release (#118)

* Changed api/gene/symbols output format and corrected doc

* bugfix: return lang_en if lang_ru empty

* OG-936: measurementMethod fix empty response

* Add updated datasets with missing experiments (#107)

* New datasets with studies that were not added

* Correct dataset for blue form

* Correct dataset for pink form

* Rename new datasets

* Change names of the datasets

* Update dataset with missing experiments

* Noissue. Do not change timestamp when gene was created

* Noissue. Don't perform delete in longevity associations script since now

* Noissue. Update confidence_level.tsv dataset

* Updated first query assignment to avoid duplicates

* OG-943: change logic and refactor code for the script binding hallmarks and GO-terms

* Added join in _form, changed filter behavior, deleted created tester router

* Update README.md

* #115. Remove GROUP BY

Co-authored-by: psnewbee <savlovp@mail.ru>
Co-authored-by: anthony <antonwowis@yandex.ru>

README.md

@@ -1,4 +1,9 @@
-# Open Genes Python API
+# Open Genes API
+
+[![API CI](https://github.com/open-genes/open-genes-api/actions/workflows/api.yml/badge.svg?branch=master)](https://github.com/open-genes/open-genes-api/actions/workflows/api.yml)
+[![CodeQL](https://github.com/open-genes/open-genes-api/actions/workflows/codeql-analysis.yml/badge.svg?branch=master)](https://github.com/open-genes/open-genes-api/actions/workflows/codeql-analysis.yml)
+
+Open Genes API is based on [FastAPI](https://fastapi.tiangolo.com/) framework and provides data for genes and experiments in Open Genes database.
 
 ## Architecture
 
@@ -17,6 +22,8 @@
 
 ## Development
 
+
+
 ### Build local development image
 
 ```

api/db/dao.py

@@ -580,6 +580,7 @@ def get_symbols(self):
 
 
 class ResearchesDAO(BaseDAO):
+
     def increase_lifespan_search(self, input):
         IncreaseLifespanSearched.__fields__['geneAliases'].outer_type_ = str
 

api/models/gene.py

@@ -158,7 +158,6 @@ class GeneCommon(BaseModel):
 LEFT JOIN gene_to_ontology ON gene.id = gene_to_ontology.gene_id
 LEFT JOIN gene_ontology_to_aging_mechanism_visible ON gene_to_ontology.gene_ontology_id = gene_ontology_to_aging_mechanism_visible.gene_ontology_id
 INNER JOIN aging_mechanism ON gene_ontology_to_aging_mechanism_visible.aging_mechanism_id = aging_mechanism.id AND aging_mechanism.name_en != ''
-GROUP BY aging_mechanism.id
 """,
         )
     ]

api/models/researches.py

@@ -600,11 +600,17 @@ class IncreaseLifespanSearchInput(PaginationInput, LanguageInput, SortInput):
             lambda value: value.split(',') + [len(value.split(','))],
         ],
         'bySpecies': [
-            lambda value: '(select count(distinct model_organism_id) from lifespan_experiment where lifespan_experiment.gene_id=gene.id and model_organism_id in ('
+            lambda value: 'model_organism.id in ('
             + ','.join(['%s' for v in value.split(',')])
-            + '))=%s',
-            lambda value: value.split(',') + [len(value.split(','))],
+            + ')',
+            lambda value: value.split(','),
         ],
+        # 'bySpecies': [
+        #     lambda value: '(select count(distinct model_organism_id) from lifespan_experiment where lifespan_experiment.gene_id=gene.id and model_organism_id in ('
+        #     + ','.join(['%s' for v in value.split(',')])
+        #     + '))=%s',
+        #     lambda value: value.split(',') + [len(value.split(','))],
+
         'byOrigin': [
             lambda value: '(select count(*) from phylum where gene.phylum_id=phylum.id and phylum.name_phylo in ('
             + ','.join(['%s' for v in value.split(',')])
@@ -662,6 +668,7 @@ class IncreaseLifespanSearched(IncreaseLifespan):
 left join statistical_significance as ssmean on ssmean.id = general_lifespan_experiment.lifespan_mean_change_stat_sign_id
 left join statistical_significance as ssmedian on ssmedian.id = general_lifespan_experiment.lifespan_median_change_stat_sign_id
 left join statistical_significance as ssmax on ssmax.id = general_lifespan_experiment.lifespan_max_change_stat_sign_id
+left join model_organism on model_organism.id = general_lifespan_experiment.model_organism_id
 @FILTERING@
 @PAGING@
 """