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Adding term build tests
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‎.github/workflows/test_vfbterms.yml‎

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name: Test VFB Terms Generation
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on:
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push:
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paths:
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- 'vfbterms.py'
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- '.github/workflows/test_vfbterms.yml'
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pull_request:
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paths:
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- 'vfbterms.py'
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- '.github/workflows/test_vfbterms.yml'
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workflow_dispatch:
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jobs:
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test:
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v3
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- name: Set up Python
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uses: actions/setup-python@v4
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with:
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python-version: '3.9'
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- name: Install dependencies
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run: |
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python -m pip install --upgrade pip
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pip install vfb-connect pandas
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- name: Run medulla test
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run: |
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python3 vfbterms.py
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- name: Archive test results
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if: always()
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uses: actions/upload-artifact@v3
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with:
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name: test-results
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path: |
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FBbt_00003748_v*.md
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retention-days: 7

‎.gitignore‎

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public/*
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.DS_Store
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/.venv

‎vfbterms.py‎

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#!/usr/bin/env python3
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import sys
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from os import listdir, chdir
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from os.path import isfile, join
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import os
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import warnings
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# Suppress the urllib3 warning about OpenSSL
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warnings.filterwarnings('ignore', category=Warning)
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# Set environment variable to skip GUI dependencies
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os.environ['VFB_SKIP_GUI'] = '1'
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from vfb_connect.cross_server_tools import VfbConnect
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import re
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@@ -296,72 +307,183 @@ def wrapStringInHTMLMac(term):
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print(whole)
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f.close()
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mypath = sys.argv[1]
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print("Updating all files in " + mypath)
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onlyfiles = [f for f in listdir(mypath) if isfile(join(mypath, f))]
302-
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chdir(mypath + 'fbbt/')
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save_terms(vc.nc.commit_list(["MATCH (n:Class) WHERE n.short_form starts with 'FBbt' WITH n.short_form as id ORDER BY id ASC RETURN collect(distinct id) as ids"])[0]['data'][0]['row'][0])
305-
chdir(mypath + 'fbbi/')
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save_terms(vc.nc.commit_list(["MATCH (n:Class) WHERE n.short_form starts with 'FBbi' WITH n.short_form as id ORDER BY id ASC RETURN collect(distinct id) as ids"])[0]['data'][0]['row'][0])
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chdir(mypath + 'fbcv/')
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save_terms(vc.nc.commit_list(["MATCH (n:Class) WHERE n.short_form starts with 'FBcv' WITH n.short_form as id ORDER BY id ASC RETURN collect(distinct id) as ids"])[0]['data'][0]['row'][0])
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chdir(mypath + 'fbdv/')
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save_terms(vc.nc.commit_list(["MATCH (n:Class) WHERE n.short_form starts with 'FBdv' WITH n.short_form as id ORDER BY id ASC RETURN collect(distinct id) as ids"])[0]['data'][0]['row'][0])
311-
chdir(mypath + 'vfb/')
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vfb = vc.nc.commit_list(["MATCH (n:Individual) WHERE n.short_form starts with 'VFB_' AND NOT n.short_form starts with 'VFB_internal' WITH n.short_form as id ORDER BY id ASC RETURN collect(distinct id) as ids"])[0]['data'][0]['row'][0]
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save_terms(vfb)
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save_terms(vc.nc.commit_list(["MATCH (n:Class) WHERE n.short_form starts with 'VFBexp_' WITH n.short_form as id ORDER BY id ASC RETURN collect(distinct id) as ids"])[0]['data'][0]['row'][0])
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# TODO: replace once VFBconnect pub queries added
317-
#save_terms(vc.nc.commit_list(["MATCH (n:pub) with n.short_form as id ORDER BY id ASC RETURN collect(distinct id) as ids"])[0]['data'][0]['row'][0])
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chdir(mypath + '../datasets/')
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save_terms(vc.nc.commit_list(["MATCH (n:DataSet) with n.short_form as id ORDER BY id ASC RETURN collect(distinct id) as ids"])[0]['data'][0]['row'][0])
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323-
chdir(mypath + 'go/')
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save_terms(vc.nc.commit_list(["MATCH (n:Class) WHERE n.short_form starts with 'GO_' WITH n.short_form as id ORDER BY id ASC RETURN collect(distinct id) as ids"])[0]['data'][0]['row'][0])
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chdir(mypath + 'so/')
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save_terms(vc.nc.commit_list(["MATCH (n:Class) WHERE n.short_form starts with 'SO_' WITH n.short_form as id ORDER BY id ASC RETURN collect(distinct id) as ids"])[0]['data'][0]['row'][0])
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chdir(mypath + 'ioa/')
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save_terms(vc.nc.commit_list(["MATCH (n:Class) WHERE n.short_form starts with 'IAO_' WITH n.short_form as id ORDER BY id ASC RETURN collect(distinct id) as ids"])[0]['data'][0]['row'][0])
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chdir(mypath + 'geno/')
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save_terms(vc.nc.commit_list(["MATCH (n:Class) WHERE n.short_form starts with 'GENO_' WITH n.short_form as id ORDER BY id ASC RETURN collect(distinct id) as ids"])[0]['data'][0]['row'][0])
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chdir(mypath + 'pato/')
336-
save_terms(vc.nc.commit_list(["MATCH (n:Class) WHERE n.short_form starts with 'PATO_' WITH n.short_form as id ORDER BY id ASC RETURN collect(distinct id) as ids"])[0]['data'][0]['row'][0])
337-
338-
chdir(mypath + 'pco/')
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save_terms(vc.nc.commit_list(["MATCH (n:Class) WHERE n.short_form starts with 'PCO_' WITH n.short_form as id ORDER BY id ASC RETURN collect(distinct id) as ids"])[0]['data'][0]['row'][0])
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chdir(mypath + 'uberon/')
342-
save_terms(vc.nc.commit_list(["MATCH (n:Class) WHERE n.short_form starts with 'UBERON_' WITH n.short_form as id ORDER BY id ASC RETURN collect(distinct id) as ids"])[0]['data'][0]['row'][0])
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def test_medulla_page():
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"""Test full term page creation for medulla using actual VFB connection"""
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expected_content = """---
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title: "medulla [FBbt_00003748]"
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linkTitle: "medulla"
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tags: [Entity,Adult,Anatomy,Class,Nervous_system,Synaptic_neuropil,Synaptic_neuropil_domain,FBbt]
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content: [term]
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date: {current_date}
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images: []
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description: >
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The second optic neuropil, sandwiched between the lamina and the lobula complex. It is divided into 10 layers: 1-6 make up the outer (distal) medulla, the seventh (or serpentine) layer exhibits a distinct architecture and layers 8-10 make up the inner (proximal) medulla (Ito et al., 2014).
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weight: 10000
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sitemap_exclude: true
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canonicalUrl: "https://www.virtualflybrain.org/term/medulla-fbbt_00003748/"
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---
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344-
chdir(mypath + 'ro/')
345-
save_terms(vc.nc.commit_list(["MATCH (n:Class) WHERE n.short_form starts with 'RO_' WITH n.short_form as id ORDER BY id ASC RETURN collect(distinct id) as ids"])[0]['data'][0]['row'][0])
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{note}
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chdir(mypath + 'obi/')
348-
save_terms(vc.nc.commit_list(["MATCH (n:Class) WHERE n.short_form starts with 'OBI_' WITH n.short_form as id ORDER BY id ASC RETURN collect(distinct id) as ids"])[0]['data'][0]['row'][0])
328+
[Open **medulla** in **VFB**](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?id=FBbt_00003748)
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350-
chdir(mypath + 'ncbitaxon/')
351-
save_terms(vc.nc.commit_list(["MATCH (n:Class) WHERE n.short_form starts with 'NCBITaxon_' WITH n.short_form as id ORDER BY id ASC RETURN collect(distinct id) as ids"])[0]['data'][0]['row'][0])
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## Term Information
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353-
chdir(mypath + 'zp/')
354-
save_terms(vc.nc.commit_list(["MATCH (n:Class) WHERE n.short_form starts with 'ZP_' WITH n.short_form as id ORDER BY id ASC RETURN collect(distinct id) as ids"])[0]['data'][0]['row'][0])
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- **ID**: FBbt_00003748
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- **Name**: medulla
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- **Definition**: The second optic neuropil, sandwiched between the lamina and the lobula complex. It is divided into 10 layers: 1-6 make up the outer (distal) medulla, the seventh (or serpentine) layer exhibits a distinct architecture and layers 8-10 make up the inner (proximal) medulla (Ito et al., 2014).
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- **Type**: Entity, Adult, Anatomy, Class, Nervous_system, Synaptic_neuropil, Synaptic_neuropil_domain
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356-
chdir(mypath + 'wbphenotype/')
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save_terms(vc.nc.commit_list(["MATCH (n:Class) WHERE n.short_form starts with 'WBPhenotype_' WITH n.short_form as id ORDER BY id ASC RETURN collect(distinct id) as ids"])[0]['data'][0]['row'][0])
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## Classification
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- [synaptic neuropil domain](https://www.virtualflybrain.org/term/synaptic-neuropil-domain-fbbt_00040007) <span class="label types"><span class="label label-Synaptic_neuropil">Synaptic neuropil</span> <span class="label label-Nervous_system">Nervous system</span></span>
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chdir(mypath + 'caro/')
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save_terms(vc.nc.commit_list(["MATCH (n:Class) WHERE n.short_form starts with 'CARO_' WITH n.short_form as id ORDER BY id ASC RETURN collect(distinct id) as ids"])[0]['data'][0]['row'][0])
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## Relationships
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- develops from [medulla anlage](https://www.virtualflybrain.org/term/medulla-anlage-fbbt_00001935) <span class="label types"><span class="label label-Nervous_system">Nervous system</span> <span class="label label-Larva">Larva</span></span>
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chdir(mypath + 'bfo/')
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save_terms(vc.nc.commit_list(["MATCH (n:Class) WHERE n.short_form starts with 'BFO_' WITH n.short_form as id ORDER BY id ASC RETURN collect(distinct id) as ids"])[0]['data'][0]['row'][0])
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## Cross References
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- [![Insect Brain DB](https://insectbraindb.org/app/assets/images/Megalopta_frontal.png) Insect Brain DB](https://insectbraindb.org/app/structures/38)
345+
- [medulla on Insect Brain DB](https://insectbraindb.org/app/structures/38)"""
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365-
chdir(mypath + 'flybase/')
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save_terms(vc.nc.commit_list(["MATCH (n:Class) WHERE n.short_form starts with 'FB' AND NOT n.short_form contains '_' WITH n.short_form as id ORDER BY id ASC RETURN collect(distinct id) as ids"])[0]['data'][0]['row'][0])
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# Get actual medulla data
348+
print("Fetching medulla data from VFB...")
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terms = vc.neo_query_wrapper.get_TermInfo(["FBbt_00003748"])
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351+
if terms.empty:
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print("ERROR: Could not fetch medulla data")
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return False
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# Generate actual content
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print("Generating medulla page...")
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import tempfile
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import os
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# Create temporary directory for test
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with tempfile.TemporaryDirectory() as tmpdir:
362+
os.chdir(tmpdir)
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364+
# Process the term
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for _, row in terms.iterrows():
366+
term_data = {
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"term": {
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"core": {
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"short_form": row.get("short_form", ""),
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"label": row.get("label", ""),
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"types": row.get("types", []),
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"iri": row.get("iri", ""),
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"symbol": row.get("symbol", "")
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},
375+
"description": [row.get("description", "")],
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"comment": [row.get("comment", "")]
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},
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"parents": row.get("parents", []),
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"relationships": row.get("relationships", []),
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"xrefs": row.get("xrefs", []),
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"pub_syn": row.get("pub_syn", []),
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"def_pubs": row.get("def_pubs", [])
383+
}
384+
wrapStringInHTMLMac(term_data)
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# Read generated file
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filename = f"FBbt_00003748_v{version}.md"
388+
if os.path.exists(filename):
389+
with open(filename, 'r') as f:
390+
actual_content = f.read()
391+
392+
# Compare content (ignoring date which will change)
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import datetime
394+
expected_with_date = expected_content.format(
395+
current_date=datetime.datetime.today().strftime("%Y-%m-%d"),
396+
note=note
397+
)
398+
399+
if actual_content.strip() == expected_with_date.strip():
400+
print("✓ Test passed: Generated content matches expected")
401+
return True
402+
else:
403+
print("✗ Test failed: Content mismatch")
404+
print("\nExpected content:")
405+
print(expected_with_date)
406+
print("\nActual content:")
407+
print(actual_content)
408+
return False
409+
else:
410+
print(f"✗ Test failed: File {filename} was not created")
411+
return False
412+
413+
if __name__ == "__main__":
414+
if len(sys.argv) > 1:
415+
mypath = sys.argv[1]
416+
print("Updating all files in " + mypath)
417+
onlyfiles = [f for f in listdir(mypath) if isfile(join(mypath, f))]
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419+
chdir(mypath + 'fbbt/')
420+
save_terms(vc.nc.commit_list(["MATCH (n:Class) WHERE n.short_form starts with 'FBbt' WITH n.short_form as id ORDER BY id ASC RETURN collect(distinct id) as ids"])[0]['data'][0]['row'][0])
421+
chdir(mypath + 'fbbi/')
422+
save_terms(vc.nc.commit_list(["MATCH (n:Class) WHERE n.short_form starts with 'FBbi' WITH n.short_form as id ORDER BY id ASC RETURN collect(distinct id) as ids"])[0]['data'][0]['row'][0])
423+
chdir(mypath + 'fbcv/')
424+
save_terms(vc.nc.commit_list(["MATCH (n:Class) WHERE n.short_form starts with 'FBcv' WITH n.short_form as id ORDER BY id ASC RETURN collect(distinct id) as ids"])[0]['data'][0]['row'][0])
425+
chdir(mypath + 'fbdv/')
426+
save_terms(vc.nc.commit_list(["MATCH (n:Class) WHERE n.short_form starts with 'FBdv' WITH n.short_form as id ORDER BY id ASC RETURN collect(distinct id) as ids"])[0]['data'][0]['row'][0])
427+
chdir(mypath + 'vfb/')
428+
vfb = vc.nc.commit_list(["MATCH (n:Individual) WHERE n.short_form starts with 'VFB_' AND NOT n.short_form starts with 'VFB_internal' WITH n.short_form as id ORDER BY id ASC RETURN collect(distinct id) as ids"])[0]['data'][0]['row'][0]
429+
save_terms(vfb)
430+
save_terms(vc.nc.commit_list(["MATCH (n:Class) WHERE n.short_form starts with 'VFBexp_' WITH n.short_form as id ORDER BY id ASC RETURN collect(distinct id) as ids"])[0]['data'][0]['row'][0])
431+
432+
# TODO: replace once VFBconnect pub queries added
433+
#save_terms(vc.nc.commit_list(["MATCH (n:pub) with n.short_form as id ORDER BY id ASC RETURN collect(distinct id) as ids"])[0]['data'][0]['row'][0])
434+
435+
chdir(mypath + '../datasets/')
436+
437+
save_terms(vc.nc.commit_list(["MATCH (n:DataSet) with n.short_form as id ORDER BY id ASC RETURN collect(distinct id) as ids"])[0]['data'][0]['row'][0])
438+
439+
chdir(mypath + 'go/')
440+
save_terms(vc.nc.commit_list(["MATCH (n:Class) WHERE n.short_form starts with 'GO_' WITH n.short_form as id ORDER BY id ASC RETURN collect(distinct id) as ids"])[0]['data'][0]['row'][0])
441+
442+
chdir(mypath + 'so/')
443+
save_terms(vc.nc.commit_list(["MATCH (n:Class) WHERE n.short_form starts with 'SO_' WITH n.short_form as id ORDER BY id ASC RETURN collect(distinct id) as ids"])[0]['data'][0]['row'][0])
444+
445+
chdir(mypath + 'ioa/')
446+
save_terms(vc.nc.commit_list(["MATCH (n:Class) WHERE n.short_form starts with 'IAO_' WITH n.short_form as id ORDER BY id ASC RETURN collect(distinct id) as ids"])[0]['data'][0]['row'][0])
447+
448+
chdir(mypath + 'geno/')
449+
save_terms(vc.nc.commit_list(["MATCH (n:Class) WHERE n.short_form starts with 'GENO_' WITH n.short_form as id ORDER BY id ASC RETURN collect(distinct id) as ids"])[0]['data'][0]['row'][0])
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451+
chdir(mypath + 'pato/')
452+
save_terms(vc.nc.commit_list(["MATCH (n:Class) WHERE n.short_form starts with 'PATO_' WITH n.short_form as id ORDER BY id ASC RETURN collect(distinct id) as ids"])[0]['data'][0]['row'][0])
453+
454+
chdir(mypath + 'pco/')
455+
save_terms(vc.nc.commit_list(["MATCH (n:Class) WHERE n.short_form starts with 'PCO_' WITH n.short_form as id ORDER BY id ASC RETURN collect(distinct id) as ids"])[0]['data'][0]['row'][0])
456+
457+
chdir(mypath + 'uberon/')
458+
save_terms(vc.nc.commit_list(["MATCH (n:Class) WHERE n.short_form starts with 'UBERON_' WITH n.short_form as id ORDER BY id ASC RETURN collect(distinct id) as ids"])[0]['data'][0]['row'][0])
459+
460+
chdir(mypath + 'ro/')
461+
save_terms(vc.nc.commit_list(["MATCH (n:Class) WHERE n.short_form starts with 'RO_' WITH n.short_form as id ORDER BY id ASC RETURN collect(distinct id) as ids"])[0]['data'][0]['row'][0])
462+
463+
chdir(mypath + 'obi/')
464+
save_terms(vc.nc.commit_list(["MATCH (n:Class) WHERE n.short_form starts with 'OBI_' WITH n.short_form as id ORDER BY id ASC RETURN collect(distinct id) as ids"])[0]['data'][0]['row'][0])
465+
466+
chdir(mypath + 'ncbitaxon/')
467+
save_terms(vc.nc.commit_list(["MATCH (n:Class) WHERE n.short_form starts with 'NCBITaxon_' WITH n.short_form as id ORDER BY id ASC RETURN collect(distinct id) as ids"])[0]['data'][0]['row'][0])
468+
469+
chdir(mypath + 'zp/')
470+
save_terms(vc.nc.commit_list(["MATCH (n:Class) WHERE n.short_form starts with 'ZP_' WITH n.short_form as id ORDER BY id ASC RETURN collect(distinct id) as ids"])[0]['data'][0]['row'][0])
471+
472+
chdir(mypath + 'wbphenotype/')
473+
save_terms(vc.nc.commit_list(["MATCH (n:Class) WHERE n.short_form starts with 'WBPhenotype_' WITH n.short_form as id ORDER BY id ASC RETURN collect(distinct id) as ids"])[0]['data'][0]['row'][0])
474+
475+
chdir(mypath + 'caro/')
476+
save_terms(vc.nc.commit_list(["MATCH (n:Class) WHERE n.short_form starts with 'CARO_' WITH n.short_form as id ORDER BY id ASC RETURN collect(distinct id) as ids"])[0]['data'][0]['row'][0])
477+
478+
chdir(mypath + 'bfo/')
479+
save_terms(vc.nc.commit_list(["MATCH (n:Class) WHERE n.short_form starts with 'BFO_' WITH n.short_form as id ORDER BY id ASC RETURN collect(distinct id) as ids"])[0]['data'][0]['row'][0])
480+
481+
chdir(mypath + 'flybase/')
482+
save_terms(vc.nc.commit_list(["MATCH (n:Class) WHERE n.short_form starts with 'FB' AND NOT n.short_form contains '_' WITH n.short_form as id ORDER BY id ASC RETURN collect(distinct id) as ids"])[0]['data'][0]['row'][0])
483+
484+
else:
485+
print("Testing medulla page generation...")
486+
success = test_medulla_page()
487+
if not success:
488+
sys.exit(1)
367489

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