SCKAN-151 feat: Replace PMID with the sentence/statement ID #143
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ddelpiano
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* #47 refactor: remove use of format_html in admin.py * #47 chore: ran black and isort * #47 chore: remove some code form testing * #47 feat: added some extra filters for sentence admin * #47 feat: added some extra filters for connectivity statement admin * chore: updated serializers openapi generation * #47 chore: create genapi.sh script for generating the frontend * #47 chore: updated openapi + js functions * chore: added missing openapi generator * fix: resized doi to 100 * chore: added doi to sentence list * chore: frontend setup * chore: change the way a user is displayed in forms * Feature/22 (#62) * #frontend set up * #22 add proxy ponting to be server in package.json * #22 feat: implement temporary development redirect on django backend server for testing * #22 feat: log the user profile to the JS console * #22 chore: update package-lock.json * #22 chore: updated .gitignore * #22 chore: some backend updates for frontend authentication * #22 feat: connect frontend to backend login * #22 fix: delete token on update of ORCID user * #22 chore: update Dockerfiles to copy frontend build * #22 refactor: nginx default.conf * #22 chore: remove default staff assignment to new users * #22 refactor: change sentences component to sentencedetails component * #22 chore: logout redirects to orcid logout Co-authored-by: Anto <“[email protected]”> * #54 refactor: renamed *View serializers to *WithDetails * chore: pin basePath to / * chore: pin basePath to / * #19 feat: Add sentence filters (#64) * #19 feat: Add sentence filters * #19 feat: Add connectivity_statement filters * #19 feat: Update and add new filters * #19 feat: Add modified date to model * #19 feat: Add sorting options * refactor: filters to use model and modelmultiplechoice Co-authored-by: Zoran Sinnema <[email protected]> * chore: pin npm packages * fix: backend issue getting the profile when (admin) user has no profile * chore: added /admin to do an ORCID login and redirect to /admin/ * FE-main-components: Main layout, topbar, sidebar (#65) chore: update logo FE-main-comp feat: Add Topbar FE-main-components fix: app main layout FE-main-components feat: add sidebar content and styling Co-authored-by: Anto <“[email protected]”> * SCKAN-32 chore: merged develop + fix merge conflicts (#66) SCKAN-32 feat: implement dynamic rjsf forms based on the django models * chore: enabled route to statement * fix: issues with statement with path not being serialized * refactor: jsonschemas from per serializer endpoint to one rest endpoint * fix: many-to-many update fix * feat: implement&finish rest api for notes and frontend noteform support * chore: small connectivity statement form change: moved modified by down * chore: formatted backend with black * fix: composer admin * SCKAN-40 feat: implement anatomical entities ingestion (#67) * fix: for protected fsm state field updates through the rest api * refactor: remove protected fsmfields from the serializer update * chore: formatted with black * fix: ingestion pmid, pmcid, doi set to None if empty or 0 * chore: added steps for anatomical entities ingestion to readme * refactor: jsonschema generation * feat: implement disabled forms depending on 'owner' of the data * SCKAN-15 feat: implement Sentences List (#68) SCKAN-15 feat: implement Sentences List SCKAN-15 feat: add retrieve paginated sentence list service SCKAN-15 feat: add home page routing subject to user profile SCKAN-15 feat: add MUI DatGrid component at SentenceList SCKAN-15 feat: server-side pagination at SentenceList SCKAN-15 fix: conflicts with develop SCKAN-15 feat: add link to sentence detail on row click SCKAN-15 feat: WIP server-side sorting SCKAN-15 refactor: sorting at sentence list SCKAN-15 refactor: implement useNavigate hook SCKAN-15 feat: add table columns and fix date format SCKAN-15 fix: cursor style to pointer at rows SCKAN-15 feat: add table header and theming SCKAN-15 feat: add filter by status SCKAN-15 feat: add Tag service SCKAN-15 feat: implement filter by tag functionality SCKAN-15 refact: small refact of states checkboxes SCKAN-15 fix: small fix on pagination SCKAN-15 chore: some minor code cleanup --------- Co-authored-by: Anto <“[email protected]”> Co-authored-by: Zoran Sinnema <[email protected]> * Feature/sckan 50 (#69) * #50 feat: WIP - Add autosave hook * #50 feat: WIP - Update queue system * #50 feat: Delete unnecessary hook * #50 feat: Update useAutoSave * #50 feat: Simplify autosave * #50 feat: Block form while saving * #50 feat: Replace debug values with prod * SCKAN-50 chore: Remove deprecated dependency, deprecated schemas and schema utilities * SCKAN-50 chore: some little tweaks on autosaving --------- Co-authored-by: Anto <“[email protected]”> Co-authored-by: Zoran Sinnema <[email protected]> * chore: added () for testing backdrop in FormBase * chore: replaced NLP Sentences by Sentences * feat: implement disable and alert for non owners on sentence and statement * feat: implement take owenership * chore: a bit friendlier confirm message statement and sentence * feat: implement tags separation from sentence and statement * feat: implement Tag form * Removes lodash dependency (#70) SCKAN-50 replace lodash debounce --------- Co-authored-by: Zoran Sinnema <[email protected]> * SCKAN-62 feat: added batch_name and external_ref to sentence (#72) * refactor: removed sentence and statement withdetails serializer * chore: add try catch for ingest NLP sentence due to wrong csv format, skipping sentences with wrong format, e.g. record id 946 * SCKAN-55 refact: implement Redux for sentence states management (#71) resolve conflicts with develop SCKAN-55 feat: install redux and store set up SCKAN-55 feat:add async Redux actions WIP SCKAN-55 refact: move pagination, sorting and filter logic to redux SCKAN-55 refac: move search logic to redux SCKAN-55 fix: minor bug fixes SCKAN-55 chore: add correct type to available state transistions to generate api enums for state choices SCKAN-55 refactor: comp breakdown, leave only query options at redux store SCKAN-55 refactor: tag filter SCKAN-55 refactor: search, sorting, pagination Co-authored-by: Anto <“[email protected]”> * SCKAN-55 chore: update package-lock.json * Feature/sckan 17 (#73) * #SCKAN-17 feat: Fix no results alignment * #SCKAN-17 feat: Fix no results styles * #SCKAN-17 feat: Add autocomplete fetch * #SCKAN-17 feat: Add swap entities * #SCKAN-17 feat: Style duplicates table * #SCKAN-17 feat: Remove MUI warning on swap entities * #SCKAN-17 fix: Fix navigation on row selection * #SCKAN-17 fix: Undo freeSolo fix * SCKAN-17 chore: fix issues after refactor remove withdetails serializer * #SCKAN-17 feat: Clean search on close * #SCKAN-17 feat: Update pmid styles * SCKAN-17 feat: also use AE aliasses for searching duplicates * #SCKAN-17 feat: Update theme * SCKAN-17 refactor: filter CS by AE origin/destination id * #SCKAN-17 chore: Refactor check for duplicates components and update styles * #SCKAN-17 feat: Fix double padding * #SCKAN-17 feat: Align rows and cols * SCKAN-17 chore: added check for duplicates to SentenceDetail page --------- Co-authored-by: Zoran Sinnema <[email protected]> * Feature/sckan 58 (#74) * #SCKAN-58 feat: Add uri to model * #SCKAN-58 feat: Make uri field mandatory * #SCKAN-58 feat: Remove regex validation * #SCKAN-58 chore: Optimize imports * #SCKAN-58 feat: Add uri to serializer * SCKAN-58 refactor: biological sex to be part of the statement serializer and admin and generated new frontend client * SCKAN-58 chore: updating connectivity statement biological sex --------- Co-authored-by: Zoran Sinnema <[email protected]> * SCKAN-15 feat: adjust style at Sentence list page (#75) SCKAN-15 feat: adjust style at sentencelist page SCKAN-15 feat: styling pagination SCKAN-15 feat: add custom pagination to check for duplicates SCKAN-15 feat: sentence cell styling SCKAN-15 feat: style last_edited column SCKAN-15 feat: add styling to notes column at sentence list SCKAN-15 feat: add tag styling at sentence list SCKAN-15 feat: styling states badges SCKAN-15 feat:add state badges at filter drawer SCKAN-15 table headers styling SCKAN-15 fix search input on focus style SCKAN-15 feat: add tag input widget at tag filter SCKAN-15 style checkbox undo file formatting changes SCKAN-15 fix double line effect when scrolling SCKAN-15 chore: remove border-bottom for last row in grid --------- Co-authored-by: Anto <“[email protected]”> Co-authored-by: Zoran Sinnema <[email protected]> * chore: added react types to package.json * refactor: state into sentencestate and statementstate * fix: change the color list of the check for duplicates to statement color list instead of sentence color list * #SCKAN-60 feat: Update title and logo (#76) * #SCKAN-60 feat: Update title and logo * #SCKAN-60 feat: Update logo * chore: changed the icon logo path * chore: logo change for django backend * chore: tweaked k8s config resources and probes * chore: disable SECURE_SSL_REDIRECT * chore: use /admin/login/ for the probes * chore: update README * chore: some performance optimalisations * SCKAN-18 feat: Implement Statement List (#77) * SCKAN-18 feat: implement statement list SCKAN-18 feat: add statement list routing for user with triage op and curator profile SCKAN-18 chore: create Pages directory SCKAN-18 feat: add statement reducer at redux store SCKAN-18 add getList at Statement Service SCKAN-18 refactor: split datagrid from sentenceList SCKAN-18 refactor: use EntityDataGrid component at the SentenceList SCKAN-18 refactor: split datagrid filters from sentencelist SCKAN-18 feat: create statement list page with working datagrid SCKAN-18 fix: state chip color subject to entity SCKAN-18 feat: add subtitle and adjust caption on Statement list header SCKAN-18 fix: searchbar input value and comment out the num of statements to be curated SCKAN-18 feat: add initial compose_now filter on statement list SCKAN-18 feat: add initial filter by compose_now for curators * SCKAN-18 feat: hide draft connectivity statements from statement list --------- Co-authored-by: Anto <“[email protected]”> Co-authored-by: Zoran Sinnema <[email protected]> * feat: added default filter for reviewer * Sckan 59: refactor NLP ingestion get title (#78) * refactor: NLP ingestion now uses the internet for title look up * chore: added missing crossref-commons * chore: README update pip to pip3 * chore: make ingest NLP a bit more robust * chore: updated the dashboard message for users without any role * refactor: for sentencelist show sentence text instead of the title * fix: typo in runserver.sh when in dev mode * SCKAN-66 feat: add journey compilation (#79) * chore: updated the frontend open apiclient * Feature/sckan 68 (#80) * SCKAN-68 feat: WIP - Update species and tags views and serializers * SCKAN-68 feature: set specie to readonly=False on CS serializer to allow specie subform * SCKAN-68 chore: update frontend api client * SCKAN-68 chore: remove specie mixin from sentence * SCKAN-68 chore: implement specieservice for retrieving all species * SCKAN-68 feat: WIP - Update doi serializers * SCKAN-68 feat: Rollback dois read_only * SCKAN-68 feat: Regenerate frontend api --------- Co-authored-by: Zoran Sinnema <[email protected]> * Feature/sckan 69 (#81) * SCKAN-69 feat: Add doi schema and mixin * SCKAN-69 feat: Update frontend api * SCKAN-69 feat: Update frontend schema model * SCKAN-63: Add sentence form (#82) * SCKAN-63 feat: Add sentence dialog * SCKAN-63 feat: add DOI field to add sentence form * SCKAN-63 refactor: move post or put logic to service * SCKAN-63 feat: navigate to sentence details after sucessful submission * SCKAN-63 refactor: add optional form validation prop at FormBase * SCKAN-63-b feat: added doi to formvalidation --------- Co-authored-by: Anto <“[email protected]”> Co-authored-by: Zoran Sinnema <[email protected]> * SCKAN-71 feat: use ORCID also for the Django Admin * SCKAN-71 feat: test on superuser exclude the admin user * SCKAN-16 triage operator sentence details page (#84) * SCKAN-16 add textField, textArea, buttonGroup widgets * add on change function for all the custom components * SCKAN-16 chore: set CS origin and destination id optional * SCKAN-16 chore: loop over sentence connectivity statements to create all forms * merge develop * SCKAN-16 chore: fix issue with anonymous user * chore: Fix frontend proxy * remove KnowledgeStatementsForm.tsx * add custom widget for chips input + add dois form and service * add dois form functionality * add NPL sentece form * add sentece form * add sentece form * fix: Remove species read only attributes * feat: Update add doi endpoint to add multiple dois * add notes form * add notes form style * chore: Regenerate client api * feat: Add biological sex GET endpoint * add species form * add species form * add knowledge statemnt form * feat: Add species name filter * chore: Update frontend api * update knowledge statement * fix: Rollback serializer changes * update/submit conectivity statement * update form style * SCKAN-16 chore: fix doi * SCKAN-16 chore: specie set ontology_uri to optional * add remove statement functionality * SCKAN-16 fix: deletion of draft ConnectivityStatements * SCKAN-16 chore: some base fixes for doi * move pages folder to src * SCKAN-16 feat: implement refresh sentence after statement or doi change * SCKAN-16 feat: implement del of doi * SCKAN-16 refactor: only update the statement when adding dois * SCKAN-16 revert: update sentence on doi insert/delete * SCKAN-16 fix: rerender dois * Merge branch 'SCKAN-16-Triage-Operator-sentence-details-page' of https://github.com/MetaCell/sckan-composer into SCKAN-16-Triage-Operator-sentence-details-page # Conflicts: # frontend/src/Pages/SentenceDetails.tsx * SCKAN-16 fix: set the defaults for the form on useEffect * Merge branch 'SCKAN-16-Triage-Operator-sentence-details-page' of https://github.com/MetaCell/sckan-composer into SCKAN-16-Triage-Operator-sentence-details-page # Conflicts: # frontend/src/Pages/SentenceDetails.tsx * refactor notes form component * update delete button for statement * add species select * SCKAN-16 refactored the create new statement + aded required setting to customtextarea * SCKAN-16 fix: add value to custom text input so the current value will be shown * SCKAN-16 chore: merged species feature * SKCAN-16 chore: reverted change of Dockerfile * SCKAN-16 refac: separate component for statement section within sentence details page * SCKAN-16 feat: enable save of draft statements from the frontend * SCKAN-16 fix: issue of sentence being set to statement in sentencedetail form * SCKAN-16 fix: clear chip input after submission * SCKAN-16 feat: set species field as chip input * SCKAN-16 feat: add autocomplete widget for species * SCKAN-16 fix label styling and spacing * SCKAN-16 feat: change autocomplete options based on selection * SCKAN-16 feat: fix clear notes * SCKAN-16 temporal fix: do not create statement until the user types the knowledge statement field * SCKAN-16 fix: autocompletewithchips in case no more options are available * SCKAN-16 refactor: ansdivisions, species and biologicalsexes list retrieval * SCKAN-16 feat: add pmcid and doi deeplinks of sentence * SCKAN-16 fix: ordering of notes --------- Co-authored-by: Salam Dalloul <[email protected]> Co-authored-by: Zoran Sinnema <[email protected]> Co-authored-by: afonso <[email protected]> Co-authored-by: Anto <“[email protected]”> * feat: sentencedetails set to be reviewed when available as first action * feat: sentencedetails set to be reviewed when available as first action, if not then use the first in the list of available transitions * SCKAN-76 fix: sort connectivity statements array by id to display them in the correct order (#85) Co-authored-by: Anto <“[email protected]”> * SCKAN-96 feat: implement path chart and journey text (#87) Co-authored-by: Anto <“[email protected]”> * chore: updated package-lock.json * Sckan 92 (#88) * view notes/tags form + statement header * SCKAN-92 fix: notes linking to statements --------- Co-authored-by: Salam Dalloul <[email protected]> Co-authored-by: Zoran Sinnema <[email protected]> * SCKAN-77 fix submit form on autosave to work in Firefox and Safari (#86) * SCKAN-77 fix: prevent referesh onsubmit in Firefox * SCKAN-77 fix: replace programatically submit not supported by Firefox and Safari * SCKAN-77 refactor: submit button at form base receiving props --------- Co-authored-by: Anto <“[email protected]”> * Sckan 99 (#89) * view statement details header + transitions button list * SCKAN-99 fix transition --------- Co-authored-by: Salam Dalloul <[email protected]> * chore: add condition for statement transition to be reviewed state * chore: fix typo in statement spieces * chore: moved statement condition to be reviewed from compsoe now to curated * chore: statement move check to be reviewed to curated state * chore: added doi uri to the rest api and the rest client * Sckan 93 (#92) * view statement details header + transitions button list * SCKAN-95 view statement details * SCKAN-95 fix style of statement details * SCKAN-95 view/update statement details section * SCKAN-93 view related NLP statements * SCKAN-93 view related NLP statements --------- Co-authored-by: Salam Dalloul <[email protected]> * fix: issue with current statement shown in the other statement list * feat: disable sentence form on statement details * Feature/sckan 57 (#91) * SCKAN-57 feat: WIP - Add export csv * SCKAN-57 feat: Refactor export service * SCKAN-57 feat: Use type display name; Add review notes * SCKAN-57 feat: Add has nerve branches column * SCKAN-57 chore: Add todos * SCKAN-57 chore: Lint and refactor based on PR feedback * SCKAN-57 fix: Fix export error on non existent folder * SCKAN-57 feat: Generalize different note type * SCKAN-57 feat: Refactor out export from command to service * SCKAN-57 feat: Add temporary mappings for unclear rows * SCKAN-57 chore: Apply linting * SCKAN-57 feat: Update export_connectivity_statements definition * SCKAN-97: implement KS at proofing tab (#93) * SCKAN-97: implement KS at proofing tab * chore: fix sall bug with put on CS * chore: removed to lower on journey --------- Co-authored-by: Anto <“[email protected]”> Co-authored-by: Zoran Sinnema <[email protected]> * fix: crash after adding tag to CS * SCKAN-88 feat: implement transitions from NPO APPROVAL & EXPORTED back to COMPOSE NOW (only for staff users) (#94) * SCKAN-82 feat: implement exported state for statement and update statement after it's been exported * SCKAN-83 feat: implement export+download statements action in admin * chore: updated rest api client + fixed issues with id being null * SCKAN-75 increase the contrast of borders + view placeholder for selects components + fix style for input base placeholders (#97) Co-authored-by: Salam Dalloul <[email protected]> * Feature/sckan 57 continuation (#98) * SCKAN-57 feat: Update destination type options * SCKAN-57 chore: Fix problematic migration * SCKAN-57 feat: Updates destination type change migrations * Feature/sckan 80 (#99) * SCKAN-80 feat: implement export batch + fix some small issues with exporting of newlines * SCKAN-80 chore: removed obsolete code * SCKAN-80 refactor: admin login url config, resolving warning urls.W003 in composer urls * SCKAN-104 feat: implement logging of transitions of sentences and connectivity statements as notes * SCKAN-80 feat: implement gexport batch graph * chore: fixed composer order of migrations * chore: fixed fix2 composer order of migrations * chore: fixed fix3 composer order of migrations * chore: fixed fix4 composer order of migrations * chore: add composer to nginx proxy to django backend * SCKAN-111 fix issue of frontend missing transitions (#100) * SCKAN-111 fix issue of frontend missing transitions * SCKAN-111 chore: remove exportmetrics from admin and fix issue with state having _ in the export metrix graphs * sckan-108 added sample test and jest/puppeteer installations * sckan-108 initial setup of the pipeline * sckan-108 fixed dockerfile.testing * sckan-108 remove work_dir * sckan-108 change base build * SCKAN-112 chore: squashed all composer migrations (#101) * chore: added filter for has_notes check to ignore system generated notes (like transitions) * SCKAN-98 feat: implement Paths builder (#102) * SCKAN-98 feat: Implement Path Builder SCKAN-98 add Path Builder container to Proofing tab SCKAN-98 feat: add origin and destination fields at path builder SCKAN-98 feat: make inline fields at parth builder destination row SCKAN-98 fix destination spacing and order SCKAN-98 feat: implement sortable table component SCKAN-98 fix spacing at paths builder rows SCKAN-98 improve path builder styling SCKAN-98 add via form WIP chore: add via type field to serializer chore: add type to via serializer SCKAN-98 fix select spacing SCKAN-98 change via serializer and display path field within statement form SCKAN-98 add via items in path builder SCKAN-98 refactor: reuse component for destination, origin and via fields SCKAN-98 fix path builder styling SCKAN-98 minor fixes SCKAN-98 implement row sorting at vias table WIP SCKAN-98 implement via rows sorting SCKAN-98 add disabled prop down the tree at statement details page SCKAN-98 disable proofing tab if there is no origin and destination SCKAN-98: remove error list on the top of the form SCKAN-98 adapt path builder to new design SCKAN-98 styling fixes SCKAN-98 refactor: prevent api calls before the data is loaded SCKAN-98 fix migration and other minors fixes SCKAN-98 fix responsive values * SCKAN-98 remove unused ViaForm * SCKAN-98 rename migration --------- Co-authored-by: Anto <“[email protected]”> * chore: updated package-lock.json * fix: change name prop by label at AnatomicalEntitiesField (#104) Co-authored-by: Anto <“[email protected]”> * linking the two together * tests change * added page.title fopr debugging * timeout * fix bug at species and path fields (#105) Co-authored-by: Anto <“[email protected]”> * SCKAN-89 implement changes at Distillation view (#103) * SCKAN-89 implement changes at Distillation view SCKAN-89 chore: change ANSDiv, Sex model name, enums of Laterality and add Projection enum field SCKAN-89 add projection field and rename BioSex and ANSDivision to Sex and Phenotype SCKAN-89 resolve conflicts with develop SCKAN-89 minor fixes * SCKAN-89 added update of laterality and projection * minor fix on migration --------- Co-authored-by: Anto <“[email protected]”> Co-authored-by: Zoran Sinnema <[email protected]> * chore: regenerate api * chore: split migrations * chore: fix migrations * SCKAN-114 (#106) * SCKAN-114 allow null on origin and destination and add border on Dois and KS fields * fix notes background --------- Co-authored-by: Anto <“[email protected]”> * SCKAN-117 feat: rework CS Dois to CS Provenances (#107) * SCKAN-117 feat: rework CS Dois to CS Provenances * SCKAN-117 feat: add protocol to Provenance uri when not submitted * fix paramenters order passed to provenance delete service --------- Co-authored-by: Anto <“[email protected]”> * added page title and url for debugging * SCKAN-119 add additional information field at statement form (#108) * SCKAN-119 add additional information field at statement form * SCKAN-119 feat: added additional info to the destillationtab --------- Co-authored-by: Anto <“[email protected]”> Co-authored-by: Zoran Sinnema <[email protected]> * added page title and url for debugging * changed selector * changed selector * changed selector * changed selector * changed selector * changed selector * puppeteer image + waitUntil * changed puppeteer version * added await * fix: crash during export due to renaming DOI to Provenance * Feature/sckan 116: add an export CS identifier (#109) * SCKAN-116 feat: implement export CS numbering --------- Co-authored-by: Anto <“[email protected]”> * chore: removed media from nginx mapping * chore: removed media from nginx mapping * SCKAN-79 fix: searchbar placeholder (#111) Co-authored-by: Anto <“[email protected]”> * SCKAN-105 feat: enable ks and provenance field at distillation and pr… (#110) * SCKAN-105 feat: enable ks and provenance field at distillation and proofing tab SCKAN-105 improve Provenance field style SCKAN-105 improve KS field style SCKAN-105 feat: enable ks and provenance field at distillation and proofing tab SCKAN-105 open external link if provenance is a valid url * fix: debounced onChange on controlled textarea --------- Co-authored-by: Anto <“[email protected]”> * SCKAN-90 fix sentence search to filter by title and text (#112) Co-authored-by: Anto <“[email protected]”> * SCKAN-118 feat: add important tag to CS when transition from NPO approved or Exported to Compose now (#113) * refactor: important tag refactor * admin workspace button to redirect to admin interface * SCKAN-107 add tooltip on sentence hover at list page * minor changes to text * SCKAN-86 add api endpoint to clonate a statement * SCKAN-86 add clone button at FE and connect to BE * SCKAN-86 replicate Provenance and Vias at the cloned statement * SCKAN-86 null proofing tab data on statement cloning * SCKAN-86 disable delete and cloning KS button for sentences at compose_now * SKCAN-85 feat: implement changes to the autosave SCKAN-85 disable autosave and add save onChange for dropdowns SCKAN-85 feat: disable autosave and add saving onblur and onchange SCKAN-85 implement autosave every 2 min for text fields- * SCKAN-78 add requirements to can_be_compose sentence state service * Fix: disable state button when there is no transitions available * undo change at package json * SCKAN-112 feat: Adds uri to phenotype model * SCKAN-112 feat: Adds data migration to add default phenotypes * SCKAN-112 feat: Use same timezone as db to exported filename * feature/sckan-108 All test steps finished * sckan-108 changed selectors and fixed import * sckan-108 removing the test steps from codefresh yaml * sckan-108 resolving conflicts * sckan-108 removed unecessary file * replace setInterval by setTimeout * fix ks cloning to also clone species * fixing package-lock out of sync * SCKAN-123 add tooltip on KS column at statement list page * SCKAN-124 fix: remove draft state from statement filter options * SCKN-126 change phenotype on_delete to SET_NULL at statement model * changes to the pipeline * fixing build * SCKAN-112 fix: Update data migration script to create or update * SCKAN-126 add migration file from previuos phenotype field change (#129) Co-authored-by: Anto <“[email protected]”> * feature/SCKAN-128 implement statement ingestion command (#130) * feature/SCKAN-128 implement statement ingestion command SCKAN-127 neurons ingestion WIP SCKAN-128 check if entities already exist in composer db SCKAN-128 create artifact sentence for each of the statements to be ingested SCKAN-128 clean unused function SCKAN-128 fix function name SCKAN-128 add reference_uri field SCKAN-128 fix create reference_uri if not provided SCKAN-128 add functiona circuit and projection phenotype fields SCKAN-128 directory structure and create sentence changes SCKAN-128 add alert note type and prepare data for ingestion WIP SCKAN-128 validate and create statements SCKAN-128 add many to many fields to new statements SCKAN-128 add sex and spec validation and warning for skipped phenotypes SCKAN-128 add direct sentence transition from OPEN to COMPOSE_NOW if user is system SCKAN-128 fix multiple provenances and add TODOs * SCKAN-128 update anatomical_entities resources and create provenance if not provided * SCKAN-128 refactor: replace circuit type mapping function with a constant * SCKAN-128 add statement transition to exported * SCKAN-128 fix do_state_transition --------- Co-authored-by: Anto <“[email protected]”> * fix: ingestion speed of anatomical entities * chore: replaced function index+unique key on AE with a new Unique Functional constraint * fix: limit the max number of characters for sentence title * fix: missing neurodm dependency * SCKAN-130 fix: ingest AE synonyms * SCKAN-129 untangle relationship-predicate at export (#132) Co-authored-by: Anto <“[email protected]”> * SCKAN-129-b add column predicate to export file (#133) Co-authored-by: Anto <“[email protected]”> * chore: ingest nlp sentence changed to , as field separator (instead of ;) * Fix export: skip projection and fcr phenotype rows if none (#134) Co-authored-by: Anto <“[email protected]”> * SCKAN-137 change details layout at statement details page (#135) SCKAN-137 replace details section for accordion at statement details page SCKAN-137 add other ks section at the bottom of statement details page SCKAN-137 only show other ks section if any SCKAN-137 move NLP sentence to the bottom of statement details page Co-authored-by: Anto <“[email protected]”> * SCKAN-145 feat: Allow check for duplicates with just one AnatomicalEntity set (#137) * SCKAN-144 feat: Update Anatomical Entity search (#136) * SCKAN-144 feat: Update Anatomical Entity search * SCKAN-145 fix: Make filter_name on anatomical entity robust * chore(): disable TZ * feat(): add ingestion of comments * feat: comment ingestion if user not found add the comment sender to the comment text between [] * chore(ingest comment): if the user is not (yet) in the system add the sender to the note text * feat(ingest nlp): add check if comments file exists * Feature/sckan 153 (#144) * SCKAN-153 feat: Add closeIcon to search bar * SCKAN-153 feat: Add closeIcon to autocomplete with chips * SCKAN-151 feat: Replace PMID with the sentence/statement ID (#143) * SCKAN-148 feat: Add move forward feature on triage step (#142) Co-authored-by: Zoran Sinnema <[email protected]> * Feature/sckan 146 (#141) * SCKAN-146 feat: Add statement preview computed value * SCKAN-146 feat: Add statement preview ui component * SCKAN-146 feat: Update statement preview ui component * SCKAN-146 feat: Update statement preview creation * fix broken build * Feature/sckan 148 enhancement (#157) * SCKAN-148 feat: Update next sentence calculation and add UI feedback * SCKAN-148 fix: Fix premature leaving of loading state * SCKAN-148 chore: Rollback unintentional code style changes * SCKAN-148 chore: Fix typo * SCKAN-148 chore: Fix indentation * SCKAN-148 fix: Stop infinite loading on errors * SCKAN-148 feat: Update no rows message on data grid * feat(ingest sentence): add merging of sentences during ingestion (#160) * feat(ingest sentence): add merging of sentences during ingestion * feat(ingestion): nlp sentence merge also use batch name * Feature/sckan 167 (#159) * SCKAN-167 feat: Add forward connection to connectivity model * SCKAN-167 feat: Add missing migration * SCKAN-167 feat: Add exclude sentence filter * SCKAN-167 fix: Fix typo * SCKAN-167 feat: Replace use of not to exclude by using negative integers * add forward connection component * connect submitting the form * add options preview * add select/deselect all functionality * SCKAN-167 feat: Connect forward connection autocomplete with backend * SCKAN-167 feat: Add forward connections to export * SCKAN-167 feat: Fix statement on save issue with forward connection * SCKAN-167 feat: Use autocomplete max fetched entries setting * SCKAN-167 feat: Move forward connection signal to state transition conditions * SCKAN-167 feat: Add errors list to connectivity statement serializer * SCKAN-167 feat: Add explicit exclude sentence filter * add no options found style * SCKAN-167 fix: Remove nested forward_connection serialization * SCKAN-167 fix: Use entityType variable instead of hardcoded value * handle error * handle error * remove unnecessary files * chore(): simplified statement update view * chore(): fixed indent * feat: updated export to support forward connections --------- Co-authored-by: Afonso Pinto <[email protected]> Co-authored-by: Zoran Sinnema <[email protected]> * fix(): ingest nlp sentences fix + fix for linking comments of sentences that are merged * fixed layout messed up on chip label, fixed hover to visit metadata on the right side * typo fixed * fixed layout messed up on chip label, fixed hover to visit metadata o… (#161) * fixed layout messed up on chip label, fixed hover to visit metadata on the right side * typo fixed * fixing wrapping of new line * fix(): issue connectivity statement api crashing because of missing request * Fixing typos (#164) --------- Co-authored-by: Dario <[email protected]> Co-authored-by: Anto <“[email protected]”> Co-authored-by: Afonso Pinto <[email protected]> Co-authored-by: Antonella Rapuano <[email protected]> Co-authored-by: Salam Dalloul <[email protected]> Co-authored-by: Salam Dalloul <[email protected]> Co-authored-by: Simão sá <[email protected]> Co-authored-by: ddelpiano <[email protected]>
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closes https://metacell.atlassian.net/browse/SCKAN-151
2023-09-06.14-46-46.mp4