Merge pull request #8 from SouthGreenPlatform/test

check.yaml was not activated, make it works
Clean all yaml mistake that wen through due to lack of "check" ci

.github/workflows/build.yaml

@@ -17,8 +17,10 @@ concurrency:
 jobs:
 
   build:
-    runs-on: ubuntu-22.04
 
+    runs-on: ubuntu-22.04
+    #if: ${{ github.event.workflow_run.conclusion == 'success' }}
+
     steps:
       - uses: actions/checkout@v3
       - uses: r-lib/actions/setup-r@v2

.github/workflows/check.yaml

@@ -1,9 +1,9 @@
 name: check
 
-on: 
-  push:
-    paths:
-      - "staff/**.yaml"
+on: push
+#  push:
+#    paths:
+#      - "trombinoscope/staff/**"
 
 concurrency:
   group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}

.github/workflows/check_scripts/check_yaml.py

@@ -15,7 +15,6 @@ def validate_category(d,f):
 
 def check_bibtex_file(d, f):
     p = pathlib.Path(f).parent.parent / 'publication'
-    print(p)
     if 'bibtex' in d and d['bibtex']:
         return (p / d['bibtex']).exists()
     return True
@@ -31,12 +30,17 @@ def validate_orcid(d, f):
 
 def validate_url(d, f):
     regex = re.compile(r'^https?://')
-    try:
-        if re.search(regex, d['homepage']):
-            return False
-    except Exception:
+    if 'homepage' in d.keys():
+        if d['homepage'] is not None:
+            if re.search(regex, d['homepage']):
+                return True
+            else: # case value do not follow specification
+                return False
+        else: # case no value provided for homepage tag
+            return True
+    else: # case no homepage tag
         return True
-    return True
+
 
 
 

.github/workflows/check_scripts/images_exist.sh

@@ -12,9 +12,9 @@ awk '/^[[:blank:]]*image: / {
         if [[ $ymlfile == *TEMPLATE* ]]; then
             continue
         fi
+        imgfile=$(tr -dc '[[:print:]]' <<< "$imgfile") # remove non printable character
         if [ ! -e "$imgfile" ]; then
-            printf '%s (from %s) does not exist\n' \
-		    "$imgfile" "$ymlfile" >&2
+            echo  "Achtung: $imgfile (from $ymlfile) does not exist\n" >&2
             success=false
         fi
     done

trombinoscope/staff/TEMPLATE.yaml

@@ -38,7 +38,7 @@ workplace: XXX University
 #
 affiliation: CNRS/INRAE/etc
 #
-# The SouthGreen facility that you are part of. 
+# The SouthGreen facility that you are part of.
 #
 facility: iTrop
 #

trombinoscope/staff/alexis-dereeper.yaml

@@ -38,7 +38,7 @@ workplace: IRD Montpellier
 #
 affiliation: IRD
 #
-# The SouthGreen facility that you are part of. 
+# The SouthGreen facility that you are part of.
 #
 facility: SouthGreen
 #
@@ -47,7 +47,7 @@ facility: SouthGreen
 # proteomics, software, statistics, structure, systems biology,
 # dataservices, administration
 #
-category: 
+category:
   - development
   - pathogen genomics
   - plant genomics
@@ -78,7 +78,7 @@ keywords:
   - perl
   - python
   - rnaseq
-  - variants 
+  - variants
   - SNP
 #
 # "role:" is the role that you play within your infrastructure.

trombinoscope/staff/gaetan-droc.yaml

@@ -1,5 +1,4 @@
-
---- 
+---
 staffname: Gaetan Droc
 
 type: staff
@@ -12,25 +11,25 @@ phone: xxx-xxx xx xx
 
 city:
   - Montpellier
-  
+
 workplace: AGAP Unit
 
 affiliation: CIRAD
 
 facility: SouthGreen
 
-category: 
+category:
   - development
   - software
   - annotation
   - genomics
   - management
- 
+
 bibtex: gaetan-droc.bib
 
 orcid: 0000-0003-1849-1269
 
-image: gaetan-droc.png
+image: gaetan-droc.jpg
 
 keywords:
   - genome annotation
@@ -39,14 +38,13 @@ keywords:
   - reproductible research
   - postgreql
   - web developpment
-  
+
 role: Bioinformatician
 
 bio:
   Research engineer in Bioinformatics, part of SouthGreen sterring comittee.
-  My work involves NGS data analysis, including genome assembly, genome annotation,
-  comparative genomics, methylation analysis, and Cut&Tag, using Snakemake.
-  I actively participate in the development Genomes Hub through the integration of
-  omics data such as banana, rice, sugarcane, vanilla, coffea, cocoa.
-
-
+  My work involves NGS data analysis, including genome assembly, genome
+  annotation, comparative genomics, methylation analysis, and Cut&Tag, using
+  Snakemake. I actively participate in the development Genomes Hub through the
+  integration of omics data such as banana, rice, sugarcane, vanilla, coffea,
+  cocoa.

trombinoscope/staff/jacques-dainat.yaml

@@ -28,6 +28,6 @@ category:
 phone: +33 (0)00 00 00 00
 city:
   - Montpellier
-affiliation: IRD-UM-CNRS
+affiliation: IRD
 workplace: IRD
 facility: SouthGreen

trombinoscope/staff/mathieu-rouard.yaml

@@ -1,32 +1,32 @@
----
-staffname: Mathieu Rouard
-type: staff
-bio:
-  Research scientist in Bioinformatics, part of SG sterring comittee
-  I am involved in genome analyses and contribute to related
-  web resources development. Strong focus on banana and genetic diversity.
-
-active: true
-email: [email protected]
-phone: xxx-xxx xx xx
-city:
-  - Montpellier
-workplace: Alliance Bioversity and CIAT
-affiliation: Bioversity International - UMR AGAP
-facility: SouthGreen
-category: 
-- genomics
-- software
-- management
-bibtex: mathieu-rouard.bib
-orcid: 0000-0003-0284-1885
-image: mathieu-rouard.jpg
-keywords:
-  - Genome Hubs
-  - Banana Genomes
-  - Orthology
-  - Gene families
-  - rnaseq
-  - Gigwa
-  - Interoperability
-role: Comité de pilotage
+---
+staffname: Mathieu Rouard
+type: staff
+bio:
+  Research scientist in Bioinformatics, part of SG sterring comittee
+  I am involved in genome analyses and contribute to related
+  web resources development. Strong focus on banana and genetic diversity.
+
+active: true
+email: [email protected]
+phone: xxx-xxx xx xx
+city:
+  - Montpellier
+workplace: Alliance Bioversity and CIAT
+affiliation: Bioversity International - UMR AGAP
+facility: SouthGreen
+category:
+  - genomics
+  - software
+  - management
+bibtex: mathieu-rouard.bib
+orcid: 0000-0003-0284-1885
+image: mathieu-rouard.jpg
+keywords:
+  - Genome Hubs
+  - Banana Genomes
+  - Orthology
+  - Gene families
+  - rnaseq
+  - Gigwa
+  - Interoperability
+role: Comité de pilotage

trombinoscope/staff/pierre-larmande.yaml

@@ -11,7 +11,7 @@
 #
 # Your real name, the exact way that you want it displayed.
 #
-staffname: Pierre Larmande 
+staffname: Pierre Larmande
 #
 # Most people will have "type: staff", but some may be "affiliate".
 #
@@ -38,7 +38,7 @@ workplace: IRD Montpellier
 #
 affiliation: IRD
 #
-# The SouthGreen facility that you are part of. 
+# The SouthGreen facility that you are part of.
 #
 facility: SouthGreen
 #
@@ -47,9 +47,9 @@ facility: SouthGreen
 # proteomics, software, statistics, structure, systems biology,
 # dataservices, administration
 #
-category: 
+category:
   - development
-  - annotation 
+  - annotation
   - dataservices
   - systems biology
 #
@@ -64,7 +64,7 @@ bibtex: pierre-larmande.bib
 #
 # If you have an ORCID ID ("NNNN-NNNN-NNNN-NNNN")
 #
-orcid: 0000-0002-2923-9790 
+orcid: 0000-0002-2923-9790
 #
 # The name of an image file in the "img" subdirectory, no more than
 # about 400 pixels wide and less than 200 KB in file size.
@@ -84,16 +84,18 @@ keywords:
 #
 # "role:" is the role that you play within your infrastructure.
 #
-role: Researcher 
+role: Researcher
 #
 bio:
-   Pierre Larmande is senior researcher at IRD, the French Public Research Institute for Sustainable Development. He is member of the DIADE Unit in Montpellier. His main research interests are Data integration, Semantic Web, plant-ontologies, semantic data linking, Knowledge management and Big Data for plant genomics.
-
-
- He obtained PhD in Informatics from the university of Montpellier in 2007 (about federated plant data integration approaches applied to agronomy) and recently obtained the habilitation to conduct research supervision (HDR) in 2020. He coordinated the Oryza Tag Line phenotypic rice mutant database and was involved in the OrygenesDB T-DNA rice database.
-
-
- Pierre Larmande is the lead PI of the Agronomic Linked Data project (AgroLD), which is a Knowledge Graph database that consists of data integrated from a variety of plant resources and ontologies. 
-
-
-
+  Pierre Larmande is senior researcher at IRD, the French Public Research
+  Institute for Sustainable Development. He is member of the DIADE Unit in
+  Montpellier. His main research interests are Data integration, Semantic Web,
+  plant-ontologies, semantic data linking, Knowledge management and Big Data
+  for plant genomics. He obtained PhD in Informatics from the university of
+  Montpellier in 2007 (about federated plant data integration approaches
+  applied to agronomy) and recently obtained the habilitation to conduct
+  research supervision (HDR) in 2020. He coordinated the Oryza Tag Line
+  phenotypic rice mutant database and was involved in the OrygenesDB T-DNA rice
+  database. Pierre Larmande is the lead PI of the Agronomic Linked Data project
+  (AgroLD), which is a Knowledge Graph database that consists of data
+  integrated from a variety of plant resources and ontologies.

trombinoscope/staff/valentin-guignon.yaml

@@ -10,9 +10,9 @@ workplace: Alliance Bioversity and CIAT
 affiliation: Bioversity International - UMR AGAP
 facility: SouthGreen
 category:
-- software
-- development
-- genomics
+  - software
+  - development
+  - genomics
 homepage: https://fr.linkedin.com/in/valentin-guignon
 orcid: 0000-0003-0903-6811
 image: valentin-guignon.jpg
@@ -45,4 +45,4 @@ bio:
   (BrAPI, Gigwa, MGIS, Banana Genome Hub, GenoRing, GreenPhyl, Tripal,...). I am
   currently part of the Tripal Advisory Committee and the BrAPI Advisory Board.
   I have strong knowledge in databases and web development with an expertise on
-  the Drupal CMS. I design algorithms, methodologies and software.
+  the Drupal CMS. I design algorithms, methodologies and software.