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create_DB.sh
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rm data/*.json
entries=(Escherichia_coli_cft073 Escherichia_coli_o157_h7_str_edl933 Escherichia_coli_str_k_12_substr_mg1655 new_coli)
for e in ${entries[*]};do
python3 src/create_json.py ${e}
done
cd genomicus
python3 manage.py makemigrations
python3 manage.py migrate
for e in ${entries[*]};do
python3 manage.py loaddata ../data/${e}_genome.json
python3 manage.py loaddata ../data/${e}_seq.json
python3 manage.py loaddata ../data/${e}_cds_dico.json
python3 manage.py loaddata ../data/${e}_cds_seq.json
python3 manage.py loaddata ../data/${e}_pep_dico.json
python3 manage.py loaddata ../data/${e}_pep_seq.json
done
# add members in the bdd
echo "from member.models import Member; Member.objects.create_member(email='clemence.sebe@universite-paris-saclay.fr', password='clemence', lastName='Sebe', firstName='Clémence')" | python3 manage.py shell
echo "from member.models import Member; Member.objects.create_member(email='ambre.baumann@universite-paris-saclay.fr', password='ambre', lastName='Baumann', firstName='Ambre')" | python3 manage.py shell
echo "from member.models import Member; m = Member.objects.filter(email='ambre.baumann@universite-paris-saclay.fr'); m.update(user_type=2) " | python3 manage.py shell
echo "from member.models import Member; Member.objects.create_member(email='lindsay.goulet@universite-paris-saclay.fr', password='lindsay', lastName='Goulet', firstName='Lindsay')" | python3 manage.py shell
echo "from member.models import Member; m = Member.objects.filter(email='lindsay.goulet@universite-paris-saclay.fr'); m.update(user_type=3) " | python3 manage.py shell
echo "from member.models import Member; Member.objects.create_member(email='george.marchment@universite-paris-saclay.fr', password='george', lastName='Marchment', firstName='George')" | python3 manage.py shell
echo "from member.models import Member; m = Member.objects.filter(email='george.marchment@universite-paris-saclay.fr'); m.update(user_type=4) " | python3 manage.py shell
echo "Members created successfully."
# add forum/discussion
echo 'from genomApp.models import Forum, CodantInfo, Genome; from member.models import Member; forum = Forum(id=CodantInfo.objects.get(id="cds_AAN80781"), id_chromosome=Genome.objects.get(id="ASM744v1"), date="2022-12-29", auteur=Member.objects.get(email = "lindsay.goulet@universite-paris-saclay.fr")); forum.save()' | python3 manage.py shell
echo 'from genomApp.models import Forum, Commentaire; from member.models import Member; c = Commentaire(id_forum=Forum.objects.get(id="cds_AAN80781"), date="2022-12-29", text="Bonjour, j'"'"'aimerai savoir qui est la personne qui a annoté le peptide AAN80781. Merci.", auteur=Member.objects.get(email = "lindsay.goulet@universite-paris-saclay.fr")); c.save()' | python3 manage.py shell
echo 'from genomApp.models import Forum, Commentaire; from member.models import Member; c = Commentaire(id_forum=Forum.objects.get(id="cds_AAN80781"), date="2023-01-12", text="Bonjour Lindsay, c'"'"'est moi qui l'"'"'ai annoté. Vous avez une question au sujet de ce qui est écrit ?", auteur=Member.objects.get(email = "ambre.baumann@universite-paris-saclay.fr")); c.save()' | python3 manage.py shell
echo 'from genomApp.models import Forum, CodantInfo, Genome; from member.models import Member; forum = Forum(id=CodantInfo.objects.get(id="cds_AAG54493"), id_chromosome=Genome.objects.get(id="ASM666v1"), date="2023-01-04", auteur=Member.objects.get(email = "ambre.baumann@universite-paris-saclay.fr")); forum.save()' | python3 manage.py shell
echo 'from genomApp.models import Forum, Commentaire; from member.models import Member; c = Commentaire(id_forum=Forum.objects.get(id="cds_AAG54493"), date="2023-01-04", text="Bonjour, j'"'"'ai une question à propos de l'"'"'annotation. Est-ce que je pourrais savoir qui a annoté et validé l'"'"'annotation ? Merci.", auteur=Member.objects.get(email = "ambre.baumann@universite-paris-saclay.fr")); c.save()' | python3 manage.py shell
echo 'from genomApp.models import Forum, Commentaire; from member.models import Member; c = Commentaire(id_forum=Forum.objects.get(id="cds_AAG54493"), date="2023-01-06", text="Bonjour Ambre, c'"'"'est moi qui l'"'"'ai annoté. Vous avez une question au sujet de ce qui est écrit ?", auteur=Member.objects.get(email = "lindsay.goulet@universite-paris-saclay.fr")); c.save()' | python3 manage.py shell
echo 'from genomApp.models import Forum, Commentaire; from member.models import Member; c = Commentaire(id_forum=Forum.objects.get(id="cds_AAG54493"), date="2023-01-10", text="Bonjour, je suis le validateur de cette annotation.", auteur=Member.objects.get(email = "george.marchment@universite-paris-saclay.fr")); c.save()' | python3 manage.py shell
echo "Forum and discussions created successfully."
# add an annotation
#Donc Ambre elle a 3 annotations à faire (une qui à déjà été) -> 2 à validé pour George (compris celui qui a déjà était annoté) et l'autre pour Lindsay
echo 'from genomApp.models import Annotation, CodantInfo; from member.models import Member; Annotation(id= CodantInfo.objects.get(id="cds_AAN80781"), gene = "", gene_symbol = "", description = "", annotateur = Member.objects.get(email="ambre.baumann@universite-paris-saclay.fr"), validateur = Member.objects.get(email="lindsay.goulet@universite-paris-saclay.fr"), already_annotated =False).save() ' | python3 manage.py shell
echo 'from genomApp.models import Annotation, CodantInfo; from member.models import Member; Annotation(id= CodantInfo.objects.get(id="cds_ABG68043"), gene = "", gene_symbol = "", description = "", annotateur = Member.objects.get(email="ambre.baumann@universite-paris-saclay.fr"), validateur = Member.objects.get(email="george.marchment@universite-paris-saclay.fr"), already_annotated =False ).save() ' | python3 manage.py shell
echo 'from genomApp.models import Annotation, CodantInfo; from member.models import Member; Annotation(id= CodantInfo.objects.get(id="cds_AAG54493"), gene = "", gene_symbol = "", description = "", annotateur = Member.objects.get(email="lindsay.goulet@universite-paris-saclay.fr"), validateur = Member.objects.get(email="george.marchment@universite-paris-saclay.fr"), already_annotated =False ).save() ' | python3 manage.py shell
echo 'from genomApp.models import Annotation, CodantInfo; from member.models import Member; Annotation(id= CodantInfo.objects.get(id="cds_ABG68044"), gene = "Gene test", gene_symbol = "Test symbol", description = "Description", annotateur = Member.objects.get(email="ambre.baumann@universite-paris-saclay.fr"), validateur = Member.objects.get(email="george.marchment@universite-paris-saclay.fr"), already_annotated =True ).save() ' | python3 manage.py shell
echo 'from genomApp.models import Annotation, CodantInfo; from member.models import Member; Annotation(id= CodantInfo.objects.get(id="cds_ABG70353"), gene = "", gene_symbol = "", description = "", annotateur = Member.objects.get(email="ambre.baumann@universite-paris-saclay.fr"), validateur = Member.objects.get(email="george.marchment@universite-paris-saclay.fr"), already_annotated =False ).save() ' | python3 manage.py shell
echo "Annotations created successfully."
cd ..