Typo fixes

SPAAM-community · Mar 28, 2024 · 907778e · 907778e
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diff --git a/docs/source/how_to/autofill.md b/docs/source/how_to/autofill.md
@@ -52,7 +52,7 @@ project_name publication_year data_publication_doi sample_name archive archive_p
 
 You will notice that some columns are missing information, especially in the sample metadata table (in this example, `samples.tsv`). Despite our best efforts, not all information is made available through ENA, and it will be up to you to fill these missing columns, from the original publication, its supplementary material, or elsewhere.
 You can do it in your favorite text editor, or table editor (like LibreOffice Calc, or Excel).
-Please refer to the AncientMetagenomeDir wiki for information on this process: [https://github.com/SPAAM-community/AncientMetagenomeDir/wiki](github.com/SPAAM-community/AncientMetagenomeDir/wiki).
+Please refer to the AncientMetagenomeDir wiki for information on this process: [https://github.com/SPAAM-community/AncientMetagenomeDir/wiki](https://github.com/SPAAM-community/AncientMetagenomeDir/wiki).
 
 > ⚠️ The sample and library names reported on sequencing archives (ENA, SRA, ...) might not be the same as the one list in the original article. Please double check before proceeding further.
 

diff --git a/docs/source/how_to/convert.md b/docs/source/how_to/convert.md
@@ -12,7 +12,7 @@ You typically will use `convert` if you are a command-line power user, and have
 
 ## How
 
-The following description assumes that you have already have a AncientMetagenomeDir **samples** table that has been filtered to the samples you wish to run through a given pipeline(s).
+The following description assumes that you have already have an AncientMetagenomeDir **samples** table that has been filtered to the samples you wish to run through a given pipeline(s).
 
 > ⚠️ _The header, and present columns etc. should match exactly that on AncientMetagenomeDir, only rows may be removed._
 

diff --git a/docs/source/how_to/index.rst b/docs/source/how_to/index.rst
@@ -13,4 +13,5 @@ All 'How Tos' assume you have already installed AMDirT following the installatio
     convert
     validate
     autofill
+    merge
     miscellaneous
diff --git a/docs/source/how_to/merge.md b/docs/source/how_to/merge.md
@@ -2,7 +2,7 @@
 
 ## What
 
-Merges a user-supplied metadata table with the latest AncientMetagenomeDir master metadata tables, with on-the-fly [validation](validation.md).
+Merges a user-supplied metadata table with the latest AncientMetagenomeDir master metadata tables, with on-the-fly [validation](/how_to/validate).
 
 ## When
 
@@ -12,7 +12,7 @@ You typically only do this if preparing a pull request to the AncientMetagenomeD
 
 ## How
 
-The following description assumes you have already prepared a AncientMetagenomeDir **samples** or **libraries** table whose rows only consist of the header and new samples to be added.
+The following description assumes you have already prepared an AncientMetagenomeDir **samples** or **libraries** table whose rows only consist of the header and new samples to be added.
 
 > ⚠️ _The header, and present columns etc. should match exactly that on the corresponding AncientMetagenomeDir table_
 

diff --git a/docs/source/how_to/validate.md b/docs/source/how_to/validate.md
@@ -2,7 +2,7 @@
 
 ## What
 
-The purpose of the `validate` command is to check that a AncientMetagenomeDir metadata file confirms the specifications of the project.
+The purpose of the `validate` command is to check that an AncientMetagenomeDir metadata file confirms the specifications of the project.
 
 ## When
 

diff --git a/docs/source/tutorials/index.rst b/docs/source/tutorials/index.rst
@@ -1,12 +1,14 @@
 Tutorials
 =============================================
 
-Introductory tutorials for each sub-command can be found below in text and/or video format.
+Introductory tutorials for sub-commands can be found below in text and/or video format.
 
 All videos can be also found on the `SPAAM Community Youtube channel <https://www.youtube.com/@spaam-community>`_.
 
 All tutorials assume you have already installed AMDirT following the installation instructions (:doc:`/README`).
 
+Note that tutorials currently exist for user-facing commands, sub-commands such as `validate` and `autofill` are generally executed by users. For these please see the respective (:doc:`/how_to/index`) page.
+
 .. toctree::
     :maxdepth: 1
     :caption: Tutorials:

diff --git a/tests/data/libraries_schema.json b/tests/data/libraries_schema.json
@@ -38,13 +38,9 @@
         "$id": "#/items/properties/project_name",
         "type": "string",
         "title": "AncientMetagenomeDir key of the publication",
-        "description": "Format: surnameYYYY (if duplicate key but different publication, add b,c,d etc. as necessary). Must match a AncientMetagenomeDir samples table entry",
+        "description": "Format: surnameYYYY (if duplicate key but different publication, add b,c,d etc. as necessary). Must match an AncientMetagenomeDir samples table entry",
         "pattern": "^[a-zA-Z]+\\d{4}[b-z]?$",
-        "examples": [
-          "Warinner2014",
-          "Muhlemann2018",
-          "Muhlemann2018a"
-        ]
+        "examples": ["Warinner2014", "Muhlemann2018", "Muhlemann2018a"]
       },
       "publication_year": {
         "$id": "#/items/properties/publication_year",
@@ -53,70 +49,53 @@
         "maximum": 2100,
         "title": "Year of publication",
         "description": "Format: YYYY",
-        "examples": [
-          2014
-        ]
+        "examples": [2014]
       },
       "publication_doi": {
         "$id": "#/items/properties/publication_doi",
         "type": "string",
         "pattern": "^10.\\d{4,9}\\/[^,]+$",
         "title": "Digital Object Identifier (DOI) of the publication.",
-        "description": "A valid DOI code (not as an URL). Must match a AncientMetagenomeDir samples table entry",
-        "examples": [
-          "10.1038/ng.2906"
-        ]
+        "description": "A valid DOI code (not as an URL). Must match an AncientMetagenomeDir samples table entry",
+        "examples": ["10.1038/ng.2906"]
       },
       "sample_name": {
         "$id": "#/items/properties/sample_name",
         "type": "string",
         "title": "Name of the sample",
-        "description": "In most cases this should be the name of the host individual. Must match a AncientMetagenomeDir samples table entry",
-        "examples": [
-          "B61"
-        ]
+        "description": "In most cases this should be the name of the host individual. Must match an AncientMetagenomeDir samples table entry",
+        "examples": ["B61"]
       },
       "archive": {
         "$id": "#/items/properties/archive",
         "type": "string",
         "title": "Archiving platform",
         "description": "Name of the nucleotide data archiving platform",
         "$ref": "https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/archive.json",
-        "examples": [
-          "ENA"
-        ]
+        "examples": ["ENA"]
       },
       "archive_project": {
         "$id": "#/items/properties/archive_project",
         "type": "string",
         "title": "Archive project accession platform",
-        "description": "Name of the nucleotide data archiving platform. Must match a AncientMetagenomeDir samples table entry",
-        "examples": [
-          "PRJNA438985",
-          "mgp13354"
-        ]
+        "description": "Name of the nucleotide data archiving platform. Must match an AncientMetagenomeDir samples table entry",
+        "examples": ["PRJNA438985", "mgp13354"]
       },
       "archive_sample_accession": {
         "$id": "#/items/properties/archive_sample_accession",
         "type": "string",
         "pattern": "^[\\S]+$",
         "title": "Archive accession number",
-        "description": "Samples archive accession numbers, multiple records can be separated with commas. No spaces allowed. . Must match a AncientMetagenomeDir samples table entry",
-        "examples": [
-          "SRS473742,SRS473743,SRS473744,SRS473745"
-        ]
+        "description": "Samples archive accession numbers, multiple records can be separated with commas. No spaces allowed. . Must match an AncientMetagenomeDir samples table entry",
+        "examples": ["SRS473742,SRS473743,SRS473744,SRS473745"]
       },
       "library_name": {
         "$id": "#/items/properties/library_name",
         "type": "string",
         "pattern": "^[\\S]+$",
         "title": "Name of the sequencing library",
         "description": "Name of the sequencing library generated from the sample. Typically matches the corresponding FASTQ file name",
-        "examples": [
-          "ElSidron1_12056",
-          "DRT001.A0301",
-          "L1"
-        ]
+        "examples": ["ElSidron1_12056", "DRT001.A0301", "L1"]
       },
       "strand_type": {
         "$id": "#/items/properties/strand_type",
@@ -125,10 +104,7 @@
         "title": "Strandedness of library",
         "description": "Strandedness of the DNA in the library, i.e. whether single or double stranded.",
         "$ref": "https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/strand_type.json",
-        "examples": [
-          "single",
-          "double"
-        ]
+        "examples": ["single", "double"]
       },
       "library_polymerase": {
         "$id": "#/items/properties/library_polymerase",
@@ -145,36 +121,20 @@
       },
       "library_treatment": {
         "$id": "#/items/properties/library_treatment",
-        "type": [
-          "string",
-          "null"
-        ],
+        "type": ["string", "null"],
         "pattern": "^[\\S]+$",
         "title": "Name of damage-removal treatment",
         "description": "Name of any established damage-removal treatment that may have been performed.",
         "$ref": "https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_treatment.json",
-        "examples": [
-          "none",
-          "half-udg",
-          "full-udg"
-        ]
+        "examples": ["none", "half-udg", "full-udg"]
       },
       "library_concentration": {
         "$id": "#/items/properties/library_concentration",
-        "type": [
-          "integer",
-          "null"
-        ],
+        "type": ["integer", "null"],
         "minimum": 0,
         "title": "Number of pre-amplification DNA copies of library per microlitre",
         "description": "Number of pre-amplification DNA copies of library per microlitre as measured by qPCR. Can be used for contamination estimation against blanks",
-        "examples": [
-          "NA",
-          0,
-          9064000,
-          15730000,
-          1331500000
-        ]
+        "examples": ["NA", 0, 9064000, 15730000, 1331500000]
       },
       "instrument_model": {
         "$id": "#/items/properties/instrument_model",
@@ -196,51 +156,30 @@
         "title": "Sequencing layout of library",
         "description": "Sequencing layout of library, i.e. either single or paired end, based on ENA controlled vocabulary (https://www.ebi.ac.uk/ena/portal/api/controlledVocab?field=library_layout",
         "$ref": "https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_layout.json",
-        "examples": [
-          "PAIRED",
-          "SINGLE"
-        ]
+        "examples": ["PAIRED", "SINGLE"]
       },
       "library_strategy": {
         "$id": "#/items/properties/library_strategy",
         "type": "string",
         "title": "Type of sequencing library",
         "description": "Type of sequencing library. Whether shotgun sequenced (WGS) or enriched using 'Target-Capture' protocols and similar.",
         "$ref": "https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_strategy.json",
-        "examples": [
-          "WGS",
-          "Target-Capture",
-          "depletion",
-          "Unknown"
-        ]
+        "examples": ["WGS", "Target-Capture", "depletion", "Unknown"]
       },
       "read_count": {
         "$id": "#/items/properties/read_count",
-        "type": [
-          "integer",
-          "null"
-        ],
+        "type": ["integer", "null"],
         "title": "Number of reads or pairs in library",
         "description": "Number of reads or pairs in library, i.e. how deep sequenced. For paired end, count pairs (should be same number for both directions)",
-        "examples": [
-          "NA",
-          10000,
-          6900000,
-          123982
-        ]
+        "examples": ["NA", 10000, 6900000, 123982]
       },
       "archive_data_accession": {
         "$id": "#/items/properties/archive_data_accession",
         "type": "string",
         "pattern": "^[\\S]+$",
         "title": "Archive run accession number",
         "description": "Run archive accession numbers, single run accession per line. TODO: improve regex",
-        "examples": [
-          "SRR13263119",
-          "SRR13263120",
-          "ERR3003613",
-          "ERR3003661"
-        ]
+        "examples": ["SRR13263119", "SRR13263120", "ERR3003613", "ERR3003661"]
       },
       "download_links": {
         "$id": "#/items/properties/download_links",
@@ -266,18 +205,12 @@
       },
       "download_sizes": {
         "$id": "#/items/properties/download_sizes",
-        "type": [
-          "string",
-          "null"
-        ],
+        "type": ["string", "null"],
         "pattern": "^[0-9]+;[0-9]+;[0-9]+$|^[0-9]+;[0-9]+$|^[0-9]+$",
         "title": "File sizes of downloads",
         "description": "File sizes of corresponding download files in bytes, to allow calculation of HDD usage. Can be semi-colon separated list for paired end. TODO: improve regex",
-        "examples": [
-          "126181389",
-          "614385694;622383780"
-        ]
+        "examples": ["126181389", "614385694;622383780"]
       }
     }
   }
-}
+}
-Original file line number
+Diff line change
@@ Expand Up @@
     ## How
-    The following description assumes that you have already have a AncientMetagenomeDir **samples** table that has been filtered to the samples you wish to run through a given pipeline(s).
+    The following description assumes that you have already have an AncientMetagenomeDir **samples** table that has been filtered to the samples you wish to run through a given pipeline(s).
     > ⚠️ _The header, and present columns etc. should match exactly that on AncientMetagenomeDir, only rows may be removed._
@@ Expand Down @@