diff --git "a/vault/Master-Works.Edouard-Br\303\274lhart.Scripts.Python.Pictures_manager.md" "b/vault/Master-Works.Edouard-Br\303\274lhart.Scripts.Python.Pictures_manager.md" index a9ed1698844..47d95367196 100644 --- "a/vault/Master-Works.Edouard-Br\303\274lhart.Scripts.Python.Pictures_manager.md" +++ "b/vault/Master-Works.Edouard-Br\303\274lhart.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). \ No newline at end of file diff --git "a/vault/Master-Works.Edouard-Br\303\274lhart.Scripts.Python.gpkg-creator.md" "b/vault/Master-Works.Edouard-Br\303\274lhart.Scripts.Python.gpkg-creator.md" index cea1ab82dd9..5a1644c45f7 100644 --- "a/vault/Master-Works.Edouard-Br\303\274lhart.Scripts.Python.gpkg-creator.md" +++ "b/vault/Master-Works.Edouard-Br\303\274lhart.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. diff --git "a/vault/Master-Works.Edouard-Br\303\274lhart.Scripts.Python.iNaturalist_import_bot.md" "b/vault/Master-Works.Edouard-Br\303\274lhart.Scripts.Python.iNaturalist_import_bot.md" index 689aa9e1f3f..1a8ddb230b3 100644 --- "a/vault/Master-Works.Edouard-Br\303\274lhart.Scripts.Python.iNaturalist_import_bot.md" +++ "b/vault/Master-Works.Edouard-Br\303\274lhart.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) + diff --git "a/vault/Master-Works.Edouard-Br\303\274lhart.Scripts.Python.inat-fetcher.md" "b/vault/Master-Works.Edouard-Br\303\274lhart.Scripts.Python.inat-fetcher.md" index ff6a7e21ee9..9aa5e6a68e1 100644 --- "a/vault/Master-Works.Edouard-Br\303\274lhart.Scripts.Python.inat-fetcher.md" +++ "b/vault/Master-Works.Edouard-Br\303\274lhart.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]] \ No newline at end of file diff --git "a/vault/Master-Works.Edouard-Br\303\274lhart.Scripts.Python.ms-metadata-fetcher.md" "b/vault/Master-Works.Edouard-Br\303\274lhart.Scripts.Python.ms-metadata-fetcher.md" index dc0f91f29da..2bc97b01756 100644 --- "a/vault/Master-Works.Edouard-Br\303\274lhart.Scripts.Python.ms-metadata-fetcher.md" +++ "b/vault/Master-Works.Edouard-Br\303\274lhart.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). \ No newline at end of file diff --git "a/vault/Master-Works.Edouard-Br\303\274lhart.Services.Directus.md" "b/vault/Master-Works.Edouard-Br\303\274lhart.Services.Directus.md" index 596fd54fee8..9129c5cefc2 100644 --- "a/vault/Master-Works.Edouard-Br\303\274lhart.Services.Directus.md" +++ "b/vault/Master-Works.Edouard-Br\303\274lhart.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. \ No newline at end of file diff --git "a/vault/Master-Works.Edouard-Br\303\274lhart.Services.MS-sample-list-creator.md" "b/vault/Master-Works.Edouard-Br\303\274lhart.Services.MS-sample-list-creator.md" index f987dce4115..c200051ddf9 100644 --- "a/vault/Master-Works.Edouard-Br\303\274lhart.Services.MS-sample-list-creator.md" +++ "b/vault/Master-Works.Edouard-Br\303\274lhart.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). \ No newline at end of file diff --git "a/vault/Master-Works.Edouard-Br\303\274lhart.Services.PostgreSQL.md" "b/vault/Master-Works.Edouard-Br\303\274lhart.Services.PostgreSQL.md" index 614a21cfef7..06f79a7d5ed 100644 --- "a/vault/Master-Works.Edouard-Br\303\274lhart.Services.PostgreSQL.md" +++ "b/vault/Master-Works.Edouard-Br\303\274lhart.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. \ No newline at end of file diff --git "a/vault/Master-Works.Edouard-Br\303\274lhart.Services.QField.md" "b/vault/Master-Works.Edouard-Br\303\274lhart.Services.QField.md" index d0bf7adaef6..5dcc57c8974 100644 --- "a/vault/Master-Works.Edouard-Br\303\274lhart.Services.QField.md" +++ "b/vault/Master-Works.Edouard-Br\303\274lhart.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) \ No newline at end of file diff --git "a/vault/Master-Works.Edouard-Br\303\274lhart.Services.QFieldCloud.md" "b/vault/Master-Works.Edouard-Br\303\274lhart.Services.QFieldCloud.md" index bf927fa3d92..2f3fdf74c1c 100644 --- "a/vault/Master-Works.Edouard-Br\303\274lhart.Services.QFieldCloud.md" +++ "b/vault/Master-Works.Edouard-Br\303\274lhart.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). \ No newline at end of file diff --git "a/vault/Master-Works.Edouard-Br\303\274lhart.Services.QGIS.md" "b/vault/Master-Works.Edouard-Br\303\274lhart.Services.QGIS.md" index ab5bc362845..8ebfdeccc2d 100644 --- "a/vault/Master-Works.Edouard-Br\303\274lhart.Services.QGIS.md" +++ "b/vault/Master-Works.Edouard-Br\303\274lhart.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). \ No newline at end of file diff --git "a/vault/Master-Works.Edouard-Br\303\274lhart.Services.label-creator.md" "b/vault/Master-Works.Edouard-Br\303\274lhart.Services.label-creator.md" index c84aaef6bda..4774ad2a2fb 100644 --- "a/vault/Master-Works.Edouard-Br\303\274lhart.Services.label-creator.md" +++ "b/vault/Master-Works.Edouard-Br\303\274lhart.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). \ No newline at end of file diff --git "a/vault/Master-Works.Edouard-Br\303\274lhart.Services.md" "b/vault/Master-Works.Edouard-Br\303\274lhart.Services.md" index 9d6b9fa6052..8cde15e5666 100644 --- "a/vault/Master-Works.Edouard-Br\303\274lhart.Services.md" +++ "b/vault/Master-Works.Edouard-Br\303\274lhart.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. \ No newline at end of file