Develop

.github/ISSUE_TEMPLATE/recipe_template.yml

@@ -0,0 +1,145 @@
+name: Recipe Template
+description: Please use this template to submit your new recipes
+title: "Recipe title"
+body:
+  - type: markdown
+    attributes:
+      value: |
+        Thanks for providing content for the FAIR Cookbook!
+  - type: dropdown
+    id: recipe-type
+    attributes:
+      label: Recipe Type
+      multiple: true
+      description: 
+      options:
+        - Background information
+        - Experience Report / Applied Example
+        - Guidance
+        - Hands-on
+        - Inventory
+        - Technical Guidance
+        - Other
+    validations:
+      required: true
+  - type: dropdown
+    id: audience
+    attributes:
+      label: Audience
+      multiple: true
+      description: Who is your target audience?
+      options:
+        - Bioinformatician
+        - Chemoinformatician
+        - Data Consumer
+        - Data Curator
+        - Data Engineer
+        - Data Manager
+        - Data Producer
+        - Data Scientist
+        - Data Steward
+        - Everyone
+        - Funder
+        - Ontologist
+        - Principal Investigator
+        - Procurement Officer
+        - Software Engineer
+        - Software Developer
+        - System Administrator
+        - Terminology Manager
+    validations:
+      required: false
+  - type: dropdown
+    id: executable_code
+    attributes:
+      label: Executable Code
+      description: Does your recipe have executable codes?
+      options:
+        - "Yes"
+        - "No"
+    validations:
+      required: false
+  - type: textarea
+    id: main_objectives
+    attributes:
+      label: Main Objectives
+      description: Please explain the main objective of the recipe. 
+    validations:
+      required: true
+  - type: textarea
+    id: graphical_overview
+    attributes:
+      label: Graphical Overview
+      description: If you have a graphical overview, please upload it. Tip, You can attach files by clicking this area to highlight it and then dragging files in.
+    validations:
+      required: false
+  - type: textarea
+    id: requirements
+    attributes:
+      label: Requirements
+      description: Please specify the technical and knowledge requirements to implement this recipe.
+    validations:
+      required: false
+  - type: textarea
+    id: fairification_objectives
+    attributes:
+      label: FAIRification Objectives, Inputs and Outputs
+      description: Examples of objectives are "formatting" and "text annotation". An example of input is "Waters MS format". An example of output is "mzML".
+    validations:
+      required: true
+  - type: textarea
+    id: data-standards
+    attributes:
+      label: Table of Data Standards
+      description: An example of "Data Formats" is "mzML". An example of "Terminologies" is "PSI-MS". 
+    validations:
+      required: false
+  - type: textarea
+    id: introduction
+    attributes:
+      label: Introduction
+      description: 
+    validations:
+      required: true
+  - type: textarea
+    id: ingredients
+    attributes:
+      label: Ingredients
+      description: Add a list of tools and software required to implement the recipe. 
+    validations:
+      required: false
+  - type: textarea
+    id: body
+    attributes:
+      label: Recipe body or step-by-step guidance 
+      description: 
+    validations:
+      required: true
+  - type: textarea
+    id: conclusion
+    attributes:
+      label: Conclusion
+      description: 
+    validations:
+      required: true
+  - type: textarea
+    id: read_next
+    attributes:
+      label: What to read next?
+      description: 
+    validations:
+      required: false
+  - type: textarea
+    id: references
+    attributes:
+      label: References
+      description: 
+    validations:
+      required: true
+  - type: textarea
+    id: authors
+    attributes:
+      label: Authors
+      description: 
+    validations:
+      required: true

_config.yml

@@ -9,7 +9,7 @@ exclude_patterns            : [.github/*, README.md, venv/*, node_modules/*, _co
 # Execution settings
 execute:
   execute_notebooks         : off  # Whether to execute notebooks at build time. Must be one of ("auto", "force", "cache", "off")
-  cache                     : ""  # A path to the jupyter cache that will be used to store execution artifacs. Defaults to `_build/.jupyter_cache/`
+  cache                     : ""  # A path to the jupyter cache that will be used to store execution artifacts. Defaults to `_build/.jupyter_cache/`
   exclude_patterns          : []  # A list of patterns to *skip* in execution (e.g. a notebook that takes a really long time)
 
 #######################################################################################

_ext/global_variables_fairplus.py

@@ -206,7 +206,7 @@
 "Hannah"            : { "github_handle" : "HEHurst",          "name" : "Hannah Hurst",               "orcid" : "",                           "affiliation" : "EMBL-EBI",                                        "type_of_affiliation" : "academia",         "elixir_node" : "embl"      }, 
 "Herman"            : { "github_handle" : "",                 "name" : "Herman Van Vlijmen",         "orcid" : "0000-0002-1915-3141",        "affiliation" : "Janssen",                                         "type_of_affiliation" : "efpia",            "elixir_node" : ""          }, 
 "Ibrahim"           : { "github_handle" : "iemam",            "name" : "Ibrahim Emam",               "orcid" : "0000-0002-7561-2787",        "affiliation" : "Imperial College London",                         "type_of_affiliation" : "academia",         "elixir_node" : "UK"        },
-"Isuru"             : { "github_handle" : "tburdett",         "name" : "Isuru Liyanage",             "orcid" : "0000-0002-4839-5158",        "affiliation" : "EMBL-EBI",                                        "type_of_affiliation" : "academia",         "elixir_node" : "embl"      },
+"Isuru"             : { "github_handle" : "",         "name" : "Isuru Liyanage",             "orcid" : "0000-0002-4839-5158",        "affiliation" : "EMBL-EBI",                                        "type_of_affiliation" : "academia",         "elixir_node" : "embl"      },
 "Ines"              : { "github_handle" : "imsachaves",       "name" : "Inês Chaves",                "orcid" : "0000-0001-7569-3495",        "affiliation" : "ITQB, NOVA University of Lisbon",                 "type_of_affiliation" : "academia",         "elixir_node" : "PT"        },
 "Jean"              : { "github_handle" : "",                 "name" : "Jean-Marc Neefs",            "orcid" : "",                           "affiliation" : "Janssen",                                         "type_of_affiliation" : "efpia",            "elixir_node" : ""          },
 "Jolanda"           : { "github_handle" : "JolandaS",         "name" : "Jolanda Strubel",            "orcid" : "0000-0001-6675-4639",        "affiliation" : "The Hyve",                                        "type_of_affiliation" : "sme",              "elixir_node" : ""          }, 
@@ -222,7 +222,7 @@
 "Mark"              : { "github_handle" : "",                 "name" : "Mark Ibberson",              "orcid" : "0000-0003-3152-5670",        "affiliation" : "SIB",                                             "type_of_affiliation" : "academia",         "elixir_node" : "CH"        }, 
 "Martin"            : { "github_handle" : "",                 "name" : "Martin Cook",                "orcid" : "",                           "affiliation" : "Elixir Europe",                                   "type_of_affiliation" : "academia",         "elixir_node" : "CH"        },
 "Melanie"           : { "github_handle" : "mcourtot",         "name" : "Melanie Courtot",            "orcid" : "0000-0002-9551-6370",        "affiliation" : "EMBL-EBI",                                        "type_of_affiliation" : "academia",         "elixir_node" : "UK"        }, 
-"Mike"              : { "github_handle" : "mikedarcy",        "name" : "Mike d'Arcy",                "orcid" : "0000-0003-2280-917X",        "affiliation" : "University of Southern California",               "type_of_affiliation" : "academia",         "elixir_node" : "embl"      }, 
+"Mike"              : { "github_handle" : "mikedarcy",        "name" : "Mike d'Arcy",                "orcid" : "0000-0003-2280-917X",        "affiliation" : "University of Southern California",               "type_of_affiliation" : "academia",         "elixir_node" : ""      }, 
 "NickJuty"          : { "github_handle" : "nsjuty",           "name" : "Nick Juty",                  "orcid" : "0000-0002-2036-8350",        "affiliation" : "University of Manchester",                        "type_of_affiliation" : "academia",         "elixir_node" : "UK"        }, 
 "NickLynch"         : { "github_handle" : "nicklynch",        "name" : "Nick Lynch",                 "orcid" : "0000-0002-8997-5298",        "affiliation" : "OpenPhacts",                                      "type_of_affiliation" : "sme",              "elixir_node" : ""          }, 
 "Nicolas"	        : { "github_handle" : "",	              "name" : "Nicolas Francillonne",	     "orcid" : "",	                         "affiliation" : "Université Paris-Saclay, INRAE, BioinfOmics",     "type_of_affiliation" : "academia",	        "elixir_node" : "FR"	    },
@@ -235,7 +235,7 @@
 "Philippe"          : { "github_handle" : "proccaserra",      "name" : "Philippe Rocca-Serra",       "orcid" : "0000-0001-9853-5668",        "affiliation" : "University of Oxford",                            "type_of_affiliation" : "academia",         "elixir_node" : "UK"        }, 
 "Ratnesh"           : { "github_handle" : "",                 "name" : "Ratnesh Sahay",              "orcid" : "",                           "affiliation" : "Astra-Zeneca",                                    "type_of_affiliation" : "efpia",            "elixir_node" : ""          }, 
 "Robert"            : { "github_handle" : "robertgiessmann",  "name" : "Robert Giessmann",           "orcid" : "0000-0002-0254-1500",        "affiliation" : "Bayer AG",                                        "type_of_affiliation" : "efpia",            "elixir_node" : ""          }, 
-"Ronald"            : { "github_handle" : "ronaldcornet",     "name" : "Ronald Cornet",              "orcid" : "0000-0002-1704-5980",        "affiliation" : "Amsterdam UMC", 									"type_of_affiliation" : "academia",         "elixir_node" : ""          },
+"Ronald"            : { "github_handle" : "ronaldcornet",     "name" : "Ronald Cornet",              "orcid" : "0000-0002-1704-5980",        "affiliation" : "Amsterdam UMC", 					"type_of_affiliation" : "academia",         "elixir_node" : "NL"          },
 "Rudi"              : { "github_handle" : "rverbeec",         "name" : "Rudi Verbeeck",              "orcid" : "0000-0001-5445-6095",        "affiliation" : "Janssen",                                         "type_of_affiliation" : "efpia",            "elixir_node" : ""          }, 
 "Salvador"          : { "github_handle" : "scapella",         "name" : "Salvador Capella Gutierrez", "orcid" : "0000-0002-0309-604X",        "affiliation" : "Barcelona Supercomputing Centre",                 "type_of_affiliation" : "academia",         "elixir_node" : "ES"        }, 
 "Scott"             : { "github_handle" : "",                 "name" : "Scott Lusher",               "orcid" : "",                           "affiliation" : "Janssen",                                         "type_of_affiliation" : "efpia",            "elixir_node" : ""          },