where the score is thought to be less-than ideal. Each one is referenced by a short ID to the table below, but the IDs can be clicked to quickly get more information. Implementation details No form is supplied to select the result set, this parameter must be supplied by the caller.
Compare peptides	/<results>/compare	Compares the results from two or more entities. Compares the results from two or more entities. No form is supplied to select the results set or entities, these parameters must be supplied by the caller.
Proteins	/<results>/proteins	Shows the full list of proteins. Shows the full list of proteins. No form is supplied to select the result set, this parameter must be supplied by the caller.
Download	/<results>/download	Downloads the results. Downloads the results. No form is supplied to select the result set, this parameter must be supplied by the caller.
Pipeline warnings	/<results>/warnings	Shows warning messages that were issued during the course of the pipeline. Shows warning messages that were issued during the course of the pipeline. No form is supplied to select the result set, this parameter must be supplied by the caller.
View cart	/<results>/cart	Allows the user to view the flagged items and create a new model from them Allows the user to view the flagged items and create a new model from them if desired. The legacy name "cart" is sometimes used, which followed Uniprot's "protein cart" terminology, but that makes it sound like the user is buying something, and they're not.
Delete	/<results>/delete	Deletes the results. Deletes the results. No form is supplied to select the result set, this parameter must be supplied by the caller.
Pipeline details	/<results>/pipeline	Shows the technical information associated with executing a pipeline. Shows the technical information associated with executing a pipeline. No form is supplied to select the result set, this parameter must be supplied by the caller.
Model index	/<results>/index	The main results screen shown after executing the pipeline. The main results screen shown after executing the pipeline. No form is supplied to select the result set, this parameter must be supplied by the caller.
Everything	/<results>/all	Shows all the entities present in a pipeline. Shows all the entities present in a pipeline. No form is supplied to select the result set, this parameter must be supplied by the caller.
View log	/<results>/log	Shows the logs recorded during pipeline execution. Shows the logs recorded during pipeline execution. This page can be viewed during the pipeline execution itself, though requires a manual refresh in order to update.

Special

Title URL Documentation

Add to cart

/alacat/add_to_cart

Handles add-to-cart AJAX requests.

The parameters must be supplied by the caller:

The result set ID

The subject ID

Whether to add or remove the subject

Pending

/alacat/pending

Displays the status of a specified task.

Note that the task ID is obtained from either the GET parameter, "task" or the routing argument of the same name.

TASK_ROUTE_ARG:	GET data field used to access the task ID
TASK_MESSAGE_META_DATA_FIELD:	If this optional field may be present in the task's meta-data The value should be an instance of `TaskMessageMetaData`.

Users

Title	URL	Documentation
Logout	/alacat/logout	Logs the user out on visit. Logs the user out on visit. Implementation details The derived class should implement `__view__`. Nothing else is required, this class logs out the current user via a call to `HatmulProtocol.login` and then redirects to the login page. !HAS_TEST_CASE
New user	/alacat/new_user	Allows the user to log in. Allows the user to log in. Implementation details The derived class should implement `__view__`, as well as the abstract methods, which register the actual user. The `HatmulProtocol.login` is then (optionally) used to perform the actual login. Important Make sure to specify POST in the `__view__`!
Login	/alacat/login	Allows the user to log in. Allows the user to log in. Implementation details The derived class must expose the `__view__` field. Nothing else is required, the form calls `HatmulProtocol.login` when a login is attempted. !HAS_TEST_CASE
History	/alacat/history	A screen that does not expect a submit, i.e. there is only an ‵on_call‵ but A screen that does not expect a submit, i.e. there is only an `on_call` but no `on_response`. Note The class is a derivative of `CallResponseScreen` for simplicity, however `on_response` is never called. The page may still pass and process its own GET data.

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Alacat site map

Entities

Help

New

Results

Qmenu, Qconcat, Qblock, Qbrick, Protein, Peptide

NLink, CLink, NNat, CNat

Choice

Warnings

Implementation details

Special

Users

Implementation details

Implementation details

Implementation details