Updated scripts and services

vault/Master-Works.Edouard-Brülhart.Scripts.Python.Pictures_manager.md

@@ -2,6 +2,26 @@
 id: drw6wxmq7cgp7sg08uf56rq
 title: Pictures_manager
 desc: ''
-updated: 1718360291283
+updated: 1719489875729
 created: 1718360291283
 ---
+
+Pictures_manager scripts permits to collect and treat metadata and pictures coming from [[Master-Works.Edouard-Brülhart.Services.QField]]:
+
+- It downloads the collection layers, convert them in CSV files
+
+- Checks that geographic coordinates are in the correct format, and if not convert them to suit the global geographic system (EPSG:4026)
+
+- Downloads the pictures and delete them from the collection server in order to keep the collection server clean
+
+- Controls if pictures are small enough, and if not compresses them
+
+- Add time, geographic coordinates and EMI code in the pictures metadata to make them ready for iNaturalist upload
+
+- Adds all these related metadata to the [[Master-Works.Edouard-Brülhart.Services.Directus]] database
+
+- Creates a copy of these pictures (possiblity to share them using nextcloud using the script)
+
+- Creates one folder for each observation containing the related pictures, that serve as input for the [[Master-Works.Edouard-Brülhart.Scripts.Python.iNaturalist_import_bot]] script
+
+You can find the source code [here](https://github.com/digital-botanical-gardens-initiative/Pictures_manager).

vault/Master-Works.Edouard-Brülhart.Scripts.Python.gpkg-creator.md

@@ -2,10 +2,10 @@
 id: ozicr87gyzuelakrzrb92fc
 title: gpkg-creator
 desc: ''
-updated: 1719414572755
+updated: 1719488538961
 created: 1719414008348
 ---
-The gpkg-creator script permits to deploy the QGIS plugin we use to create the layers for our collection cessions.
+The gpkg-creator script permits to deploy the QGIS plugin we use to create the layers for our collection sessions.
 
 You can install this plugin directly inside the QGIS interface under the name of "DBGI". You can also download it [here](https://github.com/digital-botanical-gardens-initiative/gpkg-creator/releases) and install it manually.
 

vault/Master-Works.Edouard-Brülhart.Scripts.Python.iNaturalist_import_bot.md

@@ -2,6 +2,11 @@
 id: gr7dr9ty3pmvc7y9xqmomzj
 title: iNaturalist_import_bot
 desc: ''
-updated: 1718360387011
+updated: 1719489086630
 created: 1718360387011
 ---
+
+iNaturalist_import_bot is a python script that permits to upload iNaturalist observations from QField metadata automatically. It takes as input pictures managed by [[Master-Works.Edouard-Brülhart.Scripts.Python.Pictures_manager]] script, coming from [[Master-Works.Edouard-Brülhart.Services.QFieldCloud]].
+
+You can see the source code [here](https://github.com/digital-botanical-gardens-initiative/iNaturalist_import_bot)
+

vault/Master-Works.Edouard-Brülhart.Scripts.Python.inat-fetcher.md

@@ -2,8 +2,10 @@
 id: 3bls9c5p4unqddel8t5qh41
 title: inat-fetcher
 desc: ''
-updated: 1719487425247
+updated: 1719488856995
 created: 1718355670082
 ---
+The inat-fetcher script uses the [[Master-Works.Edouard-Brülhart.Services.iNaturalist]] API to fetch [[Master-Works.Edouard-Brülhart.Services.iNaturalist]] observations for EMI projects everyday. It will add or update them to the [[Master-Works.Edouard-Brülhart.Services.Directus]] database.
+
+You can find the source code [here](https://github.com/digital-botanical-gardens-initiative/inat-fetcher).
 
-[[Bachelor-Works.Héloïse-Coen.Bachelor Thesis.report]]

vault/Master-Works.Edouard-Brülhart.Scripts.Python.ms-metadata-fetcher.md

@@ -2,6 +2,10 @@
 id: 203775wmsv2vxu1ng2jl2ic
 title: ms-metadata-fetcher
 desc: ''
-updated: 1719413980982
+updated: 1719489289984
 created: 1719413980982
 ---
+
+ms-metadata-fetcher script is a python script that makes API calls to [[Master-Works.Edouard-Brülhart.Services.Directus]] instance, in order to collect all metadata for specific samples. These informations are necessary to perform [[Master-Works.Edouard-Brülhart.Mass-spectrometry]] data processing.
+
+You can find the source code [here](https://github.com/digital-botanical-gardens-initiative/ms-metadata-fetcher).

vault/Master-Works.Edouard-Brülhart.Services.Directus.md

@@ -2,6 +2,10 @@
 id: ieyeybee3t9qu8mfy5lkpth
 title: Directus
 desc: ''
-updated: 1718357846913
+updated: 1719490223437
 created: 1718357846913
 ---
+
+[Directus](https://directus.io/) is the nocode interface we use as overlayer of our [[Master-Works.Edouard-Brülhart.Services.PostgreSQL]] database. It permits to make our database easily available online and to make API requests to it.
+
+We use [[Master-Works.Edouard-Brülhart.Scripts.directus-db]] script to create both [[Master-Works.Edouard-Brülhart.Services.PostgreSQL]] and [[Master-Works.Edouard-Brülhart.Services.Directus]] instances on our laboratory server.

vault/Master-Works.Edouard-Brülhart.Services.MS-sample-list-creator.md

@@ -2,6 +2,20 @@
 id: gijexvusskxt9okbdesvqdr
 title: MS-sample-list-creator
 desc: ''
-updated: 1719410350415
+updated: 1719492333484
 created: 1719410350415
 ---
+
+MS-sample-list-creator is a software that creates [[Master-Works.Edouard-Brülhart.Mass-spectrometry]] sample lists and adds the MS related metadata to the [[Master-Works.Edouard-Brülhart.Services.Directus]] database:
+
+- Asks directus credentials and needed metadata (operator, mass spectrometer ID, LC rack size, injection volume, data directory, method, etc)
+
+- Asks the name of the rack the user wants to fill
+
+- Permits to enter aliquots IDs manually, or to scan them using an external USB QR code scanner
+
+- Once all aliquots have been entered, generates a CSV with all the positions and needed metadata and adds these metadata do [[Master-Works.Edouard-Brülhart.Services.Directus]] database
+
+The software can be downloaded [here](https://github.com/digital-botanical-gardens-initiative/ms-sample-list-creator/releases).
+
+The source code is available [here](https://github.com/digital-botanical-gardens-initiative/ms-sample-list-creator).

vault/Master-Works.Edouard-Brülhart.Services.PostgreSQL.md

@@ -2,6 +2,8 @@
 id: cyv7yuh42dmqjbitgmqdlx7
 title: PostgreSQL
 desc: ''
-updated: 1718357832848
+updated: 1719492523846
 created: 1718357832848
 ---
+
+[PosgreSQL](https://www.postgresql.org/) is the relational database system we use to store all the EMI collection data. It has [[Master-Works.Edouard-Brülhart.Services.Directus]] as nocode overlayer to have a graphical web interface and access the [[Master-Works.Edouard-Brülhart.Database]] using API requests.

vault/Master-Works.Edouard-Brülhart.Services.QField.md

@@ -2,6 +2,13 @@
 id: w4qmirl0lfwt4035zizh3vt
 title: QField
 desc: ''
-updated: 1718360146846
+updated: 1719492695648
 created: 1718360146846
 ---
+
+QField is the field collection application we actually use for the EMI collection campains. You can download QField for QGIS on the appstore/playstore
+
+- IOS: [QField for QGIS IOS](https://apps.apple.com/us/app/qfield-for-qgis/id1531726814)
+- Android: [QField for QGIS Android](https://play.google.com/store/apps/details?id=ch.opengis.qfield&pli=1)
+
+Alternatively, on Android phones, you can download the APK file from [https://github.com/opengisch/QField/releases](https://github.com/opengisch/QField/releases)

vault/Master-Works.Edouard-Brülhart.Services.QFieldCloud.md

@@ -2,6 +2,10 @@
 id: 6c0o64alpn9ytm0qaxdfa9a
 title: QFieldCloud
 desc: ''
-updated: 1718360204611
+updated: 1719492899812
 created: 1718360204611
 ---
+
+QFieldCloud is our collection server. It permits to make the link between [[Master-Works.Edouard-Brülhart.Services.QGIS]], the computer application, and [[Master-Works.Edouard-Brülhart.Services.QField]], the field application. It also permits to collect data simultaneously on multiple devices.
+
+You can find the scripts we use to deploy it as a self-hosted instance [here](https://github.com/opengisch/qfieldcloud).

vault/Master-Works.Edouard-Brülhart.Services.QGIS.md

@@ -2,6 +2,10 @@
 id: ft1bl5lh1b90k7um0hb0xzk
 title: QGIS
 desc: ''
-updated: 1718557954125
+updated: 1719492999925
 created: 1718557954125
 ---
+
+QGIS (Quantum GIS) permits to create and manage the EMI collection projects on a computer before collection.
+
+You can download QGIS [here](https://qgis.org/fr/site/forusers/download.html).

vault/Master-Works.Edouard-Brülhart.Services.label-creator.md

@@ -2,6 +2,24 @@
 id: szi7vn6sgd6kpo53xrbiio8
 title: label-creator
 desc: ''
-updated: 1718354426445
+updated: 1719491622545
 created: 1718354426445
 ---
+
+label-creator is a little software that manages all the needed labels for the EMI projects:
+
+- Sample labels: Creates unique labels for each EMI project and adds them to the database
+
+- Mobiler containers labels: Creates unique mobile containers labels and adds them to the database
+
+- Static containers labels: Creates unique static containers labels and adds them to the database
+
+- Generic labels: Creates labels from a CSV file
+
+- Add a new site: Permits to add new university to the database as storage site for collections
+
+The software will generate a pdf containing all the labels formatted to fit [Avery L4732](https://www.avery.co.uk/product/mini-multipurpose-labels-l4732rev-25) labels sheets
+
+You can download this software [here](https://github.com/digital-botanical-gardens-initiative/label-creator/releases).
+
+You can find the source code [here](https://github.com/digital-botanical-gardens-initiative/label-creator).

vault/Master-Works.Edouard-Brülhart.Services.md

@@ -2,6 +2,8 @@
 id: byhm3lcwcs1rvvphzc8paab
 title: Services
 desc: ''
-updated: 1718357832856
+updated: 1719491816927
 created: 1718357832856
 ---
+
+This category refers all the services that are used to perform the EMI workflow from specimen to spectra.