templated from emi

.gitignore

@@ -3,4 +3,6 @@ node_modules
 build
 seeds
 .next
-pods/service-connections
+pods/service-connections
+
+.dendron.cache.*

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/

dendron.code-workspace

@@ -34,4 +34,4 @@
       "mushan.vscode-paste-image"
     ]
   }
-}
+}

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

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";
+    },
+  },
+};

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";
+    },
+  },
+};

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";
+        },
+    },
+};

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/)

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)

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.
+

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.

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).

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: 
+      - <?xml version="1.0" encoding="UTF-8"?><batch mzmine_version="4.1.0">
+
+Several batchsteps:
+      - <batchstep method="io.github.mzmine.modules.io.import_rawdata_bruker_tdf.TDFImportModule" parameter_version="1">
+          <parameter name="File names">
+              <file>/Path/to/directory/for/files</file>
+          </parameter>
+        </batchstep>
+? 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.
+  -> <preferences>
+        ....
+        <parameter name="username">robinschmid</parameter> 
+     </preferences>
+
+[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 <arg>    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
+  ->     <batchstep method="io.github.mzmine.modules.io.import_rawdata_bruker_tdf.TDFImportModule" parameter_version="1">
+            <parameter name="File names">
+                <file>/home/jopitim/test/cuso_batch_00001</file>
+            </parameter>
+        </batchstep>
+      (Line ~100)
+  -> <batchstep method="io.github.mzmine.modules.dataanalysis.feat_ms2_similarity_intra.IntraFeatureRowMs2SimilarityModule" parameter_version="1">
+        <parameter name="Feature lists" type="BATCH_LAST_FEATURELISTS"/>
+        <parameter name="Export to file" selected="false">
+            <current_file>/home/jopitim/test/mapp_batch_00106/Untitled_intra_row_MS2similarity</current_file>
+        </parameter>
+        <parameter name="m/z tolerance (MS2)">
+            <absolutetolerance>0.003</absolutetolerance>
+            <ppmtolerance>10.0</ppmtolerance>
+        </parameter>
+        <parameter name="Minimum signals">4</parameter>
+        <parameter name="Signal filters">
+            <parameter name="Remove residual precursor m/z" selected="true">10.0</parameter>
+            <parameter name="Crop to top N signals">250</parameter>
+            <parameter name="Signal threshold (intensity filter)">50</parameter>
+            <parameter name="Intensity filter at &gt;N signals">0.98</parameter>
+        </parameter>
+    </batchstep>
+    (line ~500)
+
+        
+## Todo tomorrow, one day ... or never
+
+###
+###
+###
+
+
+## Today I learned that
+
+-