diff --git a/.gitignore b/.gitignore index 77ad2f5..5b9ebd8 100644 --- a/.gitignore +++ b/.gitignore @@ -3,4 +3,6 @@ node_modules build seeds .next -pods/service-connections \ No newline at end of file +pods/service-connections + +.dendron.cache.* \ No newline at end of file diff --git a/README.md b/README.md new file mode 100644 index 0000000..8163d81 --- /dev/null +++ b/README.md @@ -0,0 +1,4 @@ +# acol-dws +The repository for the Dendron of the EMI + +https://anticipated-chemistry-of-life.github.io/acol-dws/ diff --git a/dendron.code-workspace b/dendron.code-workspace index 5844bb9..ee5cd76 100644 --- a/dendron.code-workspace +++ b/dendron.code-workspace @@ -34,4 +34,4 @@ "mushan.vscode-paste-image" ] } -} +} \ No newline at end of file diff --git a/dendron.yml b/dendron.yml index 4f9d275..c556578 100644 --- a/dendron.yml +++ b/dendron.yml @@ -71,7 +71,6 @@ workspace: maxPreviewsCached: 10 maxNoteLength: 204800 enableFullHierarchyNoteTitle: false - enablePersistentHistory: false preview: enableFMTitle: true enableNoteTitleForLink: true @@ -91,26 +90,21 @@ publishing: writeStubs: false siteRootDir: docs seo: - title: Anticipated Chemistry of Life - description: Open Notebook Science in the Anticipated Chemistry of Life project + title: Dendron + description: Personal Knowledge Space github: enableEditLink: true - editLinkText: Participate and click here to edit this page on Github ! + editLinkText: Feel free to participate and click here to edit this page on Github ! editBranch: main editViewMode: tree editRepository: /~https://github.com/anticipated-chemistry-of-life/acol-dws + enableSiteLastModified: true enableFrontmatterTags: true enableHashesForFMTags: false enableRandomlyColoredTags: true enableTaskNotes: true enablePrettyLinks: true - searchMode: lookup - enableMermaid: true - enableHierarchyDisplay: true - assetsPrefix: /dendron-dbgi + searchMode: search siteUrl: https://anticipated-chemistry-of-life.github.io - duplicateNoteBehavior: - action: useVault - payload: - - vault + assetsPrefix: /acol-dws diff --git a/noteTraits/open-notebook-emi-mjopiti.js b/noteTraits/open-notebook-emi-mjopiti.js new file mode 100644 index 0000000..8ff5770 --- /dev/null +++ b/noteTraits/open-notebook-emi-mjopiti.js @@ -0,0 +1,32 @@ +module.exports = { + OnWillCreate: { + /** + * This example sets a prefix of 'planning', and then adds a date hierarchy + * using the luxon module. + */ + setNameModifier() { + // This example sets a prefix of 'planning', and then adds a date + // hierarchy using the luxon module. + return { + name: "open-notebook.emi.mjopiti." + luxon.DateTime.local().toFormat("yyyy.MM.dd"), + promptUserForModification: true, + }; + }, + }, + OnCreate: { + setTitle(props) { + // This example will use the currentNoteName property, extract the + // yyyy.MM.dd date portion of the note name, and then reformat it with + // dashes. + return props.currentNoteName.split(".").slice(-3).join("-"); + }, + /** + * Apply a template to each note. NOTE: If you want to use this code, you + * will need a note file called `templates.planning-template.md` in your + * Dendron workspace. + */ + setTemplate: () => { + return "templates.open-notebook.emi.mjopiti"; + }, + }, +}; \ No newline at end of file diff --git a/noteTraits/open-notebook-emi-pmallard.js b/noteTraits/open-notebook-emi-pmallard.js new file mode 100644 index 0000000..cc3fbe9 --- /dev/null +++ b/noteTraits/open-notebook-emi-pmallard.js @@ -0,0 +1,32 @@ +module.exports = { + OnWillCreate: { + /** + * This example sets a prefix of 'planning', and then adds a date hierarchy + * using the luxon module. + */ + setNameModifier() { + // This example sets a prefix of 'planning', and then adds a date + // hierarchy using the luxon module. + return { + name: "open-notebook.emi.pmallard." + luxon.DateTime.local().toFormat("yyyy.MM.dd"), + promptUserForModification: true, + }; + }, + }, + OnCreate: { + setTitle(props) { + // This example will use the currentNoteName property, extract the + // yyyy.MM.dd date portion of the note name, and then reformat it with + // dashes. + return props.currentNoteName.split(".").slice(-3).join("-"); + }, + /** + * Apply a template to each note. NOTE: If you want to use this code, you + * will need a note file called `templates.planning-template.md` in your + * Dendron workspace. + */ + setTemplate: () => { + return "templates.open-notebook.emi.pmallard"; + }, + }, +}; \ No newline at end of file diff --git a/noteTraits/open-notebook-mvisani.js b/noteTraits/open-notebook-mvisani.js new file mode 100644 index 0000000..41b578a --- /dev/null +++ b/noteTraits/open-notebook-mvisani.js @@ -0,0 +1,32 @@ +module.exports = { + OnWillCreate: { + /** + * This example sets a prefix of 'planning', and then adds a date hierarchy + * using the luxon module. + */ + setNameModifier() { + // This example sets a prefix of 'planning', and then adds a date + // hierarchy using the luxon module. + return { + name: "open-notebook.dbgi.mvisani." + luxon.DateTime.local().toFormat("yyyy.MM.dd"), + promptUserForModification: true, + }; + }, + }, + OnCreate: { + setTitle(props) { + // This example will use the currentNoteName property, extract the + // yyyy.MM.dd date portion of the note name, and then reformat it with + // dashes. + return props.currentNoteName.split(".").slice(-3).join("-"); + }, + /** + * Apply a template to each note. NOTE: If you want to use this code, you + * will need a note file called `templates.planning-template.md` in your + * Dendron workspace. + */ + setTemplate: () => { + return "templates.open-notebook.dbgi.mvisani"; + }, + }, +}; \ No newline at end of file diff --git a/notes/assets/The-Global-Biodiversity-Standard-Manual-for-assessment-and-best-practices.pdf b/notes/assets/The-Global-Biodiversity-Standard-Manual-for-assessment-and-best-practices.pdf new file mode 100644 index 0000000..1484b3f Binary files /dev/null and b/notes/assets/The-Global-Biodiversity-Standard-Manual-for-assessment-and-best-practices.pdf differ diff --git a/notes/assets/images/2022-12-25-18-00-31.png b/notes/assets/images/2022-12-25-18-00-31.png new file mode 100644 index 0000000..d436064 Binary files /dev/null and b/notes/assets/images/2022-12-25-18-00-31.png differ diff --git a/notes/assets/images/2022-12-25-18-13-17.png b/notes/assets/images/2022-12-25-18-13-17.png new file mode 100644 index 0000000..fbeb210 Binary files /dev/null and b/notes/assets/images/2022-12-25-18-13-17.png differ diff --git a/notes/assets/images/2024-06-18-15-33-58.png b/notes/assets/images/2024-06-18-15-33-58.png new file mode 100644 index 0000000..9714886 Binary files /dev/null and b/notes/assets/images/2024-06-18-15-33-58.png differ diff --git a/notes/assets/images/EMI_logo_round.png b/notes/assets/images/EMI_logo_round.png new file mode 100644 index 0000000..8c1a0d3 Binary files /dev/null and b/notes/assets/images/EMI_logo_round.png differ diff --git a/notes/dendron.md b/notes/dendron.md new file mode 100644 index 0000000..87ad593 --- /dev/null +++ b/notes/dendron.md @@ -0,0 +1,20 @@ +--- +id: l03fwlci5f5rdpot3v7oli6 +title: Dendron +desc: '' +updated: 1671987314401 +created: 1671987274473 +--- +# Welcome to Dendron + +This is a dendron vault. + +## Lookup + +This section contains useful links to related resources. + +- [Getting Started Guide](https://link.dendron.so/6b25) +- [Discord](https://link.dendron.so/6b23) +- [Home Page](https://wiki.dendron.so/) +- [Github](https://link.dendron.so/6b24) +- [Developer Docs](https://docs.dendron.so/) \ No newline at end of file diff --git a/notes/manuals.md b/notes/manuals.md new file mode 100644 index 0000000..bea6505 --- /dev/null +++ b/notes/manuals.md @@ -0,0 +1,14 @@ +--- +id: gug1zw6wdzvta1evuzc5nut +title: Manuals +desc: '' +updated: 1718717434915 +created: 1718717434915 +--- + + +Mentioned by Merry + +https://www.biodiversitystandard.org/ + +Manual is [here](/assets/The-Global-Biodiversity-Standard-Manual-for-assessment-and-best-practices.pdf) \ No newline at end of file diff --git a/notes/monorepo.Backend.md b/notes/monorepo.Backend.md new file mode 100644 index 0000000..4b416b6 --- /dev/null +++ b/notes/monorepo.Backend.md @@ -0,0 +1,37 @@ +--- +id: zurlb9xvgq0nac4vckzusam +title: Backend +desc: '' +updated: 1719306973256 +created: 1719241390631 +--- + +# Monorepo : Backend +Here we describe the basic structure of the backend of the [EMI monorepo](/~https://github.com/anticipated-chemistry-of-life/emi-monorepo/tree/web). + +## `constraint_checkers` +This folder contains the metaprogramming code to check the correctness of the database, and then to generate the rust files depending on the constraints. + +## `db_data` +Folder containing csv files with the data that will be inserted into the database. For example, the file `countries.csv` contains the list of all available/allowed countries in the database. + +## `migrations` +Folder containing the SQL files that are used to create the database schema. The files are numbered in order of execution. +Here is a brief description of the types of tables: +- `create_*_table` creates a table in the database +- `create_*_sequential_index` changes the `id` column of the table from INTEGER to SERIAL +- `populate_*_table` populates the table with data from the csv files in the `db_data` folder +- `create_*_gin_index` creates an index to allow for searching in the table +- `create_*_can_x_trigger` contain a function that takes a user ID (INTEGER) and the primary keys and returns a BOOLEAN indicating whether the user can {operation} the row + +## `src` +### `api` +#### `oauth` +Directory containing the code for the OAuth2.0 authentication and its dependencies (login/logout, login providers, refresh tokens, etc). + +#### `ws` +Directory containing the code for the websockets. + +### `database` +This directory contains the code for the database connection between the backend and the database. We are using the [Diesel](https://diesel.rs/) crate to interact with the database. Most of the code in this directory is generated automatically by the `constraint_checkers` package. + diff --git a/notes/monorepo.Frontend.md b/notes/monorepo.Frontend.md new file mode 100644 index 0000000..9933ac4 --- /dev/null +++ b/notes/monorepo.Frontend.md @@ -0,0 +1,29 @@ +--- +id: 6sunjqumyp68ibjz7e4tx42 +title: Frontend +desc: '' +updated: 1719323428789 +created: 1719316421481 +--- + +# Monorepo : Frontend +Here we describe the basic structure of the frontend of the [EMI monorepo](/~https://github.com/anticipated-chemistry-of-life/emi-monorepo/tree/web). + +## `src` +### `api` +This directory contains the frontend handlers for the different authentication methods. + +### `components` +This directory contains the different components that are used in the frontend. For example, the `footer.rs` file contains the footer of the website. The `search_bar.rs` file contains the search bar that is used to search for different items in the database. + +#### `badge` +Directory defining how the entries in the database are displayed (implementation fo `RowToBadge` for each entry). + +#### `forms` +Directory defining the forms used to create, update, and delete entries in the database from the frontend. + +### `pages` +This directory contains the different pages of the website. For example, the `home.rs` file contains the home page of the website. The `login.rs` file contains the login page of the website. + +## `styles` +This directory contains the CSS files that are used to style the website. \ No newline at end of file diff --git a/notes/monorepo.Web-Common.md b/notes/monorepo.Web-Common.md new file mode 100644 index 0000000..0ce75af --- /dev/null +++ b/notes/monorepo.Web-Common.md @@ -0,0 +1,10 @@ +--- +id: 9lrxbu977wdl7qo6qxz1mkx +title: Web Common +desc: '' +updated: 1719323693593 +created: 1719323470818 +--- + +# Monorepo : Web-Common +The `Web-Common` folder contains the common code that is shared between the frontend and the backend of the [EMI monorepo](/~https://github.com/anticipated-chemistry-of-life/emi-monorepo/tree/web). \ No newline at end of file diff --git a/notes/open-notebook.emi.mjopiti.2024.07.03.md b/notes/open-notebook.emi.mjopiti.2024.07.03.md new file mode 100644 index 0000000..eb6a03a --- /dev/null +++ b/notes/open-notebook.emi.mjopiti.2024.07.03.md @@ -0,0 +1,105 @@ +--- +id: v5zls2vytueekq9twor2qck +title: '2024-07-03' +desc: '' +updated: 1720012918829 +created: 1720008914994 +traitIds: + - open-notebook-emi-mjopiti +--- + +# This is Michael's EMI open-notebook. + +Today is 2024.07.03 + +## Todo today + +### Have a look at the EMI discussion forum + - /~https://github.com/orgs/anticipated-chemistry-of-life/discussions +### +### + +## Doing +Exploring XML files to automatize mzmine batch mode + + +## File structure +Header: + - + +Several batchsteps: + - + + /Path/to/directory/for/files + + +? what do the batchsteps represent in the GUI? How can they be shortcutted for CLI? + +## Done + +## Notes +Mzmine uses academic log-in to grant the use of the application. Here's the link to [the discussion on github](/~https://github.com/mzmine/mzmine/issues/1827) +-> Summary: It is possible to define the user in the config file but we will soon push a new release that takes a user file or credentials as input. + -> + .... + robinschmid + + +[Here](https://mzmine.github.io/mzmine_documentation/services/users.html) the reference to the documentation to implement an user. +And here the help from mzmine app: + -l,--libraries spectral library files. Either defined in a .txt + text file with one file per line + or by glob pattern matching. To match all .json + or .mgf files in a path: -l "D:\Data\*.json + --list-users List all users that are available and logged in + on this system (computer or server). + --login Use command-line to login to a user. This will + open the login website in the system internet + browser, if supported, + or prompts an input for the user credentials into + the console. After successful login, + a user file will be copied to your system USER + directory in /.mzmine/users/. And the current + user will be saved to the configuration. + The created user file can be accessed with the + -user argument on the next startup. + + +Where to change the directory/file names? + -> beginning for file name + -> + + /home/jopitim/test/cuso_batch_00001 + + + (Line ~100) + -> + + + /home/jopitim/test/mapp_batch_00106/Untitled_intra_row_MS2similarity + + + 0.003 + 10.0 + + 4 + + 10.0 + 250 + 50 + 0.98 + + + (line ~500) + + +## Todo tomorrow, one day ... or never + +### +### +### + + +## Today I learned that + +- \ No newline at end of file diff --git a/notes/open-notebook.emi.mjopiti.2024.07.04.md b/notes/open-notebook.emi.mjopiti.2024.07.04.md new file mode 100644 index 0000000..2b9ebed --- /dev/null +++ b/notes/open-notebook.emi.mjopiti.2024.07.04.md @@ -0,0 +1,60 @@ +--- +id: w1apexds30hsjxfdn3fqb08 +title: '2024-07-04' +desc: '' +updated: 1720107838217 +created: 1720105488247 +traitIds: + - open-notebook-emi-mjopiti +--- + +# This is Michael's EMI open-notebook. + +Today is 2024.07.04 + +## Todo today + +### Have a look at the EMI discussion forum + - /~https://github.com/orgs/anticipated-chemistry-of-life/discussions +### +### + +## Doing +Exploring XML files to automatize mzmine batch mode - Follow up + +File used: /home/jopitim/mzmine-batch-mode-sandbox/docs/dbgi_project_00002/cuso_batch_00001/results/mzmine/cuso_batch_00001_batch.mzbatch + +The file is a nested structure, where the root is batch (possibility to extend to multiple batches?). +The problem is that nested only for: batch -> batchstep -> parameter/files/modules +Already on the second step the tree structure starts to fall apart and case per case should be studied. + + +## Batchstep structure +It is always composed of 2 attributes: +- method="io.github.mzmine.modules.somethingElse" +- parameter_version="1" or "2" + +I don't currently know what 1 and 2 means + +I should scout in the modules directory in mzmine to understand how to retrieve the modules and/or exploit some structures. +-> /~https://github.com/mzmine/mzmine.github.io + +First batchstep should always be file input? (idk but feels right), then it's up to the user. + + +## Todo tomorrow, one day ... or never + +Look if it makes sense to parse a complete XML file and then modify by removing what's not selected by the user. +- Not all parameters need to be set, some are there because the method allows it. + +I believe it should be good to create a general batchstep object which gets filled with the needed information (look into Luca's rust presetantion for not using a constructor (I forgot the right term but it's when you use points under the ::default() definition)). +- something like this has already been created in main.rs in sandbox git but it should be expanded to fit all parameters. + +### +### +### + + +## Today I learned that + +- \ No newline at end of file diff --git a/notes/open-notebook.emi.mjopiti.2024.07.05.md b/notes/open-notebook.emi.mjopiti.2024.07.05.md new file mode 100644 index 0000000..c335be2 --- /dev/null +++ b/notes/open-notebook.emi.mjopiti.2024.07.05.md @@ -0,0 +1,38 @@ +--- +id: zap4g0jyk4vokt4izqosvlw +title: '2024-07-05' +desc: '' +updated: 1720172122733 +created: 1720171753743 +traitIds: + - open-notebook-emi-mjopiti +--- +# This is Michael's EMI open-notebook. + +Today is 2024.07.05 + +## Todo today + +### Have a look at the EMI discussion forum + - /~https://github.com/orgs/anticipated-chemistry-of-life/discussions +### +### + +## Doing +The idea is to create the parameters file using command line in the form of: +- cargo build argv1 argv2 +Where odds argvs are flagging which batchstep to include (inputted by user) and followed by it's parameter/s. + +This are the modules: +- io.github.mzmine.modules.io.import_rawdata_all.AllSpectralDataImportModule +- io.github.mzmine.modules.dataprocessing.featdet_massdetection.MassDetectionModule +- io.github.mzmine.modules.dataprocessing.featdet_adapchromatogrambuilder.ModularADAPChromatogramBuilderModule +- io.github.mzmine.modules.dataprocessing.featdet_smoothing.SmoothingModule +- io.github.mzmine.modules.dataprocessing.featdet_chromatogramdeconvolution.minimumsearch.MinimumSearchFeatureResolverModule +- io.github.mzmine.modules.dataprocessing.filter_isotopegrouper.IsotopeGrouperModule +- io.github.mzmine.modules.dataprocessing.filter_rowsfilter.RowsFilterModule +- io.github.mzmine.modules.io.export_features_gnps.fbmn.GnpsFbmnExportAndSubmitModule +- io.github.mzmine.modules.io.export_features_sirius.SiriusExportModule + +I believe the flags need to be the information after io.github.mzmine.modules. as it is constant between all modules. + diff --git a/notes/open-notebook.emi.pmallard.2024.06.03.md b/notes/open-notebook.emi.pmallard.2024.06.03.md new file mode 100644 index 0000000..0ba6952 --- /dev/null +++ b/notes/open-notebook.emi.pmallard.2024.06.03.md @@ -0,0 +1,67 @@ +--- +id: 9rkr1eqpf24vq8iw30j2fdw +title: '2024-06-03' +desc: '' +updated: 1717405090391 +created: 1717404543365 +traitIds: + - open-notebook-emi-pmallard +--- + +# This is PMA's EMI open-notebook. + +Today is 2024.06.03 + +## Todo today + +### Have a look at the EMI discussion forum + - /~https://github.com/orgs/anticipated-chemistry-of-life/discussions +### +### + +## Doing + +### Draft of first post for the EMI LinkedIn page + +[https://www.linkedin.com/company/anticipated-chemistry-of-life/](https://www.linkedin.com/company/anticipated-chemistry-of-life/) + +🌍 Introducing the Earth Metabolome Initiative (EMI)! 🌿 + +Welcome to the EMI LinkedIn page! Our mission is to explore, reveal, and safeguard the life-sustaining chemistry of all known species on Earth, creating a comprehensive resource for researchers, practitioners, and enthusiasts worldwide. + +The Earth Metabolome Initiative aims to: + +- Advance Life Sciences: Systematically expand knowledge on global chemodiversity and its role in biosphere processes. +- Benefit Human Society: Develop sustainable solutions in agriculture, medicine, and beyond. +- Protect Biodiversity: Provide critical information for biodiversity monitoring and conservation efforts. + +As we face the sixth mass extinction, understanding and preserving the metabolic diversity of life is more important than ever. With cutting-edge analytical and computational technologies, and a collaborative global effort, we aim to map and share the metabolomes of Earth's species, ensuring this invaluable knowledge benefits human societies and protects biodiversity. + +Join us on this journey to unlock the secrets of life’s chemistry and drive sustainable innovations for a better future. Follow our page for updates, insights, and ways to get involved. + +πŸ”— LinkedIn page https://www.linkedin.com/company/anticipated-chemistry-of-life/ +πŸ”— EMI website https://www.earthmetabolome.org/ +πŸ”— EMI GitHub organization /~https://github.com/anticipated-chemistry-of-life + +#EarthMetabolomeInitiative #Biodiversity #Chemodiversity #Sustainability #LifeSciences #Conservation #LinkedOpenData #Metabolomics + + + +## Paused + +## Done + +Created EMI open-notebook template and note traits (as per [[open-notebook.dbgi.setup]]). + +## Notes + +## Todo tomorrow, one day ... or never + +### +### +### + + +## Today I learned that + +- \ No newline at end of file diff --git a/notes/open-notebook.emi.pmallard.2024.06.05.md b/notes/open-notebook.emi.pmallard.2024.06.05.md new file mode 100644 index 0000000..32f7d06 --- /dev/null +++ b/notes/open-notebook.emi.pmallard.2024.06.05.md @@ -0,0 +1,46 @@ +--- +id: ui5ilal57zv9w5cjdj3u45a +title: '2024-06-05' +desc: '' +updated: 1717600253778 +created: 1717600219973 +traitIds: + - open-notebook-emi-pmallard +--- + +# This is PMA's EMI open-notebook. + +Today is 2024.06.05 + +## Todo today + +### Have a look at the EMI discussion forum + - /~https://github.com/orgs/anticipated-chemistry-of-life/discussions +### +### + +## Doing + + +Post on latest activities on the EMI Linked in page + + + + +## Paused + +## Done + +## Notes + + +## Todo tomorrow, one day ... or never + +### +### +### + + +## Today I learned that + +- \ No newline at end of file diff --git a/notes/open-notebook.emi.pmallard.2024.06.18.md b/notes/open-notebook.emi.pmallard.2024.06.18.md new file mode 100644 index 0000000..c078cd7 --- /dev/null +++ b/notes/open-notebook.emi.pmallard.2024.06.18.md @@ -0,0 +1,39 @@ +--- +id: s024v9r9xzbpv07fn7oj4my +title: '2024-06-18' +desc: '' +updated: 1718717398056 +created: 1718717398056 +traitIds: + - open-notebook-emi-pmallard +--- + +# This is PMA's EMI open-notebook. + +Today is 2024.06.18 + +## Todo today + +### Have a look at the EMI discussion forum + - /~https://github.com/orgs/anticipated-chemistry-of-life/discussions +### +### + +## Doing + +## Paused + +## Done + +## Notes + +## Todo tomorrow, one day ... or never + +### +### +### + + +## Today I learned that + +- \ No newline at end of file diff --git a/notes/open-notebook.emi.pmallard.2024.06.28.md b/notes/open-notebook.emi.pmallard.2024.06.28.md new file mode 100644 index 0000000..283626f --- /dev/null +++ b/notes/open-notebook.emi.pmallard.2024.06.28.md @@ -0,0 +1,44 @@ +--- +id: pbu4snep5ly3nbpfg8gd8dl +title: '2024-06-28' +desc: '' +updated: 1719559741656 +created: 1719558052927 +traitIds: + - open-notebook-emi-pmallard +--- + +# This is PMA's EMI open-notebook. + +Today is 2024.06.28 + +## Todo today + +### Have a look at the EMI discussion forum + - /~https://github.com/orgs/anticipated-chemistry-of-life/discussions +### +### + +## Doing + +Call with Michael Jopiti, Luca and Marco + +- EMI intro +- emi-monorepo walkthrough + +## Paused + +## Done + +## Notes + +## Todo tomorrow, one day ... or never + +### +### +### + + +## Today I learned that + +- \ No newline at end of file diff --git a/notes/open-notebook.emi.pmallard.2024.07.02.md b/notes/open-notebook.emi.pmallard.2024.07.02.md new file mode 100644 index 0000000..b77689f --- /dev/null +++ b/notes/open-notebook.emi.pmallard.2024.07.02.md @@ -0,0 +1,81 @@ +--- +id: o2q8t2o2oaa2ldkf8u4bhm3 +title: '2024-07-02' +desc: '' +updated: 1719931554057 +created: 1719922654247 +traitIds: + - open-notebook-emi-pmallard +--- + +# This is PMA's EMI open-notebook. + +Today is 2024.07.02 + +## Todo today + +### Have a look at the EMI discussion forum + - /~https://github.com/orgs/anticipated-chemistry-of-life/discussions +### +### + +## Doing + +## Paused + +## Done + +## Notes + +### Discussion Tarcisio, Luca, Disha + +EMI Ontology + +RO, GO, UBERON from OBO, +TOP ids from top thesaurus https://top-thesaurus.org/ + + +Tarcisio will set a Qlever instance + +SKOS conversion of OTL + + +### Meeting Michael J + +Create user on the commons-server + + +/home/allardpm/git_repos/EMI/mzmine-batch-mode-sandbox/data/mzml/202406251749_PMA_dbgi_003101_01_01.mzML +/home/allardpm/git_repos/EMI/mzmine-batch-mode-sandbox/data/mzml/202406251749_PMA_dbgi_003140_01_01.mzML +/home/allardpm/git_repos/EMI/mzmine-batch-mode-sandbox/data/mzml/202406251749_PMA_dbgi_003151_01_01.mzML +/home/allardpm/git_repos/EMI/mzmine-batch-mode-sandbox/data/mzml/202406251749_PMA_dbgi_003154_01_01.mzML +/home/allardpm/git_repos/EMI/mzmine-batch-mode-sandbox/data/mzml/202406251749_PMA_dbgi_003155_01_01.mzML +/home/allardpm/git_repos/EMI/mzmine-batch-mode-sandbox/data/mzml/202406251749_PMA_dbgi_003164_01_01.mzML +/home/allardpm/git_repos/EMI/mzmine-batch-mode-sandbox/data/mzml/202406251749_PMA_dbgi_003179_01_01.mzML +/home/allardpm/git_repos/EMI/mzmine-batch-mode-sandbox/data/mzml/202406251749_PMA_dbgi_003180_01_01.mzML +/home/allardpm/git_repos/EMI/mzmine-batch-mode-sandbox/data/mzml/202406251749_PMA_dbgi_003185_01_01.mzML +/home/allardpm/git_repos/EMI/mzmine-batch-mode-sandbox/data/mzml/202406251749_PMA_dbgi_003187_01_01.mzML +/home/allardpm/git_repos/EMI/mzmine-batch-mode-sandbox/data/mzml/202406251749_PMA_dbgi_003196_01_01.mzML +/home/allardpm/git_repos/EMI/mzmine-batch-mode-sandbox/data/mzml/202406251749_PMA_dbgi_003198_01_01.mzML +/home/allardpm/git_repos/EMI/mzmine-batch-mode-sandbox/data/mzml/202406251749_PMA_dbgi_003214_01_01.mzML +/home/allardpm/git_repos/EMI/mzmine-batch-mode-sandbox/data/mzml/202406251749_PMA_dbgi_003223_01_01.mzML +/home/allardpm/git_repos/EMI/mzmine-batch-mode-sandbox/data/mzml/202406251749_PMA_dbgi_blk_pre01.mzML +/home/allardpm/git_repos/EMI/mzmine-batch-mode-sandbox/data/mzml/202406251749_PMA_dbgi_mapp_bk_blk_post01.mzML +/home/allardpm/git_repos/EMI/mzmine-batch-mode-sandbox/data/mzml/202406251749_PMA_dbgi_mapp_bk_blk_post02.mzML +/home/allardpm/git_repos/EMI/mzmine-batch-mode-sandbox/data/mzml/202406251749_PMA_dbgi_mapp_bk_blk_post03.mzML +/home/allardpm/git_repos/EMI/mzmine-batch-mode-sandbox/data/mzml/202406251749_PMA_dbgi_mapp_bk_blk_pre01.mzML +/home/allardpm/git_repos/EMI/mzmine-batch-mode-sandbox/data/mzml/202406251749_PMA_dbgi_mapp_bk_blk_pre02.mzML +/home/allardpm/git_repos/EMI/mzmine-batch-mode-sandbox/data/mzml/202406251749_PMA_dbgi_mapp_bk_blk_pre03.mzML + + + +## Todo tomorrow, one day ... or never + +### +### +### + + +## Today I learned that + +- \ No newline at end of file diff --git a/notes/root.md b/notes/root.md index 0419f1d..d7f36a4 100644 --- a/notes/root.md +++ b/notes/root.md @@ -1,20 +1,40 @@ --- -id: onzl28au0rqgqp6jvx6japn -title: Root +id: 3rbfqqbp7pwbkdcrgc97u7l +title: The Earth Metabolome Initiative desc: '' -updated: 1727770330761 -created: 1727770330761 +updated: 1671988421333 +created: 1671985562294 --- -# Welcome to Dendron +# Welcome to the Earth Metabolome Initiative Dendron notes -This is the root of your dendron vault. If you decide to publish your entire vault, this will be your landing page. You are free to customize any part of this page except the frontmatter on top. +Dendron is the knowledge management system we use in the EMI. We use it specifically to manage notes, lab-books and share ideas. +If you want to know more about Dendron, have a look at this section [[dendron.md]]. -## Lookup +# What is the Earth Metabolome Initiative ? -This section contains useful links to related resources. -- [Getting Started Guide](https://link.dendron.so/6b25) -- [Discord](https://link.dendron.so/6b23) -- [Home Page](https://wiki.dendron.so/) -- [Github](https://link.dendron.so/6b24) -- [Developer Docs](https://docs.dendron.so/) \ No newline at end of file +![](/assets/images/EMI_logo_round.png){max-width: 300px, display: block, margin: 0 auto} + +The Earth Metabolome Initiative, abbreviated EMI, is an Open Science initiative and a global effort to profile the metabolic content of all currently known species on our planet (~2.3 million species). We are building the required computational, scientific and organizational architecture to establish the network of ressources and humans to advance in this massive undertaking. The EMI will explore the chemical foundations of Life for a better human society within a thriving biosphere. + +# How is it related to the Digital Botanical Gardens Initiative ? + +We have started the Digital Botanical Gardens Initiative, abbreviated DBGI, as a pilot project for the EMI. You can find more details about the DBGI at . + + +# An Open Science project + +## Working with the garage door up + +A way of working briefly described by Andy Matuschak here https://notes.andymatuschak.org/z21cgR9K3UcQ5a7yPsj2RUim3oM2TzdBByZu. + +![](/assets/images/2022-12-25-18-13-17.png){max-width: 400px} + +## Open Notebook Science + +If we apply this "working with the garage door up" idea to a scientific research endeavor, we understand it as respecting the core concepts of open-science. These are in fact the principles of Open Notebook Science https://en.wikipedia.org/wiki/Open-notebook_science. + +For the projects of the DBGI, we will follow this approach in order to share early ideas and results but also the less shiny parts of the research projects. +Expect to find strange ideas, badly formulated text and poorly written code. However if you have time and interest, you should be able to participate at each step of the process. Hopefully, this will lead to enhanced collaboration and participation. Maybe yes, maybe not. Let's make it a methodological experiment! + +The pages of this website are written in Markdown and hosted on Github. You can edit them by clicking on the "Click here to edit this page on Github !" link at the bottom of the page diff --git a/notes/templates.open-notebook.dbgi.mvisani.md b/notes/templates.open-notebook.dbgi.mvisani.md new file mode 100644 index 0000000..049a339 --- /dev/null +++ b/notes/templates.open-notebook.dbgi.mvisani.md @@ -0,0 +1,27 @@ +--- +id: mz59v1zr7grqghkinjmk034 +title: Open Notebook Mvisani +desc: '' +updated: 1719324421258 +created: 1675937670620 +--- +# This is Marco's daily open-notebook. + +Today is {{ CURRENT_YEAR }}.{{ CURRENT_MONTH }}.{{ CURRENT_DAY }} + + +## Notes + + +## Todo today +- [ ] + +## Doing + + +## Done +* + + +## Todo tomorrow +- [ ] \ No newline at end of file diff --git a/notes/templates.open-notebook.emi.pmallard.md b/notes/templates.open-notebook.emi.pmallard.md new file mode 100644 index 0000000..5301c0b --- /dev/null +++ b/notes/templates.open-notebook.emi.pmallard.md @@ -0,0 +1,37 @@ +--- +id: 0wos8p8ksf7xckz27k0mswp +title: Pmallard +desc: '' +updated: 1717404523000 +created: 1717404432131 +--- + +# This is PMA's EMI open-notebook. + +Today is {{ CURRENT_YEAR }}.{{ CURRENT_MONTH }}.{{ CURRENT_DAY }} + +## Todo today + +### Have a look at the EMI discussion forum + - /~https://github.com/orgs/anticipated-chemistry-of-life/discussions +### +### + +## Doing + +## Paused + +## Done + +## Notes + +## Todo tomorrow, one day ... or never + +### +### +### + + +## Today I learned that + +- \ No newline at end of file diff --git a/open-notebook-emi-mjopiti.js b/open-notebook-emi-mjopiti.js new file mode 100644 index 0000000..8ff5770 --- /dev/null +++ b/open-notebook-emi-mjopiti.js @@ -0,0 +1,32 @@ +module.exports = { + OnWillCreate: { + /** + * This example sets a prefix of 'planning', and then adds a date hierarchy + * using the luxon module. + */ + setNameModifier() { + // This example sets a prefix of 'planning', and then adds a date + // hierarchy using the luxon module. + return { + name: "open-notebook.emi.mjopiti." + luxon.DateTime.local().toFormat("yyyy.MM.dd"), + promptUserForModification: true, + }; + }, + }, + OnCreate: { + setTitle(props) { + // This example will use the currentNoteName property, extract the + // yyyy.MM.dd date portion of the note name, and then reformat it with + // dashes. + return props.currentNoteName.split(".").slice(-3).join("-"); + }, + /** + * Apply a template to each note. NOTE: If you want to use this code, you + * will need a note file called `templates.planning-template.md` in your + * Dendron workspace. + */ + setTemplate: () => { + return "templates.open-notebook.emi.mjopiti"; + }, + }, +}; \ No newline at end of file diff --git a/open-notebook-emi-pmallard.js b/open-notebook-emi-pmallard.js new file mode 100644 index 0000000..cc3fbe9 --- /dev/null +++ b/open-notebook-emi-pmallard.js @@ -0,0 +1,32 @@ +module.exports = { + OnWillCreate: { + /** + * This example sets a prefix of 'planning', and then adds a date hierarchy + * using the luxon module. + */ + setNameModifier() { + // This example sets a prefix of 'planning', and then adds a date + // hierarchy using the luxon module. + return { + name: "open-notebook.emi.pmallard." + luxon.DateTime.local().toFormat("yyyy.MM.dd"), + promptUserForModification: true, + }; + }, + }, + OnCreate: { + setTitle(props) { + // This example will use the currentNoteName property, extract the + // yyyy.MM.dd date portion of the note name, and then reformat it with + // dashes. + return props.currentNoteName.split(".").slice(-3).join("-"); + }, + /** + * Apply a template to each note. NOTE: If you want to use this code, you + * will need a note file called `templates.planning-template.md` in your + * Dendron workspace. + */ + setTemplate: () => { + return "templates.open-notebook.emi.pmallard"; + }, + }, +}; \ No newline at end of file diff --git a/open-notebook-mvisani.js b/open-notebook-mvisani.js new file mode 100644 index 0000000..41b578a --- /dev/null +++ b/open-notebook-mvisani.js @@ -0,0 +1,32 @@ +module.exports = { + OnWillCreate: { + /** + * This example sets a prefix of 'planning', and then adds a date hierarchy + * using the luxon module. + */ + setNameModifier() { + // This example sets a prefix of 'planning', and then adds a date + // hierarchy using the luxon module. + return { + name: "open-notebook.dbgi.mvisani." + luxon.DateTime.local().toFormat("yyyy.MM.dd"), + promptUserForModification: true, + }; + }, + }, + OnCreate: { + setTitle(props) { + // This example will use the currentNoteName property, extract the + // yyyy.MM.dd date portion of the note name, and then reformat it with + // dashes. + return props.currentNoteName.split(".").slice(-3).join("-"); + }, + /** + * Apply a template to each note. NOTE: If you want to use this code, you + * will need a note file called `templates.planning-template.md` in your + * Dendron workspace. + */ + setTemplate: () => { + return "templates.open-notebook.dbgi.mvisani"; + }, + }, +}; \ No newline at end of file diff --git a/package-lock.json b/package-lock.json new file mode 100644 index 0000000..4afbff5 --- /dev/null +++ b/package-lock.json @@ -0,0 +1,13814 @@ +{ + "name": "acol-dws", + "version": "1.0.0", + "lockfileVersion": 2, + "requires": true, + "packages": { + "": { + "name": "acol-dws", + "version": "1.0.0", + "license": "ISC", + "dependencies": { + "@dendronhq/dendron-cli": "^0.119.0" + } + }, + "node_modules/@babel/code-frame": { + "version": "7.18.6", + "resolved": "https://registry.npmjs.org/@babel/code-frame/-/code-frame-7.18.6.tgz", + "integrity": "sha512-TDCmlK5eOvH+eH7cdAFlNXeVJqWIQ7gW9tY1GJIpUtFb6CmjVyq2VM3u71bOyR8CRihcCgMUYoDNyLXao3+70Q==", + "dependencies": { + "@babel/highlight": "^7.18.6" + }, + "engines": { + "node": 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"path-is-absolute": "^1.0.1", - "path-to-regexp": "^0.1.10", - "p-try": "^2.2.0", - "picocolors": "^1.1.0", - "parse5": "^6.0.1", - "picomatch": "^2.3.1", - "pino-std-serializers": "^3.2.0", - "pino": "^6.14.0", - "promise-inflight": "^1.0.1", - "pino-pretty": "^4.8.0", - "proxy-addr": "^2.0.7", - "process-warning": "^1.0.0", - "prompts": "^2.4.2", - "pseudomap": "^1.0.2", - "promise-retry": "^2.0.1", - "property-information": "^5.6.0", - "prebuild-install": "^7.1.2", - "qs": "^6.13.0", - "quick-format-unescaped": "^4.0.4", - "pump": "^3.0.2", - "quick-lru": "^5.1.1", - "querystring": "^0.2.1", - "range-parser": "^1.2.1", - "prismjs": "^1.27.0", - "rc": "^1.2.8", - "raw-body": "^2.5.2", - "react": "^17.0.2", - "react-dom": "^17.0.2", - "readable-stream": "^3.6.2", - "regenerator-runtime": "^0.14.1", - "rehype-parse": "^7.0.1", - "readdirp": "^3.6.0", - "rehype-autolink-headings": "^5.1.0", - "refractor": "^3.6.0", - "rehype-raw": "^5.1.0", - "rehype-slug": "^4.0.1", - "remark": "^12.0.1", - "rehype-stringify": "^8.0.0", - "remark-abbr": "^1.4.2", - "rehype-katex": "^5.0.0", - "remark-rehype": "^8.1.0", - "remark-gfm": "^1.0.0", - "remark-containers": "^1.2.0", - "remark-frontmatter": "^2.0.0", - "remark-toc": "^7.2.0", - "remark-parse": "^8.0.3", - "remark-math": "^3.0.1", - "remark-stringify": "^9.0.1", - "remark-variables": "^1.4.9", - "remove-trailing-slash": "^0.1.1", - "repeat-string": "^1.6.1", - "require-directory": "^2.1.1", - "require-main-filename": "^2.0.0", - "remark-wiki-link": "^0.0.4", - "require-from-string": "^2.0.2", - "resolve-alpn": "^1.2.1", - "responselike": "^2.0.1", - "resolve-from": "^5.0.0", - "restore-cursor": "^3.1.0", - "remark-footnotes": "^2.0.0", - "rfdc": "^1.4.1", - "rimraf": "^3.0.2", - "retry": "^0.12.0", - "rsync": "^0.6.1", - "safer-buffer": "^2.1.2", - "robust-predicates": "^3.0.2", - "scheduler": "^0.20.2", - "section-matter": "^1.0.0", - "send": "^0.19.0", - "serve-static": "^1.16.2", - "shebang-command": "^2.0.0", - "semver": "^7.6.3", - "set-function-length": "^1.2.2", - "set-blocking": "^2.0.0", - "shebang-regex": "^3.0.0", - "rw": "^1.3.3", - "setprototypeof": "^1.2.0", - "side-channel": "^1.0.6", - "simple-get": "^4.0.1", - "signal-exit": "^3.0.7", - "simple-concat": "^1.0.1", - "safe-buffer": "^5.2.1", - "simple-git": "^3.27.0", - "sisteransi": "^1.0.5", - "smart-buffer": "^4.2.0", - "socks": "^2.8.3", - "space-separated-tokens": "^1.1.5", - "source-map": "^0.6.1", - "socks-proxy-agent": "^6.2.1", - "split2": "^3.2.2", - "sonic-boom": "^1.4.1", - "sprintf-js": "^1.1.3", - "state-toggle": "^1.0.3", - "spark-md5": "^3.0.2", - "ssri": "^8.0.1", - "stringify-entities": "^3.1.0", - "string_decoder": "^1.3.0", - "sqlite3": "^5.1.7", - "stream": "^0.0.2", - "strip-eof": "^1.0.0", - "statuses": "^2.0.1", - "strip-ansi": "^6.0.1", - "strip-final-newline": "^2.0.0", - "string-width": "^4.2.3", - "strip-json-comments": "^3.1.1", - "tar-stream": "^2.2.0", - "supports-color": "^7.2.0", - "tar": "^6.2.1", - "tar-fs": "^2.1.1", - "strip-bom-string": "^1.0.0", - "style-to-object": "^0.3.0", - "title": "^3.5.3", - "textextensions": "^5.16.0", - "through2": "^4.0.2", - "to-regex-range": "^5.0.1", - "titleize": "^1.0.0", - "trim": "^0.0.1", - "to-vfile": "^6.1.0", - "tmp": "^0.2.3", - "tr46": "^0.0.3", - "tslib": "^1.14.1", - "toidentifier": "^1.0.1", - "trough": "^1.0.5", - "tunnel-agent": "^0.6.0", - "type-is": "^1.6.18", - "ts-json-schema-generator": "^0.95.0", - "unherit": "^1.1.3", - "typedarray": "^0.0.6", - "unist-builder": "^2.0.3", - "uglify-js": "^3.19.3", - "trim-trailing-lines": "^1.1.4", - "unique-filename": "^1.1.1", - "unique-slug": "^2.0.2", - "unified-engine": "^8.2.0", - "unist-util-find-after": "^3.0.0", - "unist-util-generated": "^1.1.6", - "unist-util-remove-position": "^2.0.1", - "unist-util-inspect": "^5.0.1", - "typescript": "^4.3.5", - "unist-util-position": "^3.1.0", - "unist-util-visit": "^2.0.3", - "unist-util-visit-parents": "^3.1.1", - "unist-util-is": "^4.1.0", - "unist-util-select": "^3.0.4", - "unist-util-map": "^1.0.5", - "universalify": "^2.0.1", - "unified": "^9.2.2", - "universal-user-agent": "^6.0.1", - "unpipe": "^1.0.0", - "unist-util-stringify-position": "^2.0.3", - "vary": "^1.1.2", - "utils-merge": "^1.0.1", - "vfile-reporter": "^6.0.2", - "vfile-sort": "^2.2.2", - "vfile": "^4.2.1", - "vfile-location": "^3.2.0", - "url-template": "^2.0.8", - "vfile-statistics": "^1.1.4", - "util-deprecate": "^1.0.2", - "wcwidth": "^1.0.1", - "uuid": "^8.3.2", - "vfile-message": "^2.0.4", - "wide-align": "^1.1.5", - "which-module": "^2.0.1", - "whatwg-url": "^5.0.0", - "web-namespaces": "^1.1.4", - "wordwrap": "^1.0.0", - "vscode-uri": "^3.0.8", - "yallist": "^4.0.0", - "wrappy": "^1.0.2", - "wrap-ansi": "^6.2.0", - "y18n": "^4.0.3", - "xtend": "^4.0.2", - "which": "^2.0.2", - "yaml": "^1.10.2", - "yargs": "^15.4.1", - "zod": "^3.19.1", - "yaml-unist-parser": "^1.3.1", - "webidl-conversions": "^3.0.1", - "yargs-parser": "^18.1.3", - "zwitch": "^1.0.5", - "zod-validation-error": "^0.1.1" - }, - "devDependencies": {}, "scripts": { "test": "echo \"Error: no test specified\" && exit 1" }, @@ -617,5 +16,8 @@ "bugs": { "url": "/~https://github.com/anticipated-chemistry-of-life/acol-dws/issues" }, - "homepage": "/~https://github.com/anticipated-chemistry-of-life/acol-dws#readme" -} + "homepage": "/~https://github.com/anticipated-chemistry-of-life/acol-dws#readme", + "dependencies": { + "@dendronhq/dendron-cli": "^0.119.0" + } +} \ No newline at end of file diff --git a/publish.yml b/publish.yml new file mode 100644 index 0000000..9f33625 --- /dev/null +++ b/publish.yml @@ -0,0 +1,52 @@ +name: Build Dendron Static Site + +on: + workflow_dispatch: # Enables on-demand/manual triggering + push: + branches: + - main + +jobs: + build: + runs-on: ubuntu-latest + steps: + - name: Checkout source + uses: actions/checkout@v2 + with: + fetch-depth: 0 + + - name: Restore Node modules cache + uses: actions/cache@v2 + id: node-modules-cache + with: + path: | + node_modules + .next/* + !.next/.next/cache + !.next/.env.* + key: ${{ runner.os }}-dendronv2-${{ hashFiles('**/yarn.lock', '**/package-lock.json') }} + + - name: Install dependencies + run: yarn + + - name: Initialize or pull nextjs template + run: "(test -d .next) && (echo 'updating dendron next...' && cd .next && git reset --hard && git pull && yarn && cd ..) || (echo 'init dendron next' && yarn dendron publish init)" + + - name: Restore Next cache + uses: actions/cache@v2 + with: + path: .next/.next/cache + # Generate a new cache whenever packages or source files change. + key: ${{ runner.os }}-nextjs-${{ hashFiles('.next/yarn.lock', '.next/package-lock.json') }}-${{ hashFiles('.next/**.[jt]s', '.next/**.[jt]sx') }} + + - name: Export notes + run: yarn dendron publish export --target github --yes + + - name: Deploy site + uses: peaceiris/actions-gh-pages@v3 + with: + github_token: ${{ secrets.GITHUB_TOKEN }} + publish_branch: pages + publish_dir: docs/ + force_orphan: true + #cname: example.com \ No newline at end of file diff --git a/workflows/publish.yml b/workflows/publish.yml new file mode 100644 index 0000000..9f33625 --- /dev/null +++ b/workflows/publish.yml @@ -0,0 +1,52 @@ +name: Build Dendron Static Site + +on: + workflow_dispatch: # Enables on-demand/manual triggering + push: + branches: + - main + +jobs: + build: + runs-on: ubuntu-latest + steps: + - name: Checkout source + uses: actions/checkout@v2 + with: + fetch-depth: 0 + + - name: Restore Node modules cache + uses: actions/cache@v2 + id: node-modules-cache + with: + path: | + node_modules + .next/* + !.next/.next/cache + !.next/.env.* + key: ${{ runner.os }}-dendronv2-${{ hashFiles('**/yarn.lock', '**/package-lock.json') }} + + - name: Install dependencies + run: yarn + + - name: Initialize or pull nextjs template + run: "(test -d .next) && (echo 'updating dendron next...' && cd .next && git reset --hard && git pull && yarn && cd ..) || (echo 'init dendron next' && yarn dendron publish init)" + + - name: Restore Next cache + uses: actions/cache@v2 + with: + path: .next/.next/cache + # Generate a new cache whenever packages or source files change. + key: ${{ runner.os }}-nextjs-${{ hashFiles('.next/yarn.lock', '.next/package-lock.json') }}-${{ hashFiles('.next/**.[jt]s', '.next/**.[jt]sx') }} + + - name: Export notes + run: yarn dendron publish export --target github --yes + + - name: Deploy site + uses: peaceiris/actions-gh-pages@v3 + with: + github_token: ${{ secrets.GITHUB_TOKEN }} + publish_branch: pages + publish_dir: docs/ + force_orphan: true + #cname: example.com \ No newline at end of file