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chore: Bump tar from 6.1.11 to 6.2.1 #95
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update package using chem-spectra-client version 0.10.11 update version of chem-spectra-client
In short: - data submission feature added to user ELN page - Review page for internal reviewing - Public page to browse published sample/reaction data Contributors: Chia-Lin Lin Pei-Chi Huang Pierre Tremouilhac
* add xvial and type check * readonly for nmr * trim data from orcid * refresh embargo list * add a button to redirect from db view to publication view * export-sample-with-https-doi * add loading module on publication search * collection label error * download analysis of publication without sign in * view sprectra of products * orig. is not required * export embargo collections * search embargo bundle number * display name on review page * embargo in reaction list * search by authors or contributors * sanitize_sql * allow users to edit spectra's content update package using chem-spectra-client version 0.10.11 update version of chem-spectra-client * deploy config mod * add xvial symlink * minor upd Gem.lock db/schema * add default profile * FE fix after rebase * update style back to original setting * use 'mass spectrometry' and 'IR' * publication embargo search * make regenerate button for all unoriginal jdx files * regenerate for reviewer only * check and fix * smiles to SMILES * add permission on repository_api reaction and sample * add validation * fix migration file for solvent * review reaction scheme * fix duplicate function name from ELN rebase; publish reaction * reaction list style * focus on style of review page * publication molecule layout * add publish date to new layouts * change style to solve overlap issue * directing to the sample of publication change wording 'xxx DOI' instead of 'DOI' * fix e.split on review page issue * fix e.split on review page issue * review submitter list issue * publication author and the link * 1. unify the terminology: use Reference(s) 2. define citation type 3. publish references * move js file to packs * bundler * migration file * rm chemscanner * chemscanner * submission validation and collection * reference desc * rm dup. decoupled * ref * spectra 0.10.14-beta.0 * Collection DOI * display the latest image * Collection DOI * Resolve "upgrade datacite schema" * nmrshiftdb solvent * add 'copy to clipboard' on collection doi * assign to embargo * Resolve "publish when segment exist" * att permission for seg * default segment of reaction, segment for publication * oai metadata * submission date * option to skip yield validation * how-to link and quill-viewer styling * 1. add a button to copy collection DOI 2. add a checkbox confirmation to ensure that people that add data without an embargo know that the data is published as soon as review is completed * reviewer-permission-with-embargo-accepted * metadata * remove regex of orcid in frontend get result from API directly * link to publications by clicking on the statics * review comment * the focus is on the selected record in the list when redirecting from a DOI * switch tab after searching by inchi * review comment r * added molecule archive * add xvial filter * add xdata to the list * count of compound * publication element index * import collection * embargo author * rename terms of service to directive * landing page updates: 1. the word 'published' next to the analyses (right side) should be given in black. 2. add a published link to the samples (left side) 3. in reaction table - space in header between name and unit - unit in squared brackets - ml should be mL - switch from g to mg as unit - bring yield in the sub header of the table * new content of project description of about * update copyright statement * linting * fix hyperlink as string issue * fix dataset doi cannot be resolved issue * add embargo link on review and copy function * fix the bug for hyperlink export * fix routing * fix collection routing and info modal * fix based on feedback * workaround for react-svg-file-zoom-pan-latest library issue * chem converter * fixed: redirect to the latest published element successfully, but no details shown * review comment fix * hide info when inchikey is dummy * embargo btns * hr to h * Update Navigation.js * converter for user * converter config file * embargo email issue * upgrade chemspectra * fix duplicated img * Resolve "porting the 3d viewer" * Revert "Merge branch '520-upgrade-chemspectra' into 'server_chemotion_net-5'" This reverts merge request !471 * upgrade chemspectra * fix duplicated img * embargo job fix * disable 3d molecule * publication page issue * fix file ext issue * resourceTypeGeneral sample * add example text on request form * increase font size * ketcher backend * add nmrium aasm_state so that files with this state from ELN v1.5 can be transferred (avoid `ActiveRecord::RecordInvalid (Validation failed: Aasm state is invalid)` on attachment save `app/api/chemotion/gate_api.rb:167` ) at this stage no event seems to be needed * metadata description of sample publication * sample representation on landing page * shibboleth and group leader review * Resolve "sync spectra" * review notification * Resolve "molecular mass descriptor in sample metadata" * group default value * fix White Screen when clicking on Analysis DOI * fix white page while doi is null * fix the incorrect license icon usage * user reivew and svg fix * group lead review update * increase font size and add space * add comp-number to published sample page * Resolve "review ui reload issue" * Resolve "compounds visibility" * anchor on publication page * add solvent to sample metadata * published year * linked-data * add original id to compound list * linked data api * Extending chemotion_ELN with Repository functions In short: - data submission feature added to user ELN page - Review page for internal reviewing - Public page to browse published sample/reaction data Contributors: Chia-Lin Lin Pei-Chi Huang Pierre Tremouilhac --------- Co-authored-by: Chia-Lin Lin <[email protected]> Co-authored-by: Pei-Chi Huang <[email protected]> Co-authored-by: Lan Le <[email protected]> Co-authored-by: PiTrem <[email protected]>
remove download zip button fix font size analys content description add bottom nav bar revamp top navbar pubchem tag in public molecule list enable search for unsigned user public search suggestionapi set var if no current user for public coll BE: search_api: serialized result for public molecule FE: public store receive search result too disable groups UI fix Nav header in ELN view navbar: remove search/element actions for non sample/react elements change routing revamp style for publication list/element change routing to publication/molecules/:id refact href to onClick change route root to pages (nginx dual site) welcome routing enable user devise confirmable FE publish sample: fix missing argument public api inchikey add params validation default analysis version to 1 if no version while comparing with params version fix sample publication -- reintroduce analyses selection for publication (broken thru dnd analyses reordering) -- fix coauthor id (broken thru reactselect upg) change default check analysis selection for sample publish publish analyses default checked using null and true instaed of boolean becasue the extended_metadata value is coerced into string fix attachment copy fix publish doi/pubchem fix sample dataset versioning for doi token loop throug sample publication tag for authors and affiliations implement new datacite schema revamp publication concern upg upd pubchem tag thru sample dedicated publication logger allow collection array arg in CollectionSample.create_in_collection Sample publication Datacite/Pubchem split process into distinct DJs fix search suggestion on publications page when logged WIP revamp PublishSampleModal WIP f job move to final collection f reverse kind analysis options wip publication tag +revamp welcome page upd last sample view with new publiation tag struct disabled checkbx analysis selection if already published tag analysis as published in extended_metadata column fix route for analysis kind having white space f pick 818eff6 REPO FACTOR s 760b833 remove download zip button fix font size analys content description add bottom nav bar revamp top navbar s 7db9740 pubchem tag in public molecule list s 40059a3 enable search for unsigned user s 08c12d2 disable groups UI s 4e939a9 change routing s e244e47 enable user devise confirmable s 2fc9ee6 FE publish sample: fix missing argument s 64f8cdd fix attachment copy s d48bf69 fix publish doi/pubchem fix sample dataset versioning for doi token loop throug sample publication tag for authors and affiliations s c1bd3b7 upg upd pubchem tag thru sample s 0cf8dd8 dedicated publication logger s 2fab086 allow collection array arg in CollectionSample.create_in_collection s 74f8d4d Sample publication Datacite/Pubchem split process into distinct DJs s 7f97cc9 fix search suggestion on publications page when logged s aaec7c1 WIP revamp PublishSampleModal s 6389a27 WIP s c76de3b f job move to final collection s d245e57 f s 403cee5 reverse kind analysis options s 4498f05 wip publication tag +revamp s 0ca4452 welcome page upd last sample view with new publiation tag struct s b725bec disabled checkbx analysis selection if already published s b02fdf1 tag analysis as published in extended_metadata column s c009c22 fix route for analysis kind having white space s 7b12b5c f hide collection management button hide shared & sync collection selection trees fix private method container publication add molecule name to public sample detail view sort molecules in public collection add publishedTag to samples in user sample lists add doi link to publication tags of published elements in ELN view hide create new collection in moving/assigning elements modal User Collections fixes hide user own collections do no create a locked 'chemotion.net' collection for new user but instead 'ELN Gate' and 'My Data' mv chemotion label to publish common tag published molecule with doi too chemotiontag revamp change ELN navbar color to gradient up collection tree nav bar font white register repo token into eln for gate data transfer remove gradient nav bar btn-unified class sample export xls: exp chemotion doi tag if present fix origanization input: disabled to readonly fix missing sync collection for new user persons correct updating chemotion molecule tag publication detail restyle xls export analyses doi fix analysis publish checkbox: reload sample after publish fix checkbox toggle log analyses selection to publish log WIP disable publish api https doi metadata upg sync_coll entity for public collections upd Terms n Conditions categorize literatures for pulbicl collection elements persons can add references to public elements through literature managmt panel as for their own elements ref are categorized as 'public' list public literature in element detail view f display cited literature wiht referer in public publication list fix lit flux api add doi table/model fix checkbox add analyses to publish do not backup uploads doi reservation : fix doi model routine fix displaying published molecule associated to published samples missing their publication tag fix bug from attachment polymorphism upgrade publish UI add accordeon rework doi model, publication concern mv publish button to publishCommon, disable btn when already published serialize user affiliation unassociate analyses doi if inchikey changed popover information for doi reservation upd doi seeding DJ params fix fatal: hash keys cannot be integer: stringify analyses id log DC metadata xml to upload as separate files in log/ WIP fix pannel after bootstrap upg fix pagination after bootstrap upg fix ci root page link to chemscanner publish reaction UI completed backend code complete, but still need testing (especially doi part) add published button on reaction list and header re-add LabelPublication on header fix the username display issue public reaction backend db/schema f fix do not expect new reaction to have tag data move publish sample/reaction out of sample/reactionAPI to dedicated repo api fix anonymous search reactionPublishBtn upg publishBtn: workaround with overlaytrigger on disabled Btns publish reaction btn on publishable reactions mount repositoryAPI clean repoAPI do not uses sample.analyses but sample.container publish analysis: fix checkbox toggle bootstrap fix table props repo publishmodal fx panel-group assistech prop warning reaction publish btn: disabling/tooltip message upg reactionPubModal fx warning iter key green header for public detail panel & welcome page upg: - in ELN view, elemt detail panel has green header instead of blue if elemt is public - rm directive content iframe, use component instead -> NB this duplicate the info - footer upg - rm footer from publications page - rm osadl partner card - change institute link to brase group - change banner color/font repository search hide reaction publishbtn disable reaction publication api add chemotion logo on welcome page fix sample doi fetcher analyses filter mv publish actions/fetchers to dedicated classes repo api mv helper repo_api upg repo api fix clean deprec residual react.proptype f search api fx to work on public page when logged in repo api wip FE fix iterator uniq key repo_api wip WIP publish sample JOB upd WIP_pubreact_DRY DRY FE repository fetchers reaction inchi routines for product only rinchi publish reaction: duplicate reaction BE logic reaction publish tag DJ reactionpublish repo api fix deletejob f_job f_job f_dj_publish f_DJ show publish reaction btn fix replacmt ElementActions by RepositoryActions reaction svg composer pass options disable green chemistry tab DJ publish fx sync public collection for new user: allow reaction details f fix dois generation when count > 10 update molecule tag: only for sample not reaction fix xml metadata reaction DJ publish reaction fix hisde pub reaction btn for public reaction repo_api reaction fix publish reaction prepare prod public reaction detail panel green header doi redirect simplified routing redirect from reaction dois ELN: error when att.copy => rm include attachment concern assm/JCAMP WIP reaction list view add Formula Reactant and starting material should not in publications Add conditions to filter out the sample which is as starting material/reactant in reaction. If a sample is published as 'Sample', it will be shown on the publication list. If a reaction is published, the 'Product'(sample) will also be published and shown on the publication list. The 'starting material' and 'reactant' will not be shown on the list. BE/FE fetch reaction list f Affiliation output: rm group from affiliation publications table: add original element WIP revamp job chain toggle for sample and reaction search reaction page Publication: added ancestry fix search_by_method and remove wellplat and screen codes Create Publication entries w ancestry for each element - rev duplicate anaylses container revamp xml metadata files WIP new publishing process job Publishing job pseudo state machine for Publication model added transition in Publication model todo: clean element tagging, doibag, xml metadata fix WIP FE check taggable_data of publication repo_api fx add 'reaction/' to reaction doi suffix remove html formatting from doi metadata search fx publishing pubchem registr routes fixes doi link deploy config fix routes doi url redirect reaction fix sample publish the latest publish sample on landing page set publish switch button size and position Publication Rinchi fixed reaction detail 10 reaction additional info backend Additional information on publication reaction Add: 1. Expand/Collapse RInChiKey information 2. Status, Start, Stop, Duration, Temperature, Additional information for publication and purification details 3. TLC-Control information Publications analyses re-layout Relayout the Sample and Reaction on publications. The details are as below: - Reaction 1. Remove title (Short Label/Name) from Reaction - Sample 1. Remove Reaction data from Sample - Sample and Reaction 1. Rename 'Datasets' as 'Analyses' 2. Expand/Collapse analyses at one click 3. Remove the outer(the first layer) border - Datasets 1. Expand/Collapse analyses at one click remove RenderAnalysis published reaction literature display provided a reaction link on sample detail for publication Analyses types in one line User can expand/collapse analyses list by clicking analyses list header. The types are listed together on the header and separate with ','. Also put the symbol in front of the type(s) to indicate its Sample or Reaction. Analyses preview function When user click on the preview image of analyses, display the original image for user. This function is available only when user sign in already. If user click the preivew but he/she does not sign in, a system notification shows up in the top center to remind him/her 'Please sign in first'. Additional updates on: 1. Only import the one which is used from 'lodash', not import all from 'lodash' 2. Remove unused imports 3. Add semicolon Analyses format Align UI elements. Add some styles to make analyses more readable. When user double click Content, more space is added and looks like it is expanded. Fix by removing the theme setting on render. Reaction in the centre and remove start stop Remove 'float: left' to set reaction image in the centre of reaction list. Remove 'Start' and 'Stop' information. Use Div instead of FormControl to make the TLC-Description looks not like an input column. Rename some panel id, e.g. use 'collapsible-panel-rinchis' instead of 'collapsible-panel-example-1'. Console warning about unique key and inline Add 'key' pop and inline='true' to fix below warnings: 1. Warning: Received 'true' for a non-boolean attribute 'inline' 2. Warning: Each child in an array or iterator should have a unique 'key' prop Public pagination and duplicate molecules When user uses switch button to list samples or reactions, the pages need to be calculated by samples or reactions. Additional: When user uses 'Search', e.g. input inchistring and then search, the duplicate molecules show on the sample list and the pages go wrong. Fix this by using '.uniq' on api and 'molecules.size' for totalElement. repository scheme fix redirect fix doi suffix generation for reaction duplicate Reaction doi route Add .version if the version exists. Test on local environment: 1. With http://localhost:3000/inchikey/reaction/SA-FUHFF-UHFFFADPSC-UHFFFADPSC-UHFFFADPSC-NUHFF-NUHFF-NUHFF-ZZZ, it goes to Reaction id 22. 2. With http://localhost:3000/inchikey/reaction/SA-FUHFF-UHFFFADPSC-UHFFFADPSC-UHFFFADPSC-NUHFF-NUHFF-NUHFF-ZZZ.1, it goes to Reaction id 23. 3. With http://localhost:3000/inchikey/RJQVSFJIBQPCLA-UHFFFAOYSA-N, it goes to Molecule 1287. 4. With http://localhost:3000/inchikey/RJQVSFJIBQPCLA-UHFFFAOYSA-N.1, it goes to Molecule 1287. scheme issue fix and layout Disable reaction publish button after publish After user use publish button to publish a reaction, this button should be disabled so user can not publish the same reaction again. The render() of ReactionDetails is not triggered properly when state is changed, so the UI remains the same and does not display correctly with the latest data. Use forceUpdate() to force execute the render(). fix sample doi reservation disable sample publish button after publish Add scroller and toggle panel into publish reaction modal Add scroller into publish reaction modal so the user can scroll up and down to view the publish details. Some styles are added to fit the modal. Add toggle function on RInChiKey, Properties. and TLC. Additional: Eliminate some ESLint warning, e.g. use textAlign not text-align, className not class, fontSize not font-size...etc. sample publish after update sample reserve dois spinning icon Toggle panel into publication reaction Add toggle on Analyses of publication reaction; publication sample also. hide ManagingAction share-button Reaction Reserve DOIs in landing page add link to spectraviewer migrate legacy published samples/analyses to table publication and sorting the taggable_data publish sample and reaction analyses check rm secrets for testing publication page description disable when no data analysis sorting fx_task Analysis preview for the public The public can preview the analysis image, no need to sign in the system. Summary: 1. copy publication image file to public folder when doing duplicate datasets and copy attachments - The file path format is 'public/images/publications/{attachment.id}/{attachment.filename}'. - Copy the one which will be in table: publications, not the original ones. 2. fetch image file from public folder if the user is from the public, otherwise, use the the original api which gets the image file from store - If the fetch file fails, use thumbnail instead so user will not get any system error. And we are aware that the image file does not exist in public folder from console log. 3. one-time task 'ver_20190128000004_copy_image_to_public' is created - Use this task to copy the image files to the public folder. It fetches the image files from table: publications with state='completed' and element_type='Container' and then copy to public folder. 4. Add preview function on Dataset Gemfile upgrade Publication Review Process upd mail config/development enable reaction publishing fix reviewing button visibility and api mv state logic to job fix typo reaction publication author display issue publish check reaction analysis publish fix change link to new repo hostname New Chemotion landing page notification for reaction and sample publish enable cap deploy slack notification root page: text change for link to repo url link updates in publication mailer message root page link to dev repo lit api fix lint_js WIP_analyses_selection_checkbox_issue typo analysis type options fix for retracted publication fix routing that cause break page add last publish reaction to previous layout version reaction and sample publish analyses checkbox issue update publish_at repo page routing update deploy config publication review f_typo routes and review fix review page with literature manual reject publication News Two new environment variables: ARTICLE_EDITOR, ARTICLE_PATH E.g. ARTICLE_EDITOR: '2,7' (user.id = 2 and user.id = 7 have the auth. to create/edit the article; if this variable does not exist, no one are allowed to create/edit articles ) E.g ARTICLE_PATH: 'public/newsroom/' (the stroge path for article content; if this variable does not exist, the code will use 'public/newsroom' as default) One new table: articles (refer to migration file) One new gem: Moneta (refer to Gemfile) Please refer to GitLab #148 for the UIs and details. analysis-by-product-on-repository-page element to review collection change-scollection-to-collection-for-the-icon-link disable-repo-qrcode-function View comment with full screen size 8 fils are committed, including 2 new files: 'ReactionDetailsRepoComment.js' and 'SampleDetailsRepoComment.js'. 'ElementDetails.js', 'ReactionDetails.js' and 'SampleDetails.js' are more ELN related and are changed to control the comment page on/off. There other files are more Repository related. doi report reload fix Fixed 'edit is not working' issue; new timeline layout of news index page symlink newsroom for deploy fix reaction display when reaction has no analyses Fix by not to nest DOM elements directly under Nav component gem upg Js warning about id, key, expanded props and validateDOMNesting Eliminate the javascrip warning below (when loading Sample or Reaction in respoitory) 1. Warning: Each child in an array or iterator should have a unique 'key' prop. 2. Warning: Failed prop type: The prop id is required to make accessible for users of assistive technologies such as screen readers. 3. Warning: validateDOMNesting(...): Whitespace text nodes cannot appear as a child of <tbody>. Make sure you don't have any extra whitespace between tags on each line of your source code. 4. Warning: Failed prop type: You have provided a prop to without an handler prop. This will render a read-only field. If the field should be mutable use . Otherwise, set . responsive page for mobile doi download fix How-To functionality Similar to function: Newsroom, only the different look. So the data is stored in public folder as one index file and the others for content. The new environment variables are added. There is no default cover image file for How-To, use css instead. Two new environment variables: GUIDANCE_EDITOR, GUIDANCE_PATH E.g. GUIDANCE_EDITOR: '2,7' (user.id = 2 and user.id = 7 have the auth. to create/edit the How-To article; if this variable does not exist, no one are allowed to create/edit How-To articles ) E.g GUIDANCE_PATH: 'public/guidance/' (the stroge path for HOW-To article index and content; if this variable does not exist, the code will use 'public/guidance' as default) Move some codes to RepoCommon for common use. How To: reword Guidance to HowTo Guidance -> HowTo guidance -> howto GUIDANCE -> HOWTO GUIDACNE -> HOWTO ArticleAPI: fix user validation add overlay ChemDoodle molfile cleaning task bcc reviewer Set default route to welcome page, no matter user sign in or not Notification/mail to submitter after review: content change do not show 1H NMR check at public analysis prevent app breaking default to root page reduce font size lnading page panel display reaction.duration if there, otherwise, display (end_time - start_time); fix blank page issue when user copy reaction and then publish in one move config/deploy/howtox Js warning on review page and published reaction Fix the warnings below: 1. Warning: Received 'true' for a non-boolean attribute 'striped'. If you want to write it to the DOM, pass a string instead: striped='true' or striped={value.toString()}. in tbody (created by RepoReview) also: bordered, hover 2. Warning: Failed prop type: You have provided a expanded prop to Panel without an onToggle handler prop. This will render a read-only field. If the field should be mutable use defaultExpanded. Otherwise, set onToggle. 3. Warning: Failed prop type: Invalid prop 'reaction' of type 'Object' supplied to 'ReactionTable', expected instance of 'Reaction'. in ReactionTable (created by ReactionInfo) also: ReactionRinChiKey, ReactionProperties, ReactionTlc 4. Remove unused variables search review list show lastest sample svg show sample svg file in the publication list add url on doi report publishing message Pubchem with no cid check if cid null Style improvement and published date on howto and news 1. add Published_At; default value is Created_At 2. the list is order by Published_At 3. set image style in quilleditor as 50vw 4. styling to fit small device add counter in collection repo-add-new-analysis-publication-fix fix pubchem metadata doi fix repo search issue readonly when reaction published Add Reviewed Collection select reference when sample or reaction publish repo search fix Use Exact mass instead of Mass refresh list after clicking review or accept fix warning: typo class/className sort analyses by extended_metadata.index push state and routing cleanup use aviator push state: absolute path no anchor clean anchor on /mydb and /home path redirecting on authenticate mydb repo logo url fix howto and newsroom path disable reaction delete button when published is_publish check fix Submit with embargo Submitter can put an embargo on his/her Sample/Reaction when he/she submits for publication. A new menu item named 'Embargoed Publications' is added on the menu. A new collection named 'Embargoed Publications' is added on the collection if user has put embargo on. Submitter can generate a temporary account by clicking on 'Anonymous acct.', and he/she will get the email with account and password from system. Submitter can release an embargo only when all elements of this embargoed collection are in state accepted. Once the embarged is released, the related anonymous accounts will become invaild. fix about page link add skip_confirmation! when creating account add alert and notification display only when temperature is given Display completed content of an analysis Includes: 1. Remove the word 'Type' and 'Content'. 2. Display all of the content of an analysis. This change is applied for: Publications page, Review page, Embargoed Publications page. Stay on submission modal and download doi Keep modal showed after clicking 'Reserve DOIs' One new button behinds 'Reserved DOIs' for downloading DOIs in csv file format. fix post processing embargo release Not recognize activeKey prop warning on review and embargoed page Warning: React does not recognize the 'activeKey' prop on a DOM element. If you intentionally want it to appear in the DOM as a custom attribute, spell it as lowercase 'activekey' instead. If you accidentally passed it from a parent component, remove it from the DOM element. It is related to Nav and Navbar/NavbarForm. Remove and add css for styling. publication decline and submitter comments add page contactÄ fix mail_reviewed_request delete embargo function clean js warning, refer to #215 for the details Add Embargo description fitler product which has no doi Analyses in review and mydb view have same sequence 1. Sorting analyses in Review and Embargo page before rendering Analyses information 2. Remove console.log 3. Replace 'dark' with 'default' to eliminate js warning decline button title fix the currentElement null issue repository license link fix upload issue with .basename and add few css for UI Metadata preview and download A new feature Metadata on Review Page, user can preview/download Metadata which send to Datacite in one zip file. Refer to https://git.scc.kit.edu/ComPlat/chemotion_REPO/issues/223 for details. process remove from all collections review add metadata download button on publication page Get first few lines, e.g. 6 lines, as sub-description state changed before job called Styling on How-To We make some updates based on the feedback from Nicole. Please refer to https://git.scc.kit.edu/ComPlat/chemotion_REPO/issues/230. Besides, Use cache: no-store to see if it works for the file cache issue. howto and news now public job to get SID by DOI icon to link pubchem sid clean db/migrate fx howto rm labels scrollbar adjustment Statistics info Add total number of Samples, total number of Reactions, and (the top 3) total number of Analyses on Welcome page. reaction-submissions-mandatory-check w disable publish button when sample is unsaved OLS for doi update Gemfile.lock fix reaction product doi display issue advanced search by author for sample sorting by published at analysis-type-join-with-synonym use trim to removes all the whitespace characters (space, tab, no-break space, etc.) and all the line terminator characters (LF, CR, etc.) upd schema advanced search by ontologies Submissions mandatory check for re-submit Apply submission checks when user re-submit reaction or sample. We still perform these checks in front-end (not as title described). When publish a sample, molecule(sample) check will be performed. When user publish a reaction, both reaction check and molecule(sample) check will be performed in one go. If user publish a sample which is associated with a reaction, the system will pop-up a message with reaction link so user can go to reaction to publish. advanced search prevent sql injection embargo pubchem cap deploy: link public/ontologies dir Creative Common License Add 'Choose license' with CC0, CC BY and CC BY-SA options on user submission; use CC BY-SA as default value. Remove 'Creative Common License' relateds from page bottom. Based on Datacite metadata schema 4.1 (which is used by chemotion_REPO), this license data will be part of metadata_xml with tag <rights> (under <rightsList>) and we will use the title/description from Creative Common, which are - Attribution-ShareAlike 4.0 International (CC BY-SA 4.0) for CC BY-SA - Attribution 4.0 International (CC BY 4.0) for CC BY - CC0 1.0 Universal for CC0 Three SVGs(CC BY-SA, CC BY, CC0) from Creative Common are added to public/images/creative_common. show state accepted to review page fix solvent calculation fix solvent submission be analyses type check Check if kind value is with | User registration: enable organisation input Use Directive: upd txt for commercial use directive in public html file - render partial from public/directives/diretives.html for new registration page - react parse html for directive tab page - content: -- add email for retraction -- precise cookie info -- adapt for commercial use license directives content: fix html reserved charactes and other typos directives: add list of available licenses Add related identifier for reaction analyses and product Add reaction analyses DOIs into relatedIdentifiers of datacite reaction xml, with relationType is 'HasPart'. Add reaction DOI into relatedIdentifiers of datacite sample xml, with relationType is 'IsPartOf'. Plus: Encode 'description' of datacite reaction xml. Consent of license Add Legal Code link for user to view the license legal code. Two checkboxes are added for CC0 license to get user's consent. fix affiliation sorting and review display A public api to get published molecule id, reference: https://git.scc.kit.edu/ComPlat/chemotion_ELN/issues/794 fix no action connected when user click How-To Editor in the dropdown add delete doi api on datacite Display authors information on published dataset page Add 'Published On', 'Authors' and affiliation information on dataset page. Select Coauthors lists ELN confirmed accounts Only confirmed accounts are listed in Select Coauthors; filter out coauthors with confirmed_at is nil when processing publish procedure. remove affiliation group code Submission check on co-author data Check if co-author is valid or not; if co-author is invalid, user will get the error message and the submission will stop. exclude 103 on sync collection label upd Gemfile.lock rm env data upd README for repo non-published-reaction-goes-to-list-view show short_label on review list fix publication search alignment and add space on author name Show under review and under embargo statics About page: upd licensing txt highligt current selected element in the list - publication, review, and embargo bug fix on review page when reviewing element has analysis without type use editor blocks instead of only one quilleditor pid routing TOS update sid job with completed only generate doi when structure changed and accept TOS upd reviewer comments save WIP Independent scroll bar in review comment panel When user clicks on 'Reviewer comment' of MyDB, the system displays MyDB data and submission data in one screen for user to view detail data and comments from the reviewer at the same time. Add scroll bar for MyDB data and submission data so user can inspect the data by scrolling the document separately. Additional: use 'pre-wrap' for summary comment. repo review button bugfix add chemspectra deploy config fix review with comments on details embargo to remove pending tag pubchem_V2000 T9 filter Export collections for mydata and elngate only Only 'My Data' collection and 'ELN Gate' collection are used in Repository. Therefore, remove other collections(incl. 'All') from 'Export collections' UI. Disable 'Import collections' from menu due to the current logic of ELN 'Import collections' function is not suitable for Repository. sort published reaction by published date chr id Search reaction function Add search function on Publications page when switch type is Reaction. Additional: 1. Set default value in case the user has no layout data. 2. Rebuild pg_search by using rake with 'rake pg_search:multisearch:rebuild[Reaction]' or in the console with 'PgSearch::Multisearch.rebuild(Reaction)' or 'PgSearch::Multisearch.rebuild(Reaction, false)'. Add features on Welcome page change from ChRx to CRx add reviewer and public collection to env setting npm: svg-zoom downgrade back to 0.1.5 typo uniq ChemRep id rename chemspectra new editor for newsroom make the reactions visible per default (instead of molecules) REPO copy to clipboard analysis desc Revert "Resolve "report-fetch-with-buffer"" This reverts commit 51ce7aa. Report: [1] fetch list by difference [2] fix load sync & share elements Update ITG to IBCS About page: - change 'Institute of Toxicology and Genetics (ITG)' to 'Institute of Biological and Chemical Systems – Functional Molecular Systems (IBCS-FMS)' - change 'Institute of Toxicology and Genetics' to 'Institute of Biological and Chemical Systems – Functional Molecular Systems' Contact page: - change 'Institute of Toxicology and Genetics (ITG)' to 'Institute of Biological and Chemical Systems – Functional Molecular Systems (IBCS-FMS)' Additional change: code linting News room for the chemotion.net page Refer to https://git.scc.kit.edu/ComPlat/Zettelkasten/issues/43 Modification: 1. Add 'Newsroom' link on the main page. 2. Clean code Duration of reaction is mandatory for submission Add validation on Duration of reaction. Duration is mandatory for submission. Note: For re-submit/publish case, the validation of Duration is already existed. Indicate the mandatory fields for publication Add 'RequiredLabel' as a common component to indicate mandatory fields for submission. review page with filter set to pending by default 13C counting: count missing signal statement wip, yield wip switch switch to tabs disable scheme-only reaction publication publishing concern: clean WIP revamp review job fix method naming when oub declined mv collection logic to pub model use state constant WIP refactor reviewing job move logic to model refactor declined thru element deletion DRY repo_api by moving logic to publication model lint tmp fix to not email some reviewers lint WIP DRY Quillviewer not to remove formating atom count in analysis NMR description allow decimal count fix H nested bracket count add scheme only on public view, env variables, and lint scheme only BE fix reject samples check if regenerate doi is needed disable reserved DOI pagination for review page f Reaction product doi display incorrect Use taggable_data scheme only yield and author DRY for sample/reaction details of repository Common: 1. split MetadataModal, ReviewModal, CommentModal, CommentBtn into files Reaction: 1. add RepoReactionDetails.js 2. replace the codes for rendering reaction details with RepoReactionDetails.js - RepoReviewDetails.js - RepoEmbargoDetails.js - RepoElementDetails.js - ReactionDetails.js - ReactionDetailsRepoComment.js Sample: 1. add RepoSampleDetails.js, RepoSample.js 1. replace the codes for rendering sample details with RepoSampleDetails.js - RepoReviewDetails.js - RepoEmbargoDetails.js - RepoElementDetails.js - SampleDetailsRepoComment.js Features: 1. User can leave the comment on ELN view now 2. User can only close the modal by clicking on Close button or the Close icon (x) on the right-top Bug-fixes: 1. Click Dataset link and get blank page 2. Get blank page on Review when switch from Publications and currentElement exists 3. Align labels on Publications view Link to mydb missing on review panel Add codes to identify enabled/disabled MyDB link from different response structure. Align content of analysis on view page Add style to align the analysis content with ID element. show fulldoi on review move embargo to another embargo bundle All validated analyses selected by default The validated analysis is checked/selected(publish=true) by default. If users uncheck/unselect the analysis, then this analysis will not be checked/selected automatically in the future even it is validated. reaction publish duration show contributor as published by as priority correct script error upd db/schema fix reaction duration set value scheme only doilink and description and properties Page margin of element detail Use the scroll of panel when element detail is basic view (not full screen) f Add codes to identify enabled/disabled MyDB link from different response structure. hidden search input by default MyDB case show user define iupac name on publication public view search tool: fix suggestion and search TODO check suggestion/search on schemOnly Style search input of publications 1. reset search input of StructureEditor 2. align elements Eager loading detected on clicking mydb Refer to https://git.scc.kit.edu/ComPlat/chemotion_REPO/-/merge_requests/292 Use .joins to get the count of Sample and Reaction change published analyses from Serializer to Entity publication preview image fix Missing reaction description on publications 1. Show 'Description' and 'Additional information' if there is any. 2. Set defaultExpanded of 'Reaction Table' as false. 3. Wording, please refer to https://git.scc.kit.edu/ComPlat/Zettelkasten/issues/65 4. Put Formula/IUPAC on a new line if any 5. Add DOI copy function on the elements of Review page modify publication validation message fix withdraw issue when original element is deleted doi copy function by default 1. add doi copy function to Product and it analyses on Review and Embargo page 2. set defaultExpanded of RInchiKey panel as false, of Reaction Table panel as true Blank page after resubmit reaction with new added product Add logic to handle user re-submit with new added product case. disable mailing to reviewer upgrade to schema 4.3 disable-jcamp-process-when-element-submit disable sending mail to reviewers REPO FACTOR Update chem_scanner gem, text in table is not used while splitting Update chem_scanner gem, treat charge independently with fragment Skip if there is any error while processing CDX Update new version of chem_scanner gem Use backend ketcher for Chemscanner Conflicts: package-lock.json Configurize ketcher URL show published scheme only reaction literature in ELN view deploy config upd fix deploy config for ketchBE Style search and smile of publications page 1. apply harsh edge to search 2. fix border and overlap 3. fix smile data goes beyond the tabs add help infomation on tabs of publications incorrect-substructure-search-data-display-on-publication rearrange statistic layout readable statistic info when resize browser window new intro style search by chemotion-id Yield validation of submission If the yield is not given in the publishing panel, there should be a warning and the submission only allowed if the yield is given. For multiple products case, at least one should be non zero. This applies for both reaction and scheme-only reaction. Note: scheme-only reaction can only be rejected or accepted; Therefore, re-submit is not applicable to scheme-only. add element_type on suggestion review history Save collapse settings Add ArchivedManagement view: manage archived/actived files Update product name while importing Chemscanner importing run as a delayed job Delete descendant source if parent is deleted Use rdkit for SVG composer for chem_scanner, update chemscanner_composer review history column history fix review-column-history-info-collapse new style for 'no preview available' case enable prediction function for view user repo review search activate Anonymous account by default activejob_dj_overrides User comments fix publishing job retry Set as default to use description field For 'scheme-only', set 'add the description field?' as checked by default fix block syntax Analysis preview thumb and image no match Issue: On publications page, user clicks on the preview image of analysis and gets thumb file in pop modal. (w/o login) On publications page, user clicks on the preview image of analysis and gets a different image in pop modal. (w/ login) Fix: 1. When user re-submits with new attachments, these attachments should be copied to publications folder 2. Refactor the preview_image: add id and filename as return value Additional: 1. DRY with previewContainerImage 2. Remove unused codes Contributor information Add an information for the scheme only submissions at the publication page assigned to the 'Contributor'. User comments for sample and reaction null analyses affiliation export doi info fix repo reaction container issue info button for table, description and additional information... field Add info for 'scheme', 'description' and 'additional information...' fields of Reaction. Display info while hovering the text for required fields; set font color as red to mark it as required field info text upd show/hide help-button and linting fix repo search bug correct email change to the right type xvial input and display add compound link update per feedback from https://git.scc.kit.edu/ComPlat/chemotion_REPO/-/merge_requests/333#note_191189 UI control and improvement on xvial Per request, - the registered sentence only appears in the cases where an X-Vial number is entered - the X-Vial number is not visible to all users - add the email address of the requesting user to the mail; send the request email to compound team and send the confirmation email to the requester - add to the information button about Youtube channel and our how-to pages Remind user to log in to send request Secret external label The external label of sample is not visible for all users (except the reviewer and the owner himeself/herself) if the sample is published. This also applies for the case when user chooses to 'Show sample external name on title'. Add DOI in SI report there is a case that collection_label of reactant is empty fixed no response on substructure search remove review history from published element eliminate js warning element-tag-doi-for-reviewing-elements element-remove-from-contributor-pending-collection-after-release send-email-when-pubchem-timeout no-process-embargo-rejected-sample fix process element move collection before deletion doi doc report: rm unnecessary whitespace delete elements fix use DOI in report supporting-information-standard-reaction Product X-Vial 1. Add X-Vial function on product 2. Add info button on X-Vial button 3. Remove X-Vial information from published reaction list add xvial to public reaction list disable instrument tex for publication and visible for reviewing increase author list to 10 eliminate js warning Analysis view button on public page Add viewing spectra function on analysis of public samples, and reaction product as well. enlarge image when hovering, and zoom function on svg of detail lizenz text gestaltung 1. text adjustment per request 2. add 'No License' option; when user chooses 'No License', there will be no license icon or wording shown on the page and the no rights data sent to dataCite. add animation on MyDB link my collaboration WIP service collaborator-current-affiliations
- Fetch data from a collection(Repo: Open Data Collection) of Compound platform. - Use compound_open_data.yml as configuration file, put aurthized user id in allowed_uids.
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OK, I won't notify you again about this release, but will get in touch when a new version is available. If you'd rather skip all updates until the next major or minor version, let me know by commenting If you change your mind, just re-open this PR and I'll resolve any conflicts on it. |
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Bumps tar from 6.1.11 to 6.2.1.
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