Commit acb9d8a3 authored by Marek Ostaszewski's avatar Marek Ostaszewski

Compartment harmonisatino, missed fixes

parent be673a43
...@@ -245,7 +245,7 @@ Metabolic interactions of the SARS-CoV-2 Nsp14 with the human galactose, nicotin ...@@ -245,7 +245,7 @@ Metabolic interactions of the SARS-CoV-2 Nsp14 with the human galactose, nicotin
<celldesigner:compartmentAlias id="ca1" compartment="c1"> <celldesigner:compartmentAlias id="ca1" compartment="c1">
<celldesigner:class>SQUARE</celldesigner:class> <celldesigner:class>SQUARE</celldesigner:class>
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...@@ -253,7 +253,7 @@ Metabolic interactions of the SARS-CoV-2 Nsp14 with the human galactose, nicotin ...@@ -253,7 +253,7 @@ Metabolic interactions of the SARS-CoV-2 Nsp14 with the human galactose, nicotin
<celldesigner:compartmentAlias id="ca2" compartment="c2"> <celldesigner:compartmentAlias id="ca2" compartment="c2">
<celldesigner:class>SQUARE</celldesigner:class> <celldesigner:class>SQUARE</celldesigner:class>
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...@@ -7427,17 +7427,26 @@ Metabolic interactions of the SARS-CoV-2 Nsp14 with the human galactose, nicotin ...@@ -7427,17 +7427,26 @@ Metabolic interactions of the SARS-CoV-2 Nsp14 with the human galactose, nicotin
</listOfUnitDefinitions> </listOfUnitDefinitions>
<listOfCompartments> <listOfCompartments>
<compartment metaid="default" id="default" size="1" units="volume"/> <compartment metaid="default" id="default" size="1" units="volume"/>
<compartment metaid="c1" id="c1" name="cytosol" size="1" units="volume" outside="default"> <compartment metaid="c1" id="c1" name="cell" size="1" units="volume" outside="default">
<annotation> <annotation>
<celldesigner:extension> <celldesigner:extension>
<celldesigner:name>cytosol</celldesigner:name> <celldesigner:name>cell</celldesigner:name>
</celldesigner:extension> </celldesigner:extension>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
<rdf:Description rdf:about="#c1">
<bqbiol:is>
<rdf:Bag>
<rdf:li rdf:resource="urn:miriam:obo.go:GO%3A0005737"/>
</rdf:Bag>
</bqbiol:is>
</rdf:Description>
</rdf:RDF>
</annotation> </annotation>
</compartment> </compartment>
<compartment metaid="c2" id="c2" name="Mitochondria" size="1" units="volume" outside="c1"> <compartment metaid="c2" id="c2" name="GO:0005739" size="1" units="volume" outside="c1">
<annotation> <annotation>
<celldesigner:extension> <celldesigner:extension>
<celldesigner:name>Mitochondria</celldesigner:name> <celldesigner:name>GO:0005739</celldesigner:name>
</celldesigner:extension> </celldesigner:extension>
</annotation> </annotation>
</compartment> </compartment>
...@@ -13438,7 +13447,7 @@ Metabolic interactions of the SARS-CoV-2 Nsp14 with the human galactose, nicotin ...@@ -13438,7 +13447,7 @@ Metabolic interactions of the SARS-CoV-2 Nsp14 with the human galactose, nicotin
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</celldesigner:listOfReactantLinks> </celldesigner:listOfReactantLinks>
...@@ -14144,7 +14153,7 @@ Metabolic interactions of the SARS-CoV-2 Nsp14 with the human galactose, nicotin ...@@ -14144,7 +14153,7 @@ Metabolic interactions of the SARS-CoV-2 Nsp14 with the human galactose, nicotin
<celldesigner:lineDirection index="2" value="horizontal"/> <celldesigner:lineDirection index="2" value="horizontal"/>
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...@@ -14166,7 +14175,7 @@ Metabolic interactions of the SARS-CoV-2 Nsp14 with the human galactose, nicotin ...@@ -14166,7 +14175,7 @@ Metabolic interactions of the SARS-CoV-2 Nsp14 with the human galactose, nicotin
<celldesigner:lineDirection index="2" value="horizontal"/> <celldesigner:lineDirection index="2" value="horizontal"/>
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</celldesigner:reactantLink> </celldesigner:reactantLink>
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...@@ -16227,7 +16236,7 @@ Metabolic interactions of the SARS-CoV-2 Nsp14 with the human galactose, nicotin ...@@ -16227,7 +16236,7 @@ Metabolic interactions of the SARS-CoV-2 Nsp14 with the human galactose, nicotin
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</celldesigner:modification> </celldesigner:modification>
<celldesigner:modification type="INHIBITION" modifiers="s132" aliases="sa213" targetLineIndex="-1,7" editPoints="0.48838794429575216,0.09570106029903513 0.5253656507051687,-0.09300600273284232"> <celldesigner:modification type="INHIBITION" modifiers="s132" aliases="sa213" targetLineIndex="-1,7" editPoints="0.48838794429575927,0.09570106029903513 0.5253656507051758,-0.09300600273284232">
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...@@ -18423,7 +18432,7 @@ Metabolic interactions of the SARS-CoV-2 Nsp14 with the human galactose, nicotin ...@@ -18423,7 +18432,7 @@ Metabolic interactions of the SARS-CoV-2 Nsp14 with the human galactose, nicotin
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...@@ -18947,7 +18956,7 @@ Metabolic interactions of the SARS-CoV-2 Nsp14 with the human galactose, nicotin ...@@ -18947,7 +18956,7 @@ Metabolic interactions of the SARS-CoV-2 Nsp14 with the human galactose, nicotin
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<celldesigner:listOfModification> <celldesigner:listOfModification>
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......
...@@ -28,7 +28,9 @@ get_default_project <- function(map_api) { ...@@ -28,7 +28,9 @@ get_default_project <- function(map_api) {
} }
### Get the components of a given map/project on the MINERVA Platform ### Get the components of a given map/project on the MINERVA Platform
get_map_components <- function(map_api, project_id = NULL) { get_map_components <- function(map_api, project_id = NULL,
e_columns = "",
r_columns = "") {
if(is.null(project_id)) { if(is.null(project_id)) {
### If project id not given, get configuration of the map, to obtain the latest (default) version ### If project id not given, get configuration of the map, to obtain the latest (default) version
project_id <- get_default_project(map_api) project_id <- get_default_project(map_api)
...@@ -41,18 +43,19 @@ get_map_components <- function(map_api, project_id = NULL) { ...@@ -41,18 +43,19 @@ get_map_components <- function(map_api, project_id = NULL) {
### Get diagrams ### Get diagrams
models <- fromJSON(ask_GET(paste0(mnv_base, "models/"))) models <- fromJSON(ask_GET(paste0(mnv_base, "models/")))
if(e_columns != "") { e_columns <- paste0("?columns=", e_columns) }
if(r_columns != "") { r_columns <- paste0("?columns=", r_columns) }
### Get elements of the chosen diagram ### Get elements of the chosen diagram
model_elements <- lapply(models$idObject, model_elements <- lapply(models$idObject,
function(x) function(x)
fromJSON(ask_GET(paste0(mnv_base,"models/",x,"/", fromJSON(ask_GET(paste0(mnv_base,"models/",x,"/","bioEntities/elements/",e_columns)),
"bioEntities/elements/?columns=id,name,type,references,elementId,complexId")),
flatten = F)) flatten = F))
### Request for reactions that have at least one top 10 element as participant ### Request for reactions that have at least one top 10 element as participant
model_reactions <- lapply(models$idObject, model_reactions <- lapply(models$idObject,
function(x) function(x)
fromJSON(ask_GET(paste0(mnv_base,"models/",x,"/", fromJSON(ask_GET(paste0(mnv_base,"models/",x,"/","bioEntities/elements/",r_columns)),
"bioEntities/reactions/?columns=modifiers,products,reactants")),
flatten = F)) flatten = F))
### Pack all into a list and return ### Pack all into a list and return
return(list(models = models, map_elements = model_elements, map_reactions = model_reactions)) return(list(models = models, map_elements = model_elements, map_reactions = model_reactions))
......
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