First draft of system to automatically update workshop pages

Using a jinja template, the workshop page is generated automatically with each HPO release.

The raw data is pulled from the workshop tracking sheet in Monarch (a google sheet).

docs/community/workshops.md

@@ -1,25 +1,27 @@
-# Workshops
-
-Since its inception in 2008, the HPO has conducted numerous workshops  (“hackathons”) with clinical experts to add content to the HPO for specific areas of medicine. Please contact the HPO team if you would like to work with us on HPO terms for an area of medicine.
-
-Participants in such workshops are invited to join the HPO team as coauthors in our regular database update articles (e.g., [PMID:24217912](https://pubmed.ncbi.nlm.nih.gov/24217912/), [PMID:27899602](https://pubmed.ncbi.nlm.nih.gov/27899602/), [PMID:33264411](https://pubmed.ncbi.nlm.nih.gov/33264411/), [PMID:37953324](https://pubmed.ncbi.nlm.nih.gov/37953324/)). Additionally, some collaborative groups have published focussed aarticles about the work to which the HPO team has contributed. These many contributions (and many others not listed here) have enormously contributed to the quality of the HPO.
-
-
-| Date        | Location                            | Topic |Coordination |
-| :---------- | :----------------------------------- | :---------- | :---------- |
-| 2009 | Sanger Institute, Hinxton, England | General review (5 day workshop with multiple topics)| [Helen Firth](https://www.sanger.ac.uk/external_person/firth-helen/){target="_blank"}, [DECIPHER consortium](https://www.deciphergenomics.org/){target="_blank"} |
-| 2012 |Charité - Universitätsmedizin Berlin, Germany |2-day workshop in Berlin, Germany, to extend dental terminology in the HPO |Prof. [Isabelle Bailleul-Forestier](https://www.eugenol.com/profils/pr-isabelle-bailleul-forestier-698){target="_blank"} (Paul Sabatier University - Toulouse, France) |
-| 2012-2016 | Work to add 80 terms and associated is-a relationships were added to HPO (See [PMID:25949529](https://www.ncbi.nlm.nih.gov/pubmed/25949529){target="_blank"}) | Abnormal bleeding  |[BRIDGE BPD Consortium](https://www.science.org/content/author/bridge-bpd-consortium){target="_blank"}, Prof. Willem Ouwehand, University of Cambridge  | 
-|2013| Charité - Universitätsmedizin Berlin, Germany |  Epilepsy phenotypes and EEG abnormalities | [Prof. Ingo Helbig](https://www.epilepsiegenetik.de/%C3%BCber-uns/ingo-helbig/){target="_blank"}  | 
-|2015|Cambridge, England |Workshop with the UK's National Institute for Health Research (NIHR) Rare Disease—Translational Research Collaboration (See [PMID:27899602](https://pubmed.ncbi.nlm.nih.gov/27899602/){target="_blank"})|Patrick Chinnery, Mareike Veltman and Roger James.|
-|2017| [National Institute for Allergy and Infectious Diseases (NIAID-NIH)](https://www.niaid.nih.gov/){target="_blank"}|Immunology| [Morgan Similuk](https://www.linkedin.com/in/morgan-butrick-similuk-66397314/){target="_blank"} |
-|2017|[Stanford University](https://www.stanford.edu/){target="_blank"} | Cardiology | [Matthew Wheeler](https://med.stanford.edu/profiles/9086){target="_blank"} |
-|2017| Mont St. Odile, France | Ophthalmology (See [PMID:30626441](https://pubmed.ncbi.nlm.nih.gov/30626441/){target="_blank"} | Panagiotis Sergouniotis, [European Reference Network for Rare Eye Diseases](https://www.ern-eye.eu/){target="_blank"} |
-|2017-2024| Ongoing onsite and virtual workshops | Nephrology (see [PMID:32939051](https://pubmed.ncbi.nlm.nih.gov/32939051/){target="_blank"} ) | [Kidney Precision Medicine Project](https://www.kpmp.org/){target="_blank"}  (KPMP) |
-|2019-2021|Three workshops, numerous teleconferences, and joint task forces|Inborn errors of immunity (IEI)|[ESID (European Society for Immunodeficiencies)](https://esid.org/)|
-|2017-2023|numerous teleconferences| Pulmonology (See [PMID:36588100](https://pubmed.ncbi.nlm.nih.gov/36588100/){target="_blank"})| [ChILD EU](https://www.ersnet.org/science-and-research/clinical-research-collaboration-application-programme/child-eu/), Matthias Griese |
-|2017| numerous teleconferences | Newborn screening (See [PMID:33264411](https://pubmed.ncbi.nlm.nih.gov/33264411/){target="_blank"})|  Newborn Screening Translational Research Network (NBSTRN), Amy Brower |
-
-
-
-
+# Workshop List
+
+| Topic | Type | Status | When | Where |
+|-------|------|--------|------|-------|
+| Mood disorder workshop #2 | Workshop | Complete | October 13, 2023 | Montreal |
+| Lymphoma | Workshop | Complete | Nov. 10, 2024 | Farmington, CT |
+| Phenopackets Vulcan HL7 | Project Event | Complete | May 31, 2024 | Online |
+| Neuropathology Mini-workshop | Workshop | Postponed | May 23 or 24, 2024 | NYC |
+| HPO-Affect (mood) workshop #1 | Workshop | Complete | June 6, 2024 | Istanbul |
+| HPO GOSH event | Showcase | Complete | June 21, 2024 | London |
+| Mood disorder workshop #1 | Workshop | Complete | June 19, 2023 | Chicago |
+| ERN-EYE | Workshop | Scheduled | July 8, 2024 | Strasbourg |
+| Neurodevelopment and behavior | Workshop | Complete | February 1, 2023 | NIMH |
+| HPO-Affect (mood) workshop #2 | Workshop | Complete | April 6, 2024 | Budapest |
+| HPO-Immunology | Workshop | Complete | 2017 | Maryland |
+| HPO-Cardiology | Workshop | Complete | 2017 | Stanford, CA |
+| HPO-Opthalmology | Workshop | Complete | 2017 | Cedex, France |
+| NIHR RD-TRC | Workshop | Complete | 2015 | United Kingdom |
+| HPO-Epilepsy | Workshop | Complete | 2013 | Unknown |
+| HPO-Bleeding | Workshop | Complete | 2012-2016 | Unknown |
+| HPO-Dental | Workshop | Complete | 2012 | Berlin, Germany |
+| Decipher | Workshop | Complete | 2009 | Hinxton, UK |
+| Neuropathology |  |  |  | New York |
+| ERN-DERMA |  | Planning |  |  |
+| ERN-RITA (Immunology) |  | Planning |  |  |
+| ERN-malformations |  |  |  |  |
+| Contractures | Workshop | Complete |  |  |

src/ontology/build-without-imports.sh

@@ -11,3 +11,6 @@ test -f tmp/hpo-annotation-data/README.md
 ODK_TAG=$ODK sh run.sh make MIR=false IMP=false prepare_release -B
 ODK_TAG=$ODK sh run.sh make hpoa -B
 ODK_TAG=$ODK sh run.sh make hpo_diff -B
+
+# Update dynamically generated documentation pages
+ODK_TAG=$ODK sh run.sh make ../../docs/community/workshops.md -B

src/ontology/config/workshops.md.jinja2

@@ -0,0 +1,7 @@
+# Workshop List
+
+| Topic | Type | Status | When | Where |
+|-------|------|--------|------|-------|
+{%- for item in workshops | sort(attribute='When', reverse=true) %}
+| {{ item.Topic }} | {{ item.Type }} | {{ item.Status }} | {{ item.When }} | {{ item.Where }} |
+{%- endfor %}

src/ontology/hp.Makefile

@@ -530,6 +530,14 @@ public_release:
 	gh release create $(GHVERSION) --title "$(VERSION) Release" --draft $(RELEASE_ASSETS_AFTER_RELEASE) --generate-notes
 
 
+tmp/workshops.csv:
+	wget "https://docs.google.com/spreadsheets/d/e/2PACX-1vQT1u_xxXqS0rHR2lAF0NmdGHEaOuCFV3XDYPmdMldelAGmpUQSGTlU93bGvCSHDWDFRkzjq4vYe609/pub?gid=1322735303&single=true&output=csv" -O $@
+
+../../docs/community/workshops.md: tmp/workshops.csv config/workshops.md.jinja2
+	pip install j2cli
+	python3 -c "import csv, json, sys; print(json.dumps({'workshops': list(csv.DictReader(open('$<')))}))" > tmp/workshops.json
+	j2 --format=json config/workshops.md.jinja2 tmp/workshops.json > $@
+
 #############################
 #### Adopt MP EQs ###########
 #############################