$cascade API round 3, including references #1131

paynejd · 2021-11-24T14:26:08Z

This ticket is a placeholder to capture the next round of work on the $cascade operation and follows up on #1122. We will add details to this in the coming days.

@bmamlin @ $cascade is now functional enough (ie recursion and map type filter) to be tested for the desired OpenMRS Dictionary Manager functionality.

A couple of examples:

This round of work focuses on the ability to create collection references with $cascade, performance, features needed to utilize $cascade in a hierarchy tree view or in the OpenMRS Dictionary Manager, and addressing any bugs identified.

Implement ability to add a $cascade request (using parameters) as a collection reference via the API
Database-level cascade query optimization: indexes that we can add? Here's long-running query that throws a 504 that could be a good test-case: https://api.qa.openconceptlab.org/orgs/CIEL/sources/CIEL/concepts/159983/$cascade/

…fying concept mappings queryset

…ading concept parent

paynejd · 2021-12-09T13:00:20Z

Adding ideas for hierarchical response.

Move concepts and mappings counts into a summary field
Use a new entry field inside a concept to add child resources

Open questions...

Handling a repeated concept will be different here than in the flat response -- we should probably show the repeated concept- in the first occurence it would show the normal cascaded response, in repeat occurrences it would include the concept, but have an additional attribute to indicate that it is repeated, and then not show any of the child entities
Might be useful to include counts in sub-entities?

// 20211209073501
// https://api.qa.openconceptlab.org/orgs/CIEL/sources/CIEL/concepts/159615/$cascade/?cascadeLevels=1&mapTypes=CONCEPT-SET,Q-AND-A

{
  "type": "Bundle",
  "bundle_type": "searchset",
  "timestamp": "2021-03-24T16:11:38.917836Z",
  "total": 174,
  "summary": {
    "concepts": 82,
    "mappings": 92
  },
  "entry": [
    {
      "uuid": "90391",
      "id": "159614",
      "type": "Concept",
      "url": "/orgs/CIEL/sources/CIEL/concepts/159614/",
      "version_url": "/orgs/CIEL/sources/CIEL/concepts/159614/90394/",
      "entry": [
        {
          "uuid": "99215",
          "id": "159615",
          "type": "Concept",
          "url": "/orgs/CIEL/sources/CIEL/concepts/159615/",
          "version_url": "/orgs/CIEL/sources/CIEL/concepts/159615/99218/"
        },
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        },
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          "version_url": "/orgs/CIEL/sources/CIEL/concepts/1081/3247/"
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          "type": "Mapping",
          "map_type": "CONCEPT-SET",
          "url": "/orgs/CIEL/sources/CIEL/mappings/287453/",
          "version_url": "/orgs/CIEL/sources/CIEL/mappings/287453/287454/"
        },
        {
          "uuid": "312175",
          "id": "312175",
          "type": "Mapping",
          "map_type": "Q-AND-A",
          "url": "/orgs/CIEL/sources/CIEL/mappings/312175/",
          "version_url": "/orgs/CIEL/sources/CIEL/mappings/312175/312176/"
        },
        {
          "uuid": "312180",
          "id": "312180",
          "type": "Mapping",
          "map_type": "Q-AND-A",
          "url": "/orgs/CIEL/sources/CIEL/mappings/312180/",
          "version_url": "/orgs/CIEL/sources/CIEL/mappings/312180/312182/"
        },
        {
          "uuid": "312185",
          "id": "312185",
          "type": "Mapping",
          "map_type": "Q-AND-A",
          "url": "/orgs/CIEL/sources/CIEL/mappings/312185/",
          "version_url": "/orgs/CIEL/sources/CIEL/mappings/312185/312186/"
        },
        {
          "uuid": "312194",
          "id": "312194",
          "type": "Mapping",
          "map_type": "Q-AND-A",
          "url": "/orgs/CIEL/sources/CIEL/mappings/312194/",
          "version_url": "/orgs/CIEL/sources/CIEL/mappings/312194/312196/"
        },
        {
          "uuid": "312199",
          "id": "312199",
          "type": "Mapping",
          "map_type": "CONCEPT-SET",
          "url": "/orgs/CIEL/sources/CIEL/mappings/312199/",
          "version_url": "/orgs/CIEL/sources/CIEL/mappings/312199/312200/"
        },
        {
          "uuid": "312203",
          "id": "312203",
          "type": "Mapping",
          "map_type": "CONCEPT-SET",
          "url": "/orgs/CIEL/sources/CIEL/mappings/312203/",
          "version_url": "/orgs/CIEL/sources/CIEL/mappings/312203/312205/"
        },
        {
          "uuid": "312208",
          "id": "312208",
          "type": "Mapping",
          "map_type": "CONCEPT-SET",
          "url": "/orgs/CIEL/sources/CIEL/mappings/312208/",
          "version_url": "/orgs/CIEL/sources/CIEL/mappings/312208/312210/"
        },
        {
          "uuid": "315977",
          "id": "315977",
          "type": "Mapping",
          "map_type": "Q-AND-A",
          "url": "/orgs/CIEL/sources/CIEL/mappings/315977/",
          "version_url": "/orgs/CIEL/sources/CIEL/mappings/315977/315978/"
        },
        {
          "uuid": "315981",
          "id": "315981",
          "type": "Mapping",
          "map_type": "Q-AND-A",
          "url": "/orgs/CIEL/sources/CIEL/mappings/315981/",
          "version_url": "/orgs/CIEL/sources/CIEL/mappings/315981/315982/"
        },
        {
          "uuid": "315985",
          "id": "315985",
          "type": "Mapping",
          "map_type": "Q-AND-A",
          "url": "/orgs/CIEL/sources/CIEL/mappings/315985/",
          "version_url": "/orgs/CIEL/sources/CIEL/mappings/315985/315986/"
        },
        {
          "uuid": "315993",
          "id": "315993",
          "type": "Mapping",
          "map_type": "Q-AND-A",
          "url": "/orgs/CIEL/sources/CIEL/mappings/315993/",
          "version_url": "/orgs/CIEL/sources/CIEL/mappings/315993/315994/"
        },
        {
          "uuid": "315997",
          "id": "315997",
          "type": "Mapping",
          "map_type": "CONCEPT-SET",
          "url": "/orgs/CIEL/sources/CIEL/mappings/315997/",
          "version_url": "/orgs/CIEL/sources/CIEL/mappings/315997/315999/"
        },
        {
          "uuid": "316001",
          "id": "316001",
          "type": "Mapping",
          "map_type": "CONCEPT-SET",
          "url": "/orgs/CIEL/sources/CIEL/mappings/316001/",
          "version_url": "/orgs/CIEL/sources/CIEL/mappings/316001/316002/"
        },
        {
          "uuid": "316007",
          "id": "316007",
          "type": "Mapping",
          "map_type": "CONCEPT-SET",
          "url": "/orgs/CIEL/sources/CIEL/mappings/316007/",
          "version_url": "/orgs/CIEL/sources/CIEL/mappings/316007/316008/"
        }
      ]
    }
 ]
}

paynejd · 2022-04-11T12:35:01Z

Pinning as high priority so that @paynejd will update to make it clear what the next steps are

paynejd · 2022-05-19T14:31:11Z

$cascade hierarchical response format (in addition to the flat response) ($cascade response as hierarchy #1168)
Restricted to $cascade to source version (Restrict $cascade to the repo version by default #1224)
Option to cascade in reverse direction (e.g. up the tree) (Implement $cascade parameter to reverse the direction #1183)
Cascade of concepts within collection context (Implement $cascade within a collection version #1295)
Ability to use $cascade request in a collection reference (TBD)
Handling the old cascade and transform request parameters (TBD)
Introduce $cascade.returnMapTypes parameter (or equivalent behavior) that probably defaults to * (return all map types) (TBD)
- Align with (and maybe reuse) existing parameters
- Goal is to specify criteria for inclusion of resources in a response separately from criteria for cascading (e.g. for any concept that is included, include all of its mappings, but only cascade Q-AND-A and CONCEPT-SET map types)

Ideas for long-term -- these will move to new tickets:

Improvements to cascade visualization (TBD)
Ability to cascade a list of results, not just one concept at a time
Ability to define more complex cascade rules, such as the rules needed for cascading a CIEL concept to include in a concept dictionary -- see https://docs.google.com/document/d/1oFlY_wyDarpPdHhfrQM7vbvkDs51hV9qQrMusBQst5A/edit#heading=h.xn5s0dnidagz:
- multiple cascade rules per result set
- different rules at different levels/for different result sets
- criteria for inclusion of a target concept
Finalize $cascade documentation (ticket TBD):
- OCL Docs: https://docs.openconceptlab.org/en/latest/oclapi/apireference/cascade.html
- Google Doc: https://docs.google.com/document/d/1oFlY_wyDarpPdHhfrQM7vbvkDs51hV9qQrMusBQst5A/edit#heading=h.gsoixrdm42qw

@snyaggarwal @rkorytkowski @jamlung-ri Please confirm the "what's next" list -- will move these into their own tickets and close this out when we have consensus

jamlung-ri · 2022-10-04T19:03:22Z

@paynejd for the list above, we should make sure we have captured all OpenMRS cascade needs. Namely, the ability to cascade down multiple levels using certain map types.

jamlung-ri · 2022-10-05T12:22:56Z

A potentially useful lo-fi drawing for a $cascade results panel: https://docs.google.com/drawings/d/19slrFyJebEKwDSve65V4tzAqKthrbA-uiP9V8vRWMcg/edit

Edit: This cascade drawing is missing some key generic functionality, particularly for controlling the number of levels down you can go and the map types that you might want to be including.

snyaggarwal · 2022-10-06T04:42:21Z

@jamlung-ri this looks good. In terms of behavior, we will need to perform $cascade request when the user is on the dialog and switching between options of the cascade. Should we disable the button to add until the results of the cascade are not displayed?

jamlung-ri · 2022-10-06T14:34:46Z

@paulsonder might have more thoughts on this (keeping in mind that some design work is likely needed here).

Makes sense that the $cascade request will occur as the user clicks the option, so there will likely be some delay as the API returns results (especially if it's a large set of results). Because of the risk for delay, I don't really want to disable the Add button, but we should at least show that the results are still loading. The user can decide if they do or don't want to wait and review the results before clicking the Add button.

paynejd · 2022-10-17T12:00:03Z

This ticket is focused only on adding OpenMRS-compatible behavior to the $cascade endpoint in the OCL API.

Design discussions to expose the new $cascade behavior in the TermBrowser are taking place here #1378. @jamlung-ri Are there details in this ticket that need to be moved over to #1378?

Goal: Specify criteria for inclusion of resources in a response separately from criteria for processing the cascade, e.g.:

I want to cascade only Q-AND-A and CONCEPT-SET map types (e.g. ?mapTypes=Q-AND-A,CONCEPT-SET)
However, for any concept that is included, I want all of its mappings to be included in the resultset

Proposed approach: Introduce $cascade.returnMapTypes parameter (or equivalent behavior)

“returnMapTypes” must also apply to “terminal concepts”
Default to “*” (return all map types) or to “mapTypes”
mapTypes = controls cascade behavior; if no value, then this is defaults to “*” (cascade everything)
returnMapTypes = controls which mappings are included in the resultset; “*” returns all of a concept’s mappings; “false”/0 will not include any mappings in the resultset; if no value, then this defaults to the “mapTypes”
includeMappings (bool) = controls whether any mappings are included in the resultset; this parameter will be deprecated

@paynejd To follow up with a visual using this concept: https://app.openconceptlab.org/#/orgs/CIEL/sources/CIEL/concepts/161499/

Example query: https://api.qa.openconceptlab.org/orgs/CIEL/sources/CIEL/concepts/159615/$cascade/?cascadeLevels=1&mapTypes=CONCEPT-SET,Q-AND-A

jamlung-ri · 2022-10-17T12:08:28Z

Design discussions to expose the new $cascade behavior in the TermBrowser are taking place here #1378. @jamlung-ri Are there details in this ticket that need to be moved over to #1378?

Just copied over some necessary details

“returnMapTypes” must also apply to “terminal concepts”

Will the address the need to go down as many levels as necessary in the $cascade operation? Or should we be mentioning that separately in the Goal section above? @paynejd

paynejd · 2022-10-18T11:40:07Z

@jamlung-ri The number of cascade levels is a separate parameter, cascadeLevels. It will also apply to returnMapTypes

paynejd · 2022-10-18T14:49:11Z

cc @snyaggarwal @jamlung-ri

Visual applies to this concept:
https://app.openconceptlab.org/#/orgs/CIEL/sources/CIEL/concepts/161499/

Visual represents this query:
https://api.openconceptlab.org/orgs/CIEL/sources/CIEL/concepts/161499/$cascade/?mapType=CONCEPT-SET,Q-AND-A&returnMapType=*

Visual:
https://docs.google.com/spreadsheets/d/1hxRMKVcgrg9LVjzSLbd_rM9R3xN6rtAflvbymXgQzKw/edit?usp=sharing

Note that this may be introducing another new behavior related to self-maps (@snyaggarwal
please confirm):

Cascade should never return a self-map target concept (because that returns itself)
Cascade may return the self-mapping, based on the value of returnMapType

snyaggarwal · 2022-10-19T06:54:10Z

@paynejd the first attempt at this is deployed on QA. Do give it a try.

jamlung-ri · 2022-10-19T12:13:44Z

Let's set up a call to get this moving. Jon and I have not had luck yet.

paynejd · 2022-10-19T13:07:59Z

2 bugs to report so far:

If no value is provided for returnMapTypes, then the value of mapTypes should automatically be applied to it. For example:

Request Params	mapTypes	returnMapTypes
None (default)	*	*
?mapTypes=Q-AND-A,CONCEPT-SET	Q-AND-A,CONCEPT-SET	*
?mapTypes=Q-AND-A,CONCEPT-SET&returnMapTypes=Q-AND-A,CONCEPT-SET	Q-AND-A,CONCEPT-SET	Q-AND-A,CONCEPT-SET

name should be the display name of a concept, not its id. See example below:

…er map types criteria

snyaggarwal · 2022-10-20T02:21:34Z

@paynejd

Updated behavior.
name field is not needed in the response since we have display_name already. Removed it.

paynejd · 2022-10-24T20:45:51Z

cc @snyaggarwal

I created a new source in QA that we can use to test cascade functionality:
https://app.qa.openconceptlab.org/#/users/ocladmin/sources/CascadeTest/

The source has the following characteristics that we want to test using cascade:

2+ levels of hierarchy
2+ levels of internal mappings for at least one maptype (e.g. such as Q-AND-A or CONCEPT-SET)
1+ levels of internal mappings for at least one other maptype (e.g. not Q-AND-A or CONCEPT-SET)
1+ external mappings
1+ Self-maps
1+ Recursive maps (where a child is associated with a concept higher up in the tree that would cause recursion if the cascade algorithm doesn’t catch it)

paynejd · 2022-10-24T20:46:01Z

Bug:

Hierarchical results only show up with HEAD or if no source version is specified -- compare these results:
- HEAD - hierarchical results are included here, even though the hierarchy was defined before releasing any versions; note that this also works if I omit HEAD, which means that Cascade may not be correctly handling latest -- https://api.qa.openconceptlab.org/users/ocladmin/sources/CascadeTest/HEAD/concepts/AA/$cascade/?cascadeLevels=1&method=sourceToConcepts&view=hierarchy&includeRetired=false
- v3 - hierarchical results are NOT included, even though the hierarchy was defined before releasing any versions -- https://api.qa.openconceptlab.org/users/ocladmin/sources/CascadeTest/v3/concepts/AA/$cascade/?cascadeLevels=1&method=sourceToConcepts&view=hierarchy&includeRetired=false

This behavior can be easily replicated in the TermBrowser too, by looking at the Associations panel in HEAD and again in v3:

paynejd · 2022-10-24T20:50:51Z

cc @snyaggarwal These are all for discussion...

What's up?

excludeMapTypes and returnMapTypes -- how do these work together?
- returnMapTypes takes on the value of mapTypes, but what if excludeMapTypes is used instead?
includeMappings is duplicative of setting returnMapTypes to false or 0 -- we should deprecate the includeMappings parameter for users
Mappings have duplicate to_concept fields and there are no from_concept fields (at least when view=hierarchy)
- to_concept_code, to_concept_url
- target_concept_code, target_concept_url, target_concept_name, target_source_owner, target_source_name

Questions

For self-maps (e.g. SAME-AS CIEL:161499 SAME-AS CIEL:161499), in hierarchical view, should cascade return the target concept again and just suppress recursion? Probably not, but I want to confirm this one as a group.
Any reason to include uuid in the response for concepts/mappings? Not sure what is the value in exposing this externally

Food for thought

Repo version must be part of the response for each concept/mapping
- Possibly just update "url" to include the source version?
- "version_url" in its current state is discouraged to be used externally
Summary response for cascade should match (approximately) the summary response for concepts and mappings individually
The combination of method, cascadeHierarchy and cascadeMappings are quite confusing (even for me and I helped define these!) -- is there a more intuitive way to model these parameters/behaviors?

…s false

snyaggarwal · 2022-10-27T05:18:11Z

@paynejd Answers/comments on each are below:

mapTypes and excludeMapTypes makes a common criteria to filter on map_type. returnMapTypes uses the same. So its considering both.
includeMappings can now be deprecated. I will make this change.
Mappings having duplicate response. This is because TermBrowser cascade visualisation needed a common key to render nodes (rather than iterating over from_concept_* and to_concept_*), so I added target_concept_* which points to to_concept_* in forward and from_concept_* in reverse cascade. It also includes from_concept_* and to_concept_* fields for backward compatibility (can be removed though).

jamlung-ri · 2022-10-27T12:54:46Z

Bug:

* Hierarchical results only show up with HEAD or if no source version is specified -- compare these results:
  
  * **HEAD** - hierarchical results are included here, even though the hierarchy was defined before releasing any versions; note that this also works if I omit HEAD, which means that Cascade may not be correctly handling `latest` -- https://api.qa.openconceptlab.org/users/ocladmin/sources/CascadeTest/HEAD/concepts/AA/$cascade/?cascadeLevels=1&method=sourceToConcepts&view=hierarchy&includeRetired=false
  * **v3** - hierarchical results are NOT included, even though the hierarchy was defined before releasing any versions -- https://api.qa.openconceptlab.org/users/ocladmin/sources/CascadeTest/v3/concepts/AA/$cascade/?cascadeLevels=1&method=sourceToConcepts&view=hierarchy&includeRetired=false

This behavior can be easily replicated in the TermBrowser too, by looking at the Associations panel in HEAD and again in v3:

* https://app.qa.openconceptlab.org/#/users/ocladmin/sources/CascadeTest/v3/concepts/AA/

* https://app.qa.openconceptlab.org/#/users/ocladmin/sources/CascadeTest/HEAD/concepts/AA/

We discovered that hierarchy_root_url attribute is not appearing in the versions of the Source. Examples: HEAD version with the attribute, and v3 version without the attribute

paynejd · 2022-10-27T15:23:19Z

Summarizing immediate next steps from the Oct 27 deep dive:

Rename target_concept_* and target_source_* fields to cascade_target_* -- this is to avoid confusion with the existing to_concept_* fields. Note that this will require updates in the TermBrowser
Remove uuid field from the response
hierarchy_root_url field is missing when getting a specific source version (e.g. GET /users/ocladmin/sources/CascadeTest/v2/), which is causing two issues:
- Cascade only includes hierarchy when looking at HEAD
- TermBrowser does not provide the "View Hierarchy" option on the Concepts tab when looking at source versions other than HEAD
Add a section at the top-level of the response that indicates cascade direction and repository version -- or, it may make sense to just include a section with all of the cascade parameters and/or the full request URL so that the response can be shared and replicated

One remaining unanswered issue for round 3:

The url attribute for concepts in the cascade response are inconsistent:
- If looking at HEAD, concept url is a version-less relative URL
- If looking at a specific repo version, url is a relative concept version URL
- Ideally, url should instead include the repo version and not the concept version -- e.g. this is what we want it to be: /users/ocladmin/sources/CascadeTest/v2/concepts/AA/
- @snyaggarwal can you estimate the level of effort required to make this shift? Is this going to break a bunch of stuff?

Once the above items are complete, we are hopefully ready to deploy after a final round of testing. Note that we still need to do round 3 testing in the context of collections.

We'll tackle these in Round 4:

Verifying & documenting the behavior of the terminal field
The combination of method, cascadeHierarchy and cascadeMappings are quite confusing (even for me and I helped define these!) -- is there a more intuitive way to model these parameters/behaviors
Additional integration tests using CascadeTest source
If we don't get to this in round 3: Adding repo version into the actual resource URLs in the result set
Consider changing duplicate resource entries to use references rather than duplicating the concepts:
- Flat view can also provide a list of references to children that are present in the JSON

…dded hierarchy root url

snyaggarwal · 2022-11-01T04:43:51Z

Rename target_concept_* and target_source_* fields to cascade_target_* -- this is to avoid confusion with the existing to_concept_* fields. Note that this will require updates in the TermBrowser

Remove uuid field from the response

hierarchy_root_url field is missing when getting a specific source version (e.g. GET /users/ocladmin/sources/CascadeTest/v2/), which is causing two issues:

Cascade only includes hierarchy when looking at HEAD

TermBrowser does not provide the "View Hierarchy" option on the Concepts tab when looking at source versions other than HEAD

Add a section at the top-level of the response that indicates cascade direction and repository version -- or, it may make sense to just include a section with all of the cascade parameters and/or the full request URL so that the response can be shared and replicated

@paynejd These are done

jamlung-ri · 2022-11-01T13:42:00Z

@snyaggarwal I was doing some testing on this source, and I am seeing different results between a new source version and HEAD. Seems like hierarchy results are still not being included? Even though the hierarchy_root_url is filled out here.

Source version link: https://api.qa.openconceptlab.org/users/ocladmin/sources/CascadeTest/v4/concepts/AA/cascade/?method=sourcetoconcepts&cascadeHierarchy=true&cascadeMappings=true&cascadeLevels=*&reverse=false&includeRetired=false - Returning 17 concepts, no hierarchical concepts
HEAD link: https://api.qa.openconceptlab.org/users/ocladmin/sources/CascadeTest/HEAD/concepts/AA/cascade/?method=sourcetoconcepts&cascadeHierarchy=true&cascadeMappings=true&cascadeLevels=*&reverse=false&includeRetired=false - Returning 33 concepts

However, the Hierarchy option is appearing on the v4 version of the source, so that part appears to be fixed.

…version cascade

snyaggarwal · 2022-11-03T04:18:36Z

@jamlung-ri this is fixed.

snyaggarwal · 2022-11-04T09:23:40Z

@jamlung-ri @paynejd this is deployed everywhere

snyaggarwal · 2022-11-17T08:01:06Z

Deployed everywhere. Closing this.

paynejd assigned snyaggarwal Nov 24, 2021

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OpenConceptLab/ocl_issues#1131 | concept cascade performance | simpli…

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OpenConceptLab/ocl_issues#1131 | integration test for all cascade levels

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OpenConceptLab/ocl_issues#1131 | reducing max results to 500

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OpenConceptLab/ocl_issues#1131 | added concepts/mappings count

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$cascade operation round 2, incl. recursion #1122

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paynejd changed the title ~~$cascade round 3, including references~~ $cascade API round 3, including references Oct 14, 2022

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Implement Advanced Add References panel #1378

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OpenConceptLab/ocl_issues#1131 | cascade returnMapTypes behaviour

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OpenConceptLab/ocl_issues#1131 | cascade returnMapTypes behaviour

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OpenConceptLab/ocl_issues#1131 | return map types | no default value

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Cascade Documentation, round 2 #1429

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snyaggarwal commented Nov 3, 2022

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snyaggarwal commented Nov 17, 2022

$cascade API round 3, including references #1131

$cascade API round 3, including references #1131

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paynejd commented Nov 24, 2021 •

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