update http handling and add pfam warning

data/data.go

@@ -24,7 +24,7 @@ import (
 )
 
 // MotifNames has human-readable names
-//  - mostly from http://pfam-legacy.xfam.org/help#tabview=tab9
+//   - mostly from http://pfam-legacy.xfam.org/help#tabview=tab9
 var MotifNames = map[string]string{
 	"disorder":       "Disordered region",
 	"low_complexity": "Low complexity region",

data/http.go

@@ -1,19 +1,28 @@
+//go:build !wasm
 // +build !wasm
 
 package data
 
 import (
+	"crypto/tls"
+	"fmt"
 	"net/http"
 	"net/url"
-    "crypto/tls"
+	"os"
 )
 
 func httpGet(url string) (*http.Response, error) {
+	return http.Get(url)
+}
+
+func httpGetInsecure(url string) (*http.Response, error) {
 	tr := &http.Transport{
-        TLSClientConfig: &tls.Config{InsecureSkipVerify: true},
-    }
-    client := &http.Client{Transport: tr}
-    return client.Get(url)
+		TLSClientConfig: &tls.Config{InsecureSkipVerify: true},
+	}
+	client := &http.Client{Transport: tr}
+	fmt.Fprintln(os.Stderr, "WARNING: making insecure request to ", url)
+	fmt.Fprintln(os.Stderr, "         eventually this will no longer work correctly!")
+	return client.Get(url)
 }
 
 func httpPostForm(url string, vals url.Values) (*http.Response, error) {

data/http_wasm.go

@@ -1,3 +1,4 @@
+//go:build wasm
 // +build wasm
 
 package data
@@ -24,6 +25,11 @@ func httpGet(url string) (*http.Response, error) {
 	return resp, err
 }
 
+func httpGetInsecure(url string) (*http.Response, error) {
+	// I am not willing to test if this can be configured in WASM.
+	return httpGet(url)
+}
+
 // implements http.PostForm but makes wasm's fetch work with CORS
 func httpPostForm(wurl string, vals url.Values) (*http.Response, error) {
 	body := strings.NewReader(vals.Encode())

data/pfam.go

@@ -29,7 +29,7 @@ const PfamGraphicURL = "https://pfam-legacy.xfam.org/protein/%s/graphic"
 
 func GetPfamGraphicData(accession string) (*GraphicResponse, error) {
 	queryURL := fmt.Sprintf(PfamGraphicURL, accession)
-	resp, err := httpGet(queryURL)
+	resp, err := httpGetInsecure(queryURL)
 	if err != nil {
 		if err, ok := err.(net.Error); ok && err.Timeout() {
 			fmt.Fprintf(os.Stderr, "Unable to connect to Pfam. Check your internet connection or try again later.")
@@ -47,9 +47,9 @@ func GetPfamGraphicData(accession string) (*GraphicResponse, error) {
 
 	data := []GraphicResponse{}
 	err = json.Unmarshal(respBytes, &data)
-	//if err != nil {
-	//	return nil, err
-	//}
+	if err != nil {
+		return nil, err
+	}
 	if len(data) != 1 {
 		return nil, fmt.Errorf("pfam returned invalid result")
 	}

data/uniprot.go

@@ -19,6 +19,7 @@ package data
 
 import (
 	"bytes"
+	"compress/gzip"
 	"encoding/json"
 	"fmt"
 	"io"
@@ -60,13 +61,27 @@ func getValueForKey(line, key string) string {
 	return ""
 }
 
+func uniprotDecompress(respBytes []byte) []byte {
+	// uniprot's REST implementation doesn't set a valid Content-Encoding header when
+	// gzipping the response, so Go's automatic gzip decompression doesn't work.
+	// since they'll probably fix it after put in this workaround, we'll just try
+	// to un-gzip and replace the content if it doesn't fail.
+
+	buf := bytes.NewReader(respBytes)
+	zrdr, err := gzip.NewReader(buf)
+	if err != nil {
+		return respBytes
+	}
+	data, err := io.ReadAll(zrdr)
+	if err == nil {
+		return data
+	}
+	return respBytes
+}
+
 func GetUniprotGraphicData(accession string) (*GraphicResponse, error) {
 	queryURL := fmt.Sprintf(UniprotDataURL, accession)
-	client := &http.Client{}
-	req, err := http.NewRequest("GET", queryURL, nil)
-	req.Header.Add("Accept-Encoding", "UTF-8")
-	resp, err := client.Do(req)
-
+	resp, err := httpGet(queryURL)
 	if err != nil {
 		if err, ok := err.(net.Error); ok && err.Timeout() {
 			fmt.Fprintf(os.Stderr, "Unable to connect to Uniprot. Check your internet connection or try again later.")
@@ -79,6 +94,7 @@ func GetUniprotGraphicData(accession string) (*GraphicResponse, error) {
 	if err != nil {
 		return nil, err
 	}
+	respBytes = uniprotDecompress(respBytes)
 	if resp.StatusCode != 200 {
 		return nil, fmt.Errorf("pfam error: %s", resp.Status)
 	}
@@ -172,26 +188,20 @@ const UNIPROTRESTURL = "https://rest.uniprot.org/uniprotkb/search?query=%s+AND+r
 
 func GetProtID(symbol string) (string, error) {
 	apiURL := fmt.Sprintf(UNIPROTRESTURL, symbol)
-	client := &http.Client{}
-	req, err := http.NewRequest("GET", apiURL, nil)
-	req.Header.Add("Accept-Encoding", "UTF-8")
-	resp, err := client.Do(req)
-	if err != nil {
-		log.Fatal(err)
-	}
-	defer resp.Body.Close()
+	resp, err := http.Get(apiURL)
 	if err != nil {
 		if err, ok := err.(net.Error); ok && err.Timeout() {
 			fmt.Fprintf(os.Stderr, "Unable to connect to Uniprot. Check your internet connection or try again later.")
 			os.Exit(1)
 		}
 		return "", err
 	}
-
+	defer resp.Body.Close()
 	respBytes, err := io.ReadAll(resp.Body)
 	if err != nil {
 		return "", err
 	}
+	respBytes = uniprotDecompress(respBytes)
 	if resp.StatusCode != 200 {
 		return "", fmt.Errorf("uniprot error: %s", resp.Status)
 	}