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first round rpprs 2023
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@matentzn
matentzn committed Mar 23, 2023
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3 changes: 3 additions & 0 deletions .gitignore
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ontologies/*
.DS_Store
78 changes: 78 additions & 0 deletions Makefile
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START_DATE_P1=2022-08-01
END_DATE_P1=2023-05-31
START_DATE_HPO=2022-07-01
END_DATE_HPO=2023-06-30

ONTOLOGIES=mondo hp maxo
GRAINYHEAD_STATS=$(patsubst %, stats/grainyhead_%.md, $(ONTOLOGIES))
DIFF_STATS=$(patsubst %, stats/%_diff_summary.txt, $(ONTOLOGIES))

all: $(GRAINYHEAD_STATS) $(DIFF_STATS)

stats/grainyhead_hp.md:
mkdir -p stats/
grainyhead -s hp metrics --from=$(START_DATE_HPO) --to=$(END_DATE_HPO) --team human-phenotype > $@

stats/grainyhead_maxo.md:
mkdir -p stats/
grainyhead -s maxo metrics --from=$(START_DATE_HPO) --to=$(END_DATE_HPO) --team monarch-ontology-team > $@

stats/grainyhead_mondo.md:
mkdir -p stats/
grainyhead -s mondo metrics --from=$(START_DATE_P1) --to=$(END_DATE_P1) --team monarch-ontology-team > $@

ontologies/mondo_%.obo:
mkdir -p ontologies/
wget "http://purl.obolibrary.org/obo/mondo/releases/$*/mondo-base.obo" -O $@

ontologies/hp_%.obo:
mkdir -p ontologies/
wget "http://purl.obolibrary.org/obo/hp/releases/$*/hp-base.obo" -O $@

ontologies/hp_2022-06-11.obo:
mkdir -p ontologies/
wget "https://raw.githubusercontent.com/obophenotype/human-phenotype-ontology/v2022-06-11/hp-base.obo" -O $@

ontologies/maxo_%.obo:
mkdir -p ontologies/
wget "http://purl.obolibrary.org/obo/maxo/releases/$*/maxo-base.obo" -O $@

stats/mondo_diff.txt:
$(eval START := 2022-08-01)
$(eval END := 2023-03-01)
$(eval ID := mondo)
make ontologies/$(ID)_$(START).obo ontologies/$(ID)_$(END).obo
#runoak -i simpleobo:ontologies/$(ID)_$(START).obo diff -X simpleobo:ontologies/$(ID)_$(END).obo -o [email protected] --statistics
robot diff --left ontologies/$(ID)_$(START).obo --right ontologies/$(ID)_$(END).obo -o $@
.PRECIOUS: stats/mondo_diff.txt

stats/maxo_diff.txt:
mkdir -p stats/
$(eval START := 2022-06-24)
$(eval END := 2023-03-09)
$(eval ID := maxo)
make ontologies/$(ID)_$(START).obo ontologies/$(ID)_$(END).obo
#runoak -i simpleobo:ontologies/$(ID)_$(START).obo diff -X simpleobo:ontologies/$(ID)_$(END).obo --statistics -o [email protected]
robot diff --left ontologies/$(ID)_$(START).obo --right ontologies/$(ID)_$(END).obo -o $@
.PRECIOUS: stats/maxo_diff.txt

stats/hp_diff.txt:
mkdir -p stats/
$(eval START := 2022-06-11)
$(eval END := 2023-01-27)
$(eval ID := hp)
make ontologies/$(ID)_$(START).obo ontologies/$(ID)_$(END).obo
#runoak -i simpleobo:ontologies/$(ID)_$(START).obo diff -X simpleobo:ontologies/$(ID)_$(END).obo --statistics -o [email protected]
robot diff --left ontologies/$(ID)_$(START).obo --right ontologies/$(ID)_$(END).obo -o $@
.PRECIOUS: stats/hp_diff.txt

stats/%_diff_summary.txt: stats/%_diff.txt
echo "New Terms: " > $@
grep "+ Declaration" $< | wc -l >> $@
echo "New or updated definitions: " >> $@
grep -E "[+] AnnotationAssertion.*IAO_0000115" $< | wc -l >> $@
echo "New or updated synonyms: " >> $@
grep -E "[+] AnnotationAssertion.*Synonym" $< | wc -l >> $@

https://github.com/obophenotype/human-phenotype-ontology/releases/download/v2023-03-01/hp-base.obo
14 changes: 14 additions & 0 deletions stats/grainyhead_hp.md
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From 2022-07-01 to 2023-06-30

| Event | Total | Internal | Inte (%) | External | Exte (%) |
| -------------------- | -------- | -------- | -------- | -------- | -------- |
| Contributors | 65 | 7 | 10.77 | 58 | 89.23 |
| Issues opened | 2061 | 1918 | 93.06 | 143 | 6.94 |
| Issues closed | 609 | 607 | 99.67 | 2 | 0.33 |
| Pull requests opened | 31 | 25 | 80.65 | 6 | 19.35 |
| Pull requests closed | 26 | 26 | 100.00 | 0 | 0.00 |
| Pull requests merged | 23 | 23 | 100.00 | 0 | 0.00 |
| Comments | 1387 | 1066 | 76.86 | 321 | 23.14 |
| Commits | 170 | 166 | 97.65 | 4 | 2.35 |
| Releases | 3 | 3 | 100.00 | 0 | 0.00 |

14 changes: 14 additions & 0 deletions stats/grainyhead_maxo.md
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From 2022-07-01 to 2023-06-30

| Event | Total | Internal | Inte (%) | External | Exte (%) |
| -------------------- | -------- | -------- | -------- | -------- | -------- |
| Contributors | 11 | 6 | 54.55 | 5 | 45.45 |
| Issues opened | 134 | 126 | 94.03 | 8 | 5.97 |
| Issues closed | 68 | 67 | 98.53 | 1 | 1.47 |
| Pull requests opened | 39 | 39 | 100.00 | 0 | 0.00 |
| Pull requests closed | 39 | 39 | 100.00 | 0 | 0.00 |
| Pull requests merged | 38 | 38 | 100.00 | 0 | 0.00 |
| Comments | 152 | 147 | 96.71 | 5 | 3.29 |
| Commits | 240 | 240 | 100.00 | 0 | 0.00 |
| Releases | 7 | 7 | 100.00 | 0 | 0.00 |

14 changes: 14 additions & 0 deletions stats/grainyhead_mondo.md
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From 2022-08-01 to 2023-05-31

| Event | Total | Internal | Inte (%) | External | Exte (%) |
| -------------------- | -------- | -------- | -------- | -------- | -------- |
| Contributors | 69 | 11 | 15.94 | 58 | 84.06 |
| Issues opened | 343 | 131 | 38.19 | 212 | 61.81 |
| Issues closed | 354 | 316 | 89.27 | 38 | 10.73 |
| Pull requests opened | 541 | 361 | 66.73 | 180 | 33.27 |
| Pull requests closed | 541 | 477 | 88.17 | 64 | 11.83 |
| Pull requests merged | 472 | 438 | 92.80 | 34 | 7.20 |
| Comments | 1104 | 679 | 61.50 | 425 | 38.50 |
| Commits | 609 | 401 | 65.85 | 208 | 34.15 |
| Releases | 9 | 4 | 44.44 | 5 | 55.56 |

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