release v1.1.1

.github/workflows/pylint.yml

@@ -0,0 +1,23 @@
+name: Pylint
+
+on: [push]
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.8", "3.9", "3.10"]
+    steps:
+    - uses: actions/checkout@v3
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v3
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install pylint
+    - name: Analysing the code with pylint
+      run: |
+        pylint $(git ls-files '*.py')

CHANGELOG.md

@@ -0,0 +1,71 @@
+Open Genes is a non-commercial public service for biologists — a biological database of human genes associated with aging and lifespan.
+
+Open Genes API is a RESTful API that allows for programmatic access to the Open Genes database:  The API provides GET endpoints for accessing data on genes associated with aging and longevity as well as detailed structured data for each experiment binding the gene and aging: For example, we provide up to 40 parameters for each lifespan experiment: Our API provides basic and additional data for each gene, such as gene evolution, associated diseases, hallmarks of aging linked with genes, and protein functions: It also includes various parameters for filtering and sorting: Our goal is to stay objective and precise while connecting a particular gene and human aging and to keep the gene selection criteria transparent: We distinguished six types of studies and 12 criteria for adding genes to the Open Genes database: Genes were divided into highest, high, moderate, low, and lowest confidence level groups based on the type of data supporting the link between the gene and aging: 
+Open Genes API is a part of Open Genes infrastructure that includes other backend services, a data management application for biologists, and a frontend application.
+Complete interactive API documentation in Swagger (OpenAPI) format can be found at https://open-genes.org/api/docs.
+
+## What's Changed
+
+### Release v1.1.1
+* OG-923: Update CHANGELOG.md
+* OG-923: Add CONTRIBUTING.md
+* OG-923: Add script for changelog generation
+
+### Release v1.1.0
+* bugfix: Fixed issue for hallmarks of aging which was caused by an empty field in API response by @psnewbee #150
+* OG-957: Fix pandas import and add a check if hallmarks are set for gene by @psnewbee #123
+* OG-957: Fix filter for byConservativeIn parameter by @psnewbee #121
+* OG-949: Output manually bound hallmarks of aging by @psnewbee #119
+* OG-910: Fix bySpecies filter in studies by @psnewbee #111
+* Output distinct hallmarks of aging entries in the API response by @const8ine #117
+* Fix query causing duplicated hallmarks of aging in response by @const8ine #108
+* OG-936: Remove a fixer for the measurement method field, fix empty response by @Anthony1128 #106
+* Add updated datasets with missing experiments for upload by @const8ine #107
+* Update hallmarks of aging dataset by @const8ine #120
+* Update confidence levels dataset by @const8ine #143
+* bugfix: Fixed issue which was caused by empty agingMechanisms field in response by @psnewbee
+* OG-346: Fix missing methods in CalorieExperimentDAO by @Anthony1128 and @const8ine #141.
+* Added filter by symbol in gene/search API endpoint by @Anthony1128
+* OG-885: Set up API response caching by @Anthony1128 #94
+* OG-863: Change config for binding GO-terms with hallmarks by @const8ine #70
+* OG-909: Duplicates scanner by @Anthony1128 #101
+* bugfix: Fix condition for the aliases splitting by @Anthony1128 #100
+* OG-908: Change confidenceLevel field format by @Anthony1128 #99
+* OG-892: confidenceLevel output field update by @const8ine #98
+* OG-906: expression-change-human-mrna dataset by @const8ine #97
+* bugfix: Fix values trimming in longevity associations dataset upload script by @Anthony1128 #96
+* OG-906: Script for uploading data from expression-change-human-mrna dataset by @Anthony1128 #95
+* OG-809: Script for uploading data from longevity associations dataset by @Anthony1128 #90
+* OG-882: SQL injection fix by @Anthony1128 #82
+* bugfix: Fix SQL query for filtering the studies on the association of gene variants or expression levels with longevity by @Anthony1128 #92
+* OG-889: Confidence level in api/gene/search API endpoint response by @Anthony1128 #87
+* OG-901: Study filter placeholder by @Anthony1128 #88
+* OG-898: Fix typing for AgeRelatedChangeOfGene model by @const8ine #84
+* OG-887: Add filters to lifespan-change API endpoint by @psnewbee #83
+* OG-877: Add isHidden param to api/diet by @Anthony1128 #78
+* OG-881: gene/suggestions API endpoint suggestHidden param by @Anthony1128 #81
+* OG-873: Add linter by @Anthony1128 #77
+* OG-838: Fix filter logic by @Anthony1128 #74
+* OG-851: Always output tissueSpecificPromoter field in response by @const8ine #64
+* OG-589: Fix absent 'significance' field in pink form by @const8ine #66
+* OG-589: Add new fields to studies on the association of gene variants or expression levels with longevity by @tinymage #57
+* OG-589: Delete modelOrganism field from GeneAssociatedWithLongevityEffect response by @tinymage #54
+* OG-763: Add Wormbase orthologs parser by @zheld #55
+* bugfix: Fix empty HPA issue by @kergma #53
+* bugfix: Fix empty terms that broke a single gene response by @kergma #52
+* bugfix: Fix orthologs parser for studies on calorie restriction diets by @lannoyy #28
+* OG-376: Fix response for studies on age-related changes in gene expression, methylation or protein activity by @kergma #50
+* OG-617: Add bySuggestions parameter to api/gene/search API endpoint by @zheld #36
+* OG-617: Implement modular models approach for API by @kergma #36
+
+## Contributors
+* @imhelle made their first contribution #10
+* @dglubokov made their first contribution #1
+* @kergma made their first contribution #27
+* @lannoyy made their first contribution #3
+* @zheld made their first contribution #31
+* @tinymage made their first contribution #49
+* @const8ine made their first contribution #102
+
+
+

CONTRIBUTING.md

@@ -0,0 +1,16 @@
+# Release cycle
+
+## Before Making a PR
+Remember to update a changelog after working on a feature. 
+
+```bash
+sh generate-changelog.sh <tag>
+```
+
+Example:
+
+```bash
+sh generate-changelog.sh 1.0.0
+```
+
+Commit an updated CHANGELOG.md and push it to your feature branch.

api/endpoints/gene.py

@@ -153,7 +153,8 @@ async def gene_search(
             status_code=404,
             detail='Gene not found',
         )
-    search_result["agingMechanisms"] = pd.DataFrame(search_result["agingMechanisms"], dtype=object).drop_duplicates().sort_values(by=['id', 'uuid'], ascending=True).to_dict('records')
+    if search_result["agingMechanisms"]:
+        search_result["agingMechanisms"] = pd.DataFrame(search_result["agingMechanisms"], dtype=object).drop_duplicates().sort_values(by=['id', 'uuid'], ascending=True).to_dict('records')
     return search_result
 
 

generate-changelog.sh

@@ -0,0 +1,17 @@
+#!/bin/sh
+
+if [ $# -lt 1 ]; then
+  echo "Usage: $0 <tag>"
+  exit 1
+fi
+
+tag=$1
+changelogFile='CHANGELOG.md'
+
+logOutput=$(git log $tag..HEAD --pretty=format:"- %s" --no-merges | sed 's/#//g')
+
+echo "#Release v$tag" >> $changelogFile
+echo "" >> $changelogFile
+echo "$logOutput" >> $changelogFile
+
+echo "Changelog has been updated and saved to $changelogFile"

scripts/aging_mechanisms/go_and_mechanisms.tsv

@@ -5,7 +5,7 @@ go_terms	name_en	name_ru
 ['telomere maintenance']	telomere attrition	укорочение теломер
 ['histone modification']	alterations in histone modifications	изменения модификаций гистонов
 ['chromatin remodeling']	chromatin remodeling	ремоделирование хроматина
-['DNA-templated transcription']	transcriptional alterations	транскрипционные изменения
+['DNA-templated transcription', 'regulation of transcription by RNA polymerase II', 'negative regulation of transcription by RNA polymerase II', 'positive regulation of transcription by RNA polymerase II']	transcriptional alterations	транскрипционные изменения
 ['DNA methylation', 'DNA methylation on cytosine', 'DNA methylation on adenine', 'DNA methylation-dependent heterochromatin assembly', 'DNA methylation or demethylation', 'changes to DNA methylation involved in embryo development', 'gene silencing by RNA-directed DNA methylation', 'maintenance of DNA methylation', 'regulation of DNA methylation']	alterations in DNA methylation	изменения метилирования ДНК
 ['protein folding chaperone', 'chaperone-mediated protein folding', 'regulation of chaperone-mediated protein folding', 'ATP-dependent protein folding chaperone']	impairment of proteins folding and stability	нарушения фолдинга и стабильности белков
 ['proteolysis']	degradation of proteolytic systems	деградация протеолитических систем
@@ -17,6 +17,7 @@ go_terms	name_en	name_ru
 ['regulation of replicative senescence', 'replicative senescence', 'negative regulation of replicative senescence', 'positive regulation of replicative senescence', 'cellular senescence', 'regulation of cellular senescence', 'positive regulation of cellular senescence', 'negative regulation of cellular senescence', 'cell aging', 'regulation of cell aging', 'negative regulation of cell aging', 'positive regulation of cell aging', 'oncogene-induced cell senescence', 'stress-induced premature senescence', 'oxidative stress-induced premature senescence', 'progressive alteration of chromatin involved in cell aging', 'extrachromosomal circular DNA accumulation involved in cell aging', 'extrachromosomal circular DNA localization involved in cell aging']	senescent cells accumulation	накопление сенесцентных клеток
 ['stem cell differentiation', 'stem cell division', 'stem cell population maintenance']	stem cell exhaustion	истощение пула стволовых клеток
 ['transposition']	transposon activity	транспозонная активность
-['inflammatory response', 'production of molecular mediator involved in inflammatory response']	sterile inflammation	стерильное воспаление
+['inflammatory response', 'production of molecular mediator involved in inflammatory response', 'I-kappaB kinase/NF-kappaB signaling']	sterile inflammation	стерильное воспаление
 ['cell communication']	intercellular communication impairment	нарушения межклеточного взаимодействия
-['extracellular matrix assembly', 'extracellular matrix disassembly', 'extracellular matrix constituent secretion', 'dentin extracellular matrix secretion', 'extracellular matrix structural constituent']	changes in the extracellular matrix structure	изменения структуры межклеточного матрикса
+['extracellular matrix assembly', 'extracellular matrix disassembly', 'extracellular matrix constituent secretion', 'dentin extracellular matrix secretion', 'extracellular matrix structural constituent']	changes in the extracellular matrix structure	изменения структуры межклеточного матрикса
+['autophagy', 'autophagosome assembly', 'autophagy of mitochondrion']	disabled macroautophagy	отключение макроаутофагии

scripts/confidence_level/confidence_level.tsv

@@ -5,7 +5,7 @@ AKT1	highest
 GH1	highest
 GHR	highest
 GHRHR	highest
-GRN	highest
+HSPA1A	highest
 HTT	highest
 IGF1R	highest
 INSR	highest
@@ -48,8 +48,8 @@ G6PD	high
 GDF15	high
 GHRH	high
 GPX4	high
+GRN	high
 GSTA4	high
-HSPA1A	high
 HSPA1B	high
 IGF1	high
 IGFBP2	high
@@ -83,7 +83,7 @@ ADAMTS20	moderate
 AKT3	moderate
 ATP5O	moderate
 ATR	moderate
-BCL2L1	moderate
+BCL2L2	moderate
 BUB3	moderate
 CHRNA7	moderate
 CLU	moderate
@@ -93,8 +93,7 @@ DUSP10	moderate
 E2F1	moderate
 EEF1A1	moderate
 EEF2	moderate
-EGR1	moderate
-EIF5A2	moderate
+EIF5A	moderate
 ERCC4	moderate
 EZH2	moderate
 FOXO1	moderate
@@ -119,15 +118,12 @@ INS	moderate
 ITGB1	moderate
 JAK1	moderate
 JAK2	moderate
-LMNA	moderate
-LMNB1	moderate
 MAPK10	moderate
 MAPK14	moderate
 MAPK8	moderate
 MAPK9	moderate
 MRPS5	moderate
 MSRA	moderate
-MT-CO1	moderate
 MXD1	moderate
 NFE2L1	moderate
 NOTCH1	moderate
@@ -204,13 +200,15 @@ DBN1	low
 DMD	low
 EEF1E1	low
 EFEMP1	low
+EIF5A2	low
 EGFR	low
 EIF4EBP1	low
 ELN	low
 ERBB2	low
 ERCC1	low
 ERCC2	low
 ERCC5	low
+ERCC8	low
 ESR1	low
 FADS1	low
 FBN1	low
@@ -244,6 +242,8 @@ IL6R	low
 IL7	low
 ITGB3	low
 JUND	low
+LMNA	low
+LMNB1	low
 LOX	low
 MAP3K5	low
 MDM2	low
@@ -279,6 +279,7 @@ POLG	low
 PON1	low
 PPARA	low
 PPM1D	low
+PPP1CA	low
 PRKCB	low
 PRKCD	low
 PRKCH	low
@@ -304,6 +305,7 @@ SLC19A1	low
 SOCS2	low
 SOD3	low
 STAT3	low
+STAT5B	low
 SUB1	low
 TERC	low
 TERF1	low