Fixes #2302 bug influx #2327
Fixes #2302 bug influx #2327
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| CREATE TABLE tab_known_transporters_containers | ||
| ( | ||
| gene text, | ||
| species text, | ||
| container_type text, | ||
| container_name text, | ||
| transport_type text, | ||
| membrane text, | ||
| constraint tab_known_transporters_containers_pk | ||
| primary key (gene, species, container_type, container_name), | ||
| constraint tab_known_transporters_containers_tab_known_transporters_gene_species_fk | ||
| foreign key (gene, species) references tab_known_transporters (gene, species) | ||
| ); |
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Missing in the table definition:
- Foreign Key
{container_type, container_name} => tab_container_names - transport_type: constraint with allowed types (Influx, Efflux, ...)
- Actually it would be better to define a new table "tab_active_transport_types" with just 1 column "transport_type"
(with foreign keytab_active_transport_types.transport_type => tab_process_types.process_type)
And then define foreign keytab_known_transporters_containers.transport_type => tab_active_transport_types
- Actually it would be better to define a new table "tab_active_transport_types" with just 1 column "transport_type"
- membrane: constraint (Apical, Basolateral)
If you want, we can merge as is and I will add the FKs/Constraints after that.
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Yes please. I just copied the table that we had before so it somewhat should have taken over the relationship. I don't think we had constraints on columns at all
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Membrane is also brain barrier etc.
| INSERT INTO tab_known_transporters_containers VALUES('ABCC6','Human','COMPARTMENT','Periportal','Efflux','Basolateral'); | ||
| INSERT INTO tab_known_transporters_containers VALUES('SLC22A9','Human','COMPARTMENT','Pericentral','Efflux','Basolateral'); | ||
| INSERT INTO tab_known_transporters_containers VALUES('SLC22A9','Human','COMPARTMENT','Periportal','Efflux','Basolateral'); | ||
| CREATE TABLE tab_transport_directions (transport_direction text CONSTRAINT tab_transport_directions_pk PRIMARY KEY, display_name text NOT NULL, description text NOT NULL, icon text DEFAULT Influx); |
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...icon text DEFAULT Influx
The default value for the icon does not really make sense here, right?
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This was from before. No idea what this is.
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I know, just noticed it only now :)
| INSERT INTO tab_transport_directions VALUES('EffluxBloodCellsToPlasma','Efflux Blood Cells to Plasma','Efflux transport from blood cells to blood plasma across blood cell membrane','Efflux'); | ||
| INSERT INTO tab_transport_directions VALUES('InfluxInterstitialToIntracellular','Influx Interstitial to Intracellular','Influx transport from interstitial into intracellular space across cell membrane','Influx'); | ||
| INSERT INTO tab_transport_directions VALUES('EffluxIntracellularToInterstitial','Efflux Intracellular to Interstitial','Efflux transport from intracellular into interstitial space across cell membrane','Efflux'); | ||
| INSERT INTO tab_transport_directions VALUES('InfluxLumenToMucosaIntracellular','Influx Lumen To Mucosa/Intracellular','Active uptake from gastrointestinal lumen into mucosal cells','Influx'); |
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'Influx Lumen To Mucosa/Intracellular'
Replace "To" with "to"
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also stuff from before. If you look at the dump, this is a dump o the db
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Same. Old error, but I didn't notice it before
| INSERT INTO tab_transport_directions VALUES('InfluxBrainPlasmaToInterstitial','Influx Plasma to Interstitial','Influx transport from blood plasma to interstitial space across the blood-brain-barrier','Influx'); | ||
| INSERT INTO tab_transport_directions VALUES('EffluxBrainInterstitialToPlasma','Efflux Interstitial to Plasma','Efflux transport from interstitial space to blood plasma across the blood-brain-barrier','Efflux'); | ||
| INSERT INTO tab_transport_directions VALUES('PgpBrainInterstitialToPlasma','[DEPRECATED] Pgp Interstitial to plasma','[DEPRECATED] Pgp transport from interstitial space to blood plasma across the blood-brain-barrier accounting for the structural peculiarity of P-gp transporter. Will be removed in version 12 of the software','Pgp'); | ||
| INSERT INTO tab_transport_directions VALUES('None','','',''); |
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Why do we need this "None"-entry?
| var transportType = _transporterTemplateRepository.TransportTypeFor(speciesName, transporterName); | ||
| transporter.TransportType = transportType; | ||
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| if (!_transporterTemplateRepository.HasTransporterTemplateFor(speciesName, transporterName)) | ||
| { | ||
| //No template was found for the given name. Raise event warning | ||
| _eventPublisher.PublishEvent(new NoTransporterTemplateAvailableEvent(transporter)); | ||
| return; | ||
| } |
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why are the lines 45-46 called BEFORE the lines 48-53?
I would expect the opposite order: transporter type from template is set only if the template exists
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Well there is still a default being returned if not found. in the TemplateRepository. ,Maywe we should rename to TransportTypeOrDefault
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yep, would be good to rename it, otherwise the code here looking strange (without going in the called functions)
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ok, just created some additional issues.
If you rename TransportTypeFor=>TransportTypeOrDefault we can merge I think
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Most comments here are unrelated to the PR. Can you create an issue for those and fix (even better )? |
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@Yuri05 Done: |
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