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bug #7745

closed

Subtree filter for dataportal services

Added by Andreas Müller over 4 years ago. Updated about 2 years ago.

Status:
Closed
Priority:
Highest
Category:
cdmlib-remote
Target version:
Start date:
Due date:
% Done:

100%

Estimated time:
Severity:
normal
Found in Version:

Description

This is a bit similar to the publish flag filter for data portal (#3560) and other services (#7492)


Related issues

Related to EDIT - task #3560: Withheld unpublished taxa from webservice used in E+M dataportalResolvedAndreas Müller

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Related to EDIT - feature request #7492: Withheld unpublished taxa from webservice used in other webservicesNewAndreas Müller

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Related to EDIT - bug #7759: classification subtreefilter settings in portalClosedAndreas Kohlbecker

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Related to EDIT - feature request #8875: Filter data portal by taxonomic rankNewAndreas Kohlbecker

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Related to EDIT - feature request #8977: Allow filtering webservices on multiple taxon subtreesNewAndreas Müller

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Copied to EDIT - task #9402: Subtree filter for polytomousKey and polytomousKeyNode servicesNewAndreas Kohlbecker

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Actions #1

Updated by Andreas Müller over 4 years ago

  • Related to task #3560: Withheld unpublished taxa from webservice used in E+M dataportal added
Actions #2

Updated by Andreas Müller over 4 years ago

  • Description updated (diff)
Actions #3

Updated by Andreas Müller over 4 years ago

  • Related to feature request #7492: Withheld unpublished taxa from webservice used in other webservices added
Actions #4

Updated by Andreas Müller over 4 years ago

  • Status changed from New to In Progress
  • Target version changed from Unassigned CDM tickets to Release 5.3
  • % Done changed from 0 to 20
Actions #5

Updated by Andreas Müller over 4 years ago

Subtree filter is now implemented for (rankSpecific)rootNotes and simple taxon search. API exists also for freetext search (but filter not yet implemented)

Actions #6

Updated by Andreas Kohlbecker over 4 years ago

  • Related to bug #7759: classification subtreefilter settings in portal added
Actions #7

Updated by Andreas Kohlbecker over 4 years ago

the query parameter should be the same in all webservice uris: subtree

Actions #8

Updated by Andreas Kohlbecker over 4 years ago

Andreas Kohlbecker wrote:

the query parameter should be the same in all webservice uris: subtree

DONE: 905f70dc

Actions #9

Updated by Andreas Kohlbecker over 4 years ago

Also the following webservices need to get a subtree filter:

  • /portal/taxon/{uuid}
  • /portal/taxon/{uuid}/taxonNodes
  • /portal/classification/{uuid}/pathFrom/{uuid}/toRank/{uuid}
  • /classification/{uuid}/childNodesOf/{uuid}
Actions #10

Updated by Andreas Müller over 4 years ago

  • Status changed from In Progress to Resolved
Actions #11

Updated by Andreas Müller over 4 years ago

  • % Done changed from 20 to 50
Actions #12

Updated by Andreas Müller over 4 years ago

  • Status changed from Resolved to Closed

From all what I tested it works. I never got an "external" taxon.

Actions #13

Updated by Andreas Müller over 4 years ago

  • Assignee changed from Andreas Müller to Andreas Kohlbecker
  • % Done changed from 50 to 100
Actions #14

Updated by Andreas Müller over 4 years ago

  • Status changed from Closed to Feedback
  • Assignee changed from Andreas Kohlbecker to Andreas Müller
  • % Done changed from 100 to 70

Have to reopen. Freetext search on context does not yet work as expected. Searching for "All" returns no result with subtree filter on Ranunculaceae on test.cyprus. Without filter we get a 100% result for Staphisagria macrosperma which is a taxon in Ranunculaceae. Need to check if this is an error in the search itself or has to do with portal code.

(anyway I closed the wrong ticket ;-), I wanted to close the portal ticket )

Actions #15

Updated by Andreas Müller over 4 years ago

  • Status changed from Feedback to Resolved
  • Assignee changed from Andreas Müller to Andreas Kohlbecker
  • % Done changed from 70 to 80

Can you please do the final review and close if everything works as expected (but we will probably get user feedback anyway if something does not work such)

Actions #16

Updated by Andreas Müller over 4 years ago

  • Tags changed from caryophyllales to caryophyllales, search
Actions #17

Updated by Andreas Kohlbecker over 4 years ago

  • Status changed from Resolved to Feedback
  • Assignee changed from Andreas Kohlbecker to Andreas Müller
Actions #18

Updated by Andreas Müller over 4 years ago

Andreas Kohlbecker wrote:

Open issues:

tested with subtree filter Plumbaginaceae Juss. [#t10#1986#28#] uuid=0ad45274-c5cf-4a95-aa1b-dc698e78f53a

1) http://api.cybertaxonomy.org/caryophyllales_spp/portal/classification/9edc58b5-de3b-43aa-9f31-1ede7c009c2b/childNodesAt/ac470211-1586-4b24-95ca-1038050b618d?subtree=0ad45274-c5cf-4a95-aa1b-dc698e78f53a

returns the taxon set as filter! I think this should be supressesd

Why should it be suppressed? Where does it lead to problems and where is it used. Isn't this the root node for the tree and therefore should appear?

Actions #19

Updated by Andreas Müller over 4 years ago

Andreas Kohlbecker wrote:

Open issues:

2) http://api.cybertaxonomy.org/caryophyllales_spp/portal/taxon/7114a8f3-6610-411d-b559-c28e7821cf1c/synonymy?subtree=0ad45274-c5cf-4a95-aa1b-dc698e78f53a'

not yet with filter parameter

I do not understand why this is required. The webservice is not used as primary input for a taxon page or any other portal site. So we do not need to filter it.
However I implemented it (cdmlib|bc9db6bf23) as it was more or less copy and paste from taxon/uuid . Please do review. I did not test with live data

Actions #20

Updated by Andreas Müller over 4 years ago

Andreas Kohlbecker wrote:

Open issues:

3) http://api.cybertaxonomy.org/caryophyllales_spp/portal/taxon/7114a8f3-6610-411d-b559-c28e7821cf1c/toNameRelationships?subtree=0ad45274-c5cf-4a95-aa1b-dc698e78f53a

not yet with filter parameter

Again I do not understand why this needs to be filtered. If necessary we can do it the same way as the synonymy (3 lines of code), but it is not necessary. We do not want to filter webservices but data portals. For this it is not needed. Otherwise please give a dataportal link which is not protected because of this service.

Actions #21

Updated by Andreas Müller over 4 years ago

  • Status changed from Feedback to Resolved
  • Assignee changed from Andreas Müller to Andreas Kohlbecker

By the way there might be not implemented webservices that need to be protected, e.g. for PolytomousKeys. I think they have an own entry point so should be protected. Can you check this.

But we should open a new ticket for these new issues.

Actions #22

Updated by Andreas Kohlbecker over 4 years ago

To the issues 1) - 3) reported in #7745#note-17:

1) You are right, this web service behaves ok.

2) I reported this because the webservice is being used during the composition of the taxon page. It is not really required to protect it at the moment, but it could become more relavant once the data portal taxon pages are more modularized and rendered anynchonously. Anyway, thanks for filtering this webservice also. Implementation looks ok

3) I agree, this is not really needed a the moment.

Actions #23

Updated by Andreas Müller over 4 years ago

So can we close the ticket?

Actions #24

Updated by Andreas Kohlbecker over 4 years ago

Andreas Müller wrote:

So can we close the ticket?

You were too fast ;-)

Actions #25

Updated by Andreas Kohlbecker over 4 years ago

For the polytomous keys the following webservices need to be filtered by the subTree to avoid unpublished taxa showing up in the key:

  • polytomousKey/{uuid}.json --> suppress the whole key if it a) targets any taxon which needs to be suppressed or b) the taxonomic scope includes taxa to be suppressed?
  • polytomousKeyNode/{uuid}/taxon.json --> suppress target taxa per polytomousKeyNode

we need to decide if keys need to be suppressed completely or if only specific nodes are to be shown incompletely? I think the whole key needs to be hidden if it is not 100% included in the classification subtree.

I suggest to open a new ticket for the remaining issues

Actions #26

Updated by Andreas Müller almost 3 years ago

Actions #27

Updated by Andreas Müller almost 3 years ago

Actions #28

Updated by Andreas Kohlbecker about 2 years ago

Andreas Kohlbecker wrote:

For the polytomous keys the following webservices need to be filtered by the subTree to avoid unpublished taxa showing up in the key:

  • polytomousKey/{uuid}.json --> suppress the whole key if it a) targets any taxon which needs to be suppressed or b) the taxonomic scope includes taxa to be suppressed?
  • polytomousKeyNode/{uuid}/taxon.json --> suppress target taxa per polytomousKeyNode

we need to decide if keys need to be suppressed completely or if only specific nodes are to be shown incompletely? I think the whole key needs to be hidden if it is not 100% included in the classification subtree.

I suggest to open a new ticket for the remaining issues

copied to new ticket: #9402

Actions #29

Updated by Andreas Kohlbecker about 2 years ago

  • Copied to task #9402: Subtree filter for polytomousKey and polytomousKeyNode services added
Actions #30

Updated by Andreas Kohlbecker about 2 years ago

  • Status changed from Resolved to Closed
  • % Done changed from 80 to 100
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