Adapts files to new framework structure (collections, root and collections/admin)
#14
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themerekat
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Oct 7, 2021
Various updates pushed from Symbiota-light into CCH2 code repository
mandrewj
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Jan 7, 2022
GregoryPost
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Oct 11, 2022
Minor spacing adjustments
egbot
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Jul 9, 2023
* Adds existing citation formats * Re-formats code and passes dynProps to coll meta Change in code in line 43: ``` // if($k != 'dynamicProperties') ``` * Adds EDI url if collection is pushed there and not to GBIF Also some re-formatting * Creates EDI citation format and passes to coll profile Related to #14 * Modifies EDI citation format * Adds dynProps field to datasets table To allow insertion of values related to EDI publishing * Re-formats `datasets/public.php` * Adds a comma to EDI citation format * Adds a check for edi key in dynProps * Re-formats code and adds dynProps to dataset Alters function `getPublicDatasetMetadata($dsid)` to include `dynamicProperties` filed in dataset metadata array. * Adds EDI information and citation to public dataset page Closes #18
egbot
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Sep 26, 2023
Merge BioKIC/Symbiota-light developments into SEINet code repository
GregoryPost
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Aug 2, 2024
refresh codebase from BioKIC/Symbiota
Atticus29
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Aug 6, 2024
# This is the 1st commit message: begin to implement front end of association-based search # This is the commit message #2: continue fleshing out the front and back end of association-based search # This is the commit message #3: rename some variables to be more accurate and fix a few array-vs-string handlers # This is the commit message #4: remove assistive-text lines # This is the commit message #5: fix issue with taxa suggest # This is the commit message #6: DRY up taxa suggest in a way that is usable for more than one element on the same page # This is the commit message #7: fix bug where reverse relationship was not returning results correctly # This is the commit message #8: begin to flesh out populating readRequestVariables with association-related data # This is the commit message #9: continue making progress with writing setAssociationRequestVariable method # This is the commit message #10: continue working on setAssociationRequestVariable and subfunctions # This is the commit message #11: continue subfunctionalizing # This is the commit message #12: continue fleshing out the associated-taxon query # This is the commit message #13: continue to make progress on the new search-by-association query infrastructure # This is the commit message #14: get search results to display # This is the commit message #15: Get the search criteria to display # This is the commit message #16: Update harvester.php (#1447) Modifies logic to display available boundary tool when no active geographic thesaurus exist in the DB # This is the commit message #17: CSS drop-down menus (#1452) * CSS drop-down menus Add styling to header.css that enables top drop-down menus # This is the commit message #18: Update OmCollections.php (#1455) Errant line of code short circuiting collection meta data update. # This is the commit message #19: closes #1449 which was preventing checklist polyaid from opening (#1458) # This is the commit message #20: Occurrence editor crowdsource adjustments - Add formatting for eventDate2 - Adjust exsicati - Remove from display: additional identifiers, behavior, vitality # This is the commit message #21: occurrence editor crowdsource adjustments - Add vertical-align to crowdsource css to override value set within reset.css - Force refresh of crowdsource.css within client's browsers # This is the commit message #22: crowdsource editor styling issue - resolve vertical-align issue, which persisted when opening in crowdsourcing mode and then switching between long and short forms - Fix fieldset padding issue within image popout # This is the commit message #23: Api media 2024 06 (#1463) - Fix route bug interfering with POST write calls - Add recordID UUID to POST call - Improve error output media object isn't found (400 error) - Improve standardization of all response output - Add sort fields to api documentation - Add function that attempts to determine mime type via file header. Has added benefit of ensuring input file exists. - Update swagger documentation # This is the commit message #24: Media API - Add ability to match images based on recordID UUID within PATCH call # This is the commit message #25: added confirmation windows for project and editor delete icons (#1454) # This is the commit message #26: [3.1] -burpsuite-fix: do not add taxa to query if there are special characters or quotes (#1436) * do not add taxa to query if there are special characters or quotes * cherry pick fix in 6250abd where getTaxonWhereFrag was getting un-cleaned taxon string * respond to code review feedback
Atticus29
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Aug 6, 2024
# This is the 1st commit message: begin to implement front end of association-based search # This is the commit message #2: continue fleshing out the front and back end of association-based search # This is the commit message #3: rename some variables to be more accurate and fix a few array-vs-string handlers # This is the commit message #4: remove assistive-text lines # This is the commit message #5: fix issue with taxa suggest # This is the commit message #6: DRY up taxa suggest in a way that is usable for more than one element on the same page # This is the commit message #7: fix bug where reverse relationship was not returning results correctly # This is the commit message #8: begin to flesh out populating readRequestVariables with association-related data # This is the commit message #9: continue making progress with writing setAssociationRequestVariable method # This is the commit message #10: continue working on setAssociationRequestVariable and subfunctions # This is the commit message #11: continue subfunctionalizing # This is the commit message #12: continue fleshing out the associated-taxon query # This is the commit message #13: continue to make progress on the new search-by-association query infrastructure # This is the commit message #14: get search results to display # This is the commit message #15: Get the search criteria to display # This is the commit message #16: Update harvester.php (#1447) Modifies logic to display available boundary tool when no active geographic thesaurus exist in the DB # This is the commit message #17: CSS drop-down menus (#1452) * CSS drop-down menus Add styling to header.css that enables top drop-down menus # This is the commit message #18: Update OmCollections.php (#1455) Errant line of code short circuiting collection meta data update. # This is the commit message #19: closes #1449 which was preventing checklist polyaid from opening (#1458) # This is the commit message #20: Occurrence editor crowdsource adjustments - Add formatting for eventDate2 - Adjust exsicati - Remove from display: additional identifiers, behavior, vitality # This is the commit message #21: occurrence editor crowdsource adjustments - Add vertical-align to crowdsource css to override value set within reset.css - Force refresh of crowdsource.css within client's browsers # This is the commit message #22: crowdsource editor styling issue - resolve vertical-align issue, which persisted when opening in crowdsourcing mode and then switching between long and short forms - Fix fieldset padding issue within image popout # This is the commit message #23: Api media 2024 06 (#1463) - Fix route bug interfering with POST write calls - Add recordID UUID to POST call - Improve error output media object isn't found (400 error) - Improve standardization of all response output - Add sort fields to api documentation - Add function that attempts to determine mime type via file header. Has added benefit of ensuring input file exists. - Update swagger documentation # This is the commit message #24: Media API - Add ability to match images based on recordID UUID within PATCH call # This is the commit message #25: added confirmation windows for project and editor delete icons (#1454) # This is the commit message #26: [3.1] -burpsuite-fix: do not add taxa to query if there are special characters or quotes (#1436) * do not add taxa to query if there are special characters or quotes * cherry pick fix in 6250abd where getTaxonWhereFrag was getting un-cleaned taxon string * respond to code review feedback # This is the commit message #27: Occurrence download bug (#1478) - searchvar term is being sanitized prior to being set as a session variable, which is converting & to &, thus interfering with parsing of all terms after the first term. Translating & to & fixes the issue. - The cleanOutStr function santizes output using htmlspecialchars. The htmlspecialchars on line 638 will double sanitize output, thus converting "east & west" to "east & west". - Variable is getting sanitized within index.php with htmlspecialchars twice. Once on line 12 and again on line 205 Addresses GH issue: #1470 # This is the commit message #28: subfunctionalize the chip button click to the handleRemoval method
Atticus29
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Aug 6, 2024
# This is the 1st commit message: begin to implement front end of association-based search # This is the commit message #2: continue fleshing out the front and back end of association-based search # This is the commit message #3: rename some variables to be more accurate and fix a few array-vs-string handlers # This is the commit message #4: remove assistive-text lines # This is the commit message #5: fix issue with taxa suggest # This is the commit message #6: DRY up taxa suggest in a way that is usable for more than one element on the same page # This is the commit message #7: fix bug where reverse relationship was not returning results correctly # This is the commit message #8: begin to flesh out populating readRequestVariables with association-related data # This is the commit message #9: continue making progress with writing setAssociationRequestVariable method # This is the commit message #10: continue working on setAssociationRequestVariable and subfunctions # This is the commit message #11: continue subfunctionalizing # This is the commit message #12: continue fleshing out the associated-taxon query # This is the commit message #13: continue to make progress on the new search-by-association query infrastructure # This is the commit message #14: get search results to display # This is the commit message #15: Get the search criteria to display # This is the commit message #16: Update harvester.php (#1447) Modifies logic to display available boundary tool when no active geographic thesaurus exist in the DB # This is the commit message #17: CSS drop-down menus (#1452) * CSS drop-down menus Add styling to header.css that enables top drop-down menus # This is the commit message #18: Update OmCollections.php (#1455) Errant line of code short circuiting collection meta data update. # This is the commit message #19: closes #1449 which was preventing checklist polyaid from opening (#1458) # This is the commit message #20: Occurrence editor crowdsource adjustments - Add formatting for eventDate2 - Adjust exsicati - Remove from display: additional identifiers, behavior, vitality # This is the commit message #21: occurrence editor crowdsource adjustments - Add vertical-align to crowdsource css to override value set within reset.css - Force refresh of crowdsource.css within client's browsers # This is the commit message #22: crowdsource editor styling issue - resolve vertical-align issue, which persisted when opening in crowdsourcing mode and then switching between long and short forms - Fix fieldset padding issue within image popout # This is the commit message #23: Api media 2024 06 (#1463) - Fix route bug interfering with POST write calls - Add recordID UUID to POST call - Improve error output media object isn't found (400 error) - Improve standardization of all response output - Add sort fields to api documentation - Add function that attempts to determine mime type via file header. Has added benefit of ensuring input file exists. - Update swagger documentation # This is the commit message #24: Media API - Add ability to match images based on recordID UUID within PATCH call # This is the commit message #25: added confirmation windows for project and editor delete icons (#1454) # This is the commit message #26: [3.1] -burpsuite-fix: do not add taxa to query if there are special characters or quotes (#1436) * do not add taxa to query if there are special characters or quotes * cherry pick fix in 6250abd where getTaxonWhereFrag was getting un-cleaned taxon string * respond to code review feedback # This is the commit message #27: Occurrence download bug (#1478) - searchvar term is being sanitized prior to being set as a session variable, which is converting & to &, thus interfering with parsing of all terms after the first term. Translating & to & fixes the issue. - The cleanOutStr function santizes output using htmlspecialchars. The htmlspecialchars on line 638 will double sanitize output, thus converting "east & west" to "east & west". - Variable is getting sanitized within index.php with htmlspecialchars twice. Once on line 12 and again on line 205 Addresses GH issue: #1470 # This is the commit message #28: subfunctionalize the chip button click to the handleRemoval method # This is the commit message #29: only run getAssociatedTaxaSqlFragment when the relevant form field values are present in the query # This is the commit message #30: fix the behavior of the chip removal # This is the commit message #31: persist search terms # This is the commit message #32: fix the non-persisting taxon type selection # This is the commit message #33: remove var_dump # This is the commit message #34: fix bug where association search is not playing well with taxon accordion # This is the commit message #35: get the synonym searching to work
Atticus29
added a commit
that referenced
this pull request
Aug 6, 2024
# This is the 1st commit message: begin to implement front end of association-based search # This is the commit message #2: continue fleshing out the front and back end of association-based search # This is the commit message #3: rename some variables to be more accurate and fix a few array-vs-string handlers # This is the commit message #4: remove assistive-text lines # This is the commit message #5: fix issue with taxa suggest # This is the commit message #6: DRY up taxa suggest in a way that is usable for more than one element on the same page # This is the commit message #7: fix bug where reverse relationship was not returning results correctly # This is the commit message #8: begin to flesh out populating readRequestVariables with association-related data # This is the commit message #9: continue making progress with writing setAssociationRequestVariable method # This is the commit message #10: continue working on setAssociationRequestVariable and subfunctions # This is the commit message #11: continue subfunctionalizing # This is the commit message #12: continue fleshing out the associated-taxon query # This is the commit message #13: continue to make progress on the new search-by-association query infrastructure # This is the commit message #14: get search results to display # This is the commit message #15: Get the search criteria to display # This is the commit message #16: Update harvester.php (#1447) Modifies logic to display available boundary tool when no active geographic thesaurus exist in the DB # This is the commit message #17: CSS drop-down menus (#1452) * CSS drop-down menus Add styling to header.css that enables top drop-down menus # This is the commit message #18: Update OmCollections.php (#1455) Errant line of code short circuiting collection meta data update. # This is the commit message #19: closes #1449 which was preventing checklist polyaid from opening (#1458) # This is the commit message #20: Occurrence editor crowdsource adjustments - Add formatting for eventDate2 - Adjust exsicati - Remove from display: additional identifiers, behavior, vitality # This is the commit message #21: occurrence editor crowdsource adjustments - Add vertical-align to crowdsource css to override value set within reset.css - Force refresh of crowdsource.css within client's browsers # This is the commit message #22: crowdsource editor styling issue - resolve vertical-align issue, which persisted when opening in crowdsourcing mode and then switching between long and short forms - Fix fieldset padding issue within image popout # This is the commit message #23: Api media 2024 06 (#1463) - Fix route bug interfering with POST write calls - Add recordID UUID to POST call - Improve error output media object isn't found (400 error) - Improve standardization of all response output - Add sort fields to api documentation - Add function that attempts to determine mime type via file header. Has added benefit of ensuring input file exists. - Update swagger documentation # This is the commit message #24: Media API - Add ability to match images based on recordID UUID within PATCH call # This is the commit message #25: added confirmation windows for project and editor delete icons (#1454) # This is the commit message #26: [3.1] -burpsuite-fix: do not add taxa to query if there are special characters or quotes (#1436) * do not add taxa to query if there are special characters or quotes * cherry pick fix in 6250abd where getTaxonWhereFrag was getting un-cleaned taxon string * respond to code review feedback # This is the commit message #27: Occurrence download bug (#1478) - searchvar term is being sanitized prior to being set as a session variable, which is converting & to &, thus interfering with parsing of all terms after the first term. Translating & to & fixes the issue. - The cleanOutStr function santizes output using htmlspecialchars. The htmlspecialchars on line 638 will double sanitize output, thus converting "east & west" to "east & west". - Variable is getting sanitized within index.php with htmlspecialchars twice. Once on line 12 and again on line 205 Addresses GH issue: #1470 # This is the commit message #28: subfunctionalize the chip button click to the handleRemoval method # This is the commit message #29: only run getAssociatedTaxaSqlFragment when the relevant form field values are present in the query # This is the commit message #30: fix the behavior of the chip removal # This is the commit message #31: persist search terms # This is the commit message #32: fix the non-persisting taxon type selection # This is the commit message #33: remove var_dump # This is the commit message #34: fix bug where association search is not playing well with taxon accordion # This is the commit message #35: get the synonym searching to work # This is the commit message #36: get the sql command for wider taxa to work but not to display successfully on the UI yet # This is the commit message #37: remove spurious TODO and correct issue where usethes-associations and usethes were reversed # This is the commit message #38: Fix bug where synonym choice is not being respected # This is the commit message #39: Fix bug where synonym choice is not being respected # This is the commit message #40: Add all reciprocal relationships to drop down menu and Exclude non-relevant controlled vocabulary from the association dropdown list
Atticus29
added a commit
that referenced
this pull request
Aug 6, 2024
# This is the 1st commit message: begin to implement front end of association-based search # This is the commit message #2: continue fleshing out the front and back end of association-based search # This is the commit message #3: rename some variables to be more accurate and fix a few array-vs-string handlers # This is the commit message #4: remove assistive-text lines # This is the commit message #5: fix issue with taxa suggest # This is the commit message #6: DRY up taxa suggest in a way that is usable for more than one element on the same page # This is the commit message #7: fix bug where reverse relationship was not returning results correctly # This is the commit message #8: begin to flesh out populating readRequestVariables with association-related data # This is the commit message #9: continue making progress with writing setAssociationRequestVariable method # This is the commit message #10: continue working on setAssociationRequestVariable and subfunctions # This is the commit message #11: continue subfunctionalizing # This is the commit message #12: continue fleshing out the associated-taxon query # This is the commit message #13: continue to make progress on the new search-by-association query infrastructure # This is the commit message #14: get search results to display # This is the commit message #15: Get the search criteria to display # This is the commit message #16: Update harvester.php (#1447) Modifies logic to display available boundary tool when no active geographic thesaurus exist in the DB # This is the commit message #17: CSS drop-down menus (#1452) * CSS drop-down menus Add styling to header.css that enables top drop-down menus # This is the commit message #18: Update OmCollections.php (#1455) Errant line of code short circuiting collection meta data update. # This is the commit message #19: closes #1449 which was preventing checklist polyaid from opening (#1458) # This is the commit message #20: Occurrence editor crowdsource adjustments - Add formatting for eventDate2 - Adjust exsicati - Remove from display: additional identifiers, behavior, vitality # This is the commit message #21: occurrence editor crowdsource adjustments - Add vertical-align to crowdsource css to override value set within reset.css - Force refresh of crowdsource.css within client's browsers # This is the commit message #22: crowdsource editor styling issue - resolve vertical-align issue, which persisted when opening in crowdsourcing mode and then switching between long and short forms - Fix fieldset padding issue within image popout # This is the commit message #23: Api media 2024 06 (#1463) - Fix route bug interfering with POST write calls - Add recordID UUID to POST call - Improve error output media object isn't found (400 error) - Improve standardization of all response output - Add sort fields to api documentation - Add function that attempts to determine mime type via file header. Has added benefit of ensuring input file exists. - Update swagger documentation # This is the commit message #24: Media API - Add ability to match images based on recordID UUID within PATCH call # This is the commit message #25: added confirmation windows for project and editor delete icons (#1454) # This is the commit message #26: [3.1] -burpsuite-fix: do not add taxa to query if there are special characters or quotes (#1436) * do not add taxa to query if there are special characters or quotes * cherry pick fix in 6250abd where getTaxonWhereFrag was getting un-cleaned taxon string * respond to code review feedback # This is the commit message #27: Occurrence download bug (#1478) - searchvar term is being sanitized prior to being set as a session variable, which is converting & to &, thus interfering with parsing of all terms after the first term. Translating & to & fixes the issue. - The cleanOutStr function santizes output using htmlspecialchars. The htmlspecialchars on line 638 will double sanitize output, thus converting "east & west" to "east & west". - Variable is getting sanitized within index.php with htmlspecialchars twice. Once on line 12 and again on line 205 Addresses GH issue: #1470 # This is the commit message #28: subfunctionalize the chip button click to the handleRemoval method # This is the commit message #29: only run getAssociatedTaxaSqlFragment when the relevant form field values are present in the query # This is the commit message #30: fix the behavior of the chip removal # This is the commit message #31: persist search terms # This is the commit message #32: fix the non-persisting taxon type selection # This is the commit message #33: remove var_dump # This is the commit message #34: fix bug where association search is not playing well with taxon accordion # This is the commit message #35: get the synonym searching to work # This is the commit message #36: get the sql command for wider taxa to work but not to display successfully on the UI yet # This is the commit message #37: remove spurious TODO and correct issue where usethes-associations and usethes were reversed # This is the commit message #38: Fix bug where synonym choice is not being respected # This is the commit message #39: Fix bug where synonym choice is not being respected # This is the commit message #40: Add all reciprocal relationships to drop down menu and Exclude non-relevant controlled vocabulary from the association dropdown list # This is the commit message #41: Accommodate no particular relationship in the search # This is the commit message #42: Accommodate no particular taxon in the search # This is the commit message #43: remove print statement # This is the commit message #44: add none as an option to the association dropdown and handle its logic # This is the commit message #45: remove cruft from classes/AssociationManager.php # This is the commit message #46: clean up OccurrenceListManager # This is the commit message #47: fix bug where family-based search was not working # This is the commit message #48: make the taxstatus join only happen when family is selected from the dropdown # This is the commit message #49: fix bug where there were duplicates in the relationship dropdown
GregoryPost
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Sep 12, 2024
Merge Symbiota 3.0.10 fixes
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