clean up and update

Author: sofyalaski

Dockerfile

@@ -12,7 +12,11 @@ RUN go mod download
 
 # Copy the source code
 COPY main.go ./
-COPY /data/conversions.csv /app/data/conversions.csv
+
+# Download conversions.csv from OSCEM GitHub repository
+RUN mkdir -p /app/data && \
+    curl -L https://raw.githubusercontent.com/osc-em/Converter/main/csv/pdb_conversions.csv -o /app/data/conversions.csv
+
 COPY /data/mmcif_pdbx_v50.dic /app/data/mmcif_pdbx_v50.dic
 COPY depositions/onedep ./depositions/onedep
 COPY docs ./docs
@@ -70,7 +74,7 @@ RUN pip install --upgrade pip && \
 WORKDIR /app
 
 ENV PORT=8080
-ENV ALLOW_ORIGINS=http://localhost:4201
+ENV ALLOW_ORIGINS=http://localhost:4200
 ENV RCSBROOT=/app/scripts/packages/maxit-v11.300-prod-src
 
 EXPOSE 8080

depositions/onedep/config.go

@@ -18,12 +18,13 @@ const (
 )
 
 type RequestCreate struct {
-	Email    string   `json:"email" binding:"required,email"`
-	OrcidIds []string `json:"orcidIds" binding:"required"`
-	Password string   `json:"password" binding:"-"`
-	Country  string   `json:"country" binding:"required"`
-	Method   string   `json:"method" binding:"required"`
-	JWTToken string   `json:"jwtToken" binding:"required"`
+	Email       string   `json:"email" binding:"required,email"`
+	OrcidIds    []string `json:"orcidIds" binding:"required"`
+	Password    string   `json:"password"`
+	Country     string   `json:"country" binding:"required"`
+	Method      string   `json:"method" binding:"required"`
+	JWTToken    string   `json:"jwtToken" binding:"required"`
+	Coordinates bool     `json:"coordinates"`
 }
 
 type FileMetadata struct {
@@ -44,8 +45,11 @@ type UploadedFile struct {
 	FileID string `json:"FileID"`
 }
 type EmMethod struct {
-	Type    string `json:"type"`
-	Subtype string `json:"subtype,omitempty"`
+	Type        string `json:"type"`
+	Subtype     string `json:"subtype,omitempty"`
+	Coordinates bool   `json:"coordinates"`
+	SfOnly      bool   `json:"sf_only"`
+	RelatedEmdb string `json:"related_emdb,omitempty"`
 }
 type EmMethodExtended struct {
 	Type        string `json:"type"`
@@ -71,10 +75,10 @@ type UserInfo struct {
 }
 
 type FileUpload struct {
-	Name    string  `json:"name"`
-	Type    string  `json:"type"`
-	Contour float32 `json:"contour"`
-	Details string  `json:"details"`
+	Name    string     `json:"name"`
+	Type    OneDepType `json:"type"`
+	Contour float32    `json:"contour"`
+	Details string     `json:"details"`
 }
 
 type DepositionFile struct {
@@ -126,6 +130,7 @@ type OneDepType string
 const (
 	ADD_MAP     OneDepType = "add-map"
 	CO_CIF      OneDepType = "co-cif"
+	MD_CIF      OneDepType = "md-cif"
 	CO_PDB      OneDepType = "co-pdb"
 	FSC_XML     OneDepType = "fsc-xml"
 	HALF_MAP    OneDepType = "half-map"

depositions/onedep/onedep.go

@@ -81,7 +81,13 @@ func CreateDeposition(client *http.Client, userInput UserInfo, token string) (De
 
 // creates a new instance of DepositionFile
 func NewDepositionFile(depositionID string, fileUpload FileUpload) *DepositionFile {
-	fD := DepositionFile{depositionID, 0, fileUpload.Name, fileUpload.Type, [3]float32{}, fileUpload.Contour, fileUpload.Details}
+	fD := DepositionFile{depositionID,
+		0,
+		fileUpload.Name,
+		string(fileUpload.Type),
+		[3]float32{},
+		fileUpload.Contour,
+		fileUpload.Details}
 	return &fD
 }
 
@@ -335,19 +341,18 @@ func ProcessDeposition(client *http.Client, deposition string, token string) (st
 	if err != nil {
 		return "", fmt.Errorf("errored when sending request to the server: %v", err)
 	}
+	defer resp.Body.Close()
+
 	statusCode := resp.StatusCode
-	err = resp.Body.Close()
-	if err != nil {
-		return "", fmt.Errorf("error closing response body: %v", err)
-	}
 	if statusCode == 200 || statusCode == 201 {
 		return "success", nil
-	} else {
-		body, err := io.ReadAll(resp.Body)
-		if err != nil {
-			return "", fmt.Errorf("create: failed to create new deposition: status code %v, status %s, unreadable body", resp.StatusCode, resp.Status)
-		}
-		return "", fmt.Errorf("create: failed to create new deposition: status code %v, status %s, body %s", resp.StatusCode, resp.Status, string(body))
 	}
 
+	// Read error response body before it's closed
+	body, err := io.ReadAll(resp.Body)
+	if err != nil {
+		return "", fmt.Errorf("process: failed to process deposition: status code %v, status %s, unreadable body", resp.StatusCode, resp.Status)
+	}
+	return "", fmt.Errorf("process: failed to process deposition: status code %v, status %s, body %s", resp.StatusCode, resp.Status, string(body))
+
 }

docs/docs.go

@@ -676,6 +676,7 @@ const docTemplate = `{
             "enum": [
                 "add-map",
                 "co-cif",
+                "md-cif",
                 "co-pdb",
                 "fsc-xml",
                 "half-map",
@@ -710,6 +711,7 @@ const docTemplate = `{
             "x-enum-varnames": [
                 "ADD_MAP",
                 "CO_CIF",
+                "MD_CIF",
                 "CO_PDB",
                 "FSC_XML",
                 "HALF_MAP",
@@ -752,6 +754,9 @@ const docTemplate = `{
                 "orcidIds"
             ],
             "properties": {
+                "coordinates": {
+                    "type": "boolean"
+                },
                 "country": {
                     "type": "string"
                 },

docs/swagger.json

@@ -668,6 +668,7 @@
             "enum": [
                 "add-map",
                 "co-cif",
+                "md-cif",
                 "co-pdb",
                 "fsc-xml",
                 "half-map",
@@ -702,6 +703,7 @@
             "x-enum-varnames": [
                 "ADD_MAP",
                 "CO_CIF",
+                "MD_CIF",
                 "CO_PDB",
                 "FSC_XML",
                 "HALF_MAP",
@@ -744,6 +746,9 @@
                 "orcidIds"
             ],
             "properties": {
+                "coordinates": {
+                    "type": "boolean"
+                },
                 "country": {
                     "type": "string"
                 },

docs/swagger.yaml

@@ -110,6 +110,7 @@ definitions:
     enum:
     - add-map
     - co-cif
+    - md-cif
     - co-pdb
     - fsc-xml
     - half-map
@@ -144,6 +145,7 @@ definitions:
     x-enum-varnames:
     - ADD_MAP
     - CO_CIF
+    - MD_CIF
     - CO_PDB
     - FSC_XML
     - HALF_MAP
@@ -176,6 +178,8 @@ definitions:
     - XS_MTZ
   onedep.RequestCreate:
     properties:
+      coordinates:
+        type: boolean
       country:
         type: string
       email:

go.mod

@@ -7,7 +7,7 @@ toolchain go1.23.8
 require (
 	github.com/gin-contrib/cors v1.7.3
 	github.com/gin-gonic/gin v1.10.0
-	github.com/osc-em/converter-OSCEM-to-mmCIF v1.1.6
+	github.com/osc-em/converter-OSCEM-to-mmCIF v1.1.8
 	github.com/swaggo/files v1.0.1
 	github.com/swaggo/gin-swagger v1.6.0
 	github.com/swaggo/swag v1.16.4

go.sum

@@ -65,8 +65,8 @@ github.com/modern-go/concurrent v0.0.0-20180306012644-bacd9c7ef1dd h1:TRLaZ9cD/w
 github.com/modern-go/concurrent v0.0.0-20180306012644-bacd9c7ef1dd/go.mod h1:6dJC0mAP4ikYIbvyc7fijjWJddQyLn8Ig3JB5CqoB9Q=
 github.com/modern-go/reflect2 v1.0.2 h1:xBagoLtFs94CBntxluKeaWgTMpvLxC4ur3nMaC9Gz0M=
 github.com/modern-go/reflect2 v1.0.2/go.mod h1:yWuevngMOJpCy52FWWMvUC8ws7m/LJsjYzDa0/r8luk=
-github.com/osc-em/converter-OSCEM-to-mmCIF v1.1.6 h1:OxIRwRl5+/B13iSJc9/Z55ai1Q8GuK0I76ycublB+XE=
-github.com/osc-em/converter-OSCEM-to-mmCIF v1.1.6/go.mod h1:DO+6haNZuJjZgNwafIZdznFWzXPWazSG5iSKjhdBKPw=
+github.com/osc-em/converter-OSCEM-to-mmCIF v1.1.8 h1:ZT9usrIWucBG6GxiVVFHutdp6M761vVsX6FCNJyl4mA=
+github.com/osc-em/converter-OSCEM-to-mmCIF v1.1.8/go.mod h1:DO+6haNZuJjZgNwafIZdznFWzXPWazSG5iSKjhdBKPw=
 github.com/pelletier/go-toml/v2 v2.2.3 h1:YmeHyLY8mFWbdkNWwpr+qIL2bEqT0o95WSdkNHvL12M=
 github.com/pelletier/go-toml/v2 v2.2.3/go.mod h1:MfCQTFTvCcUyyvvwm1+G6H/jORL20Xlb6rzQu9GuUkc=
 github.com/pmezard/go-difflib v1.0.0 h1:4DBwDE0NGyQoBHbLQYPwSUPoCMWR5BEzIk/f1lZbAQM=