Merge pull request #133 from gleanerio/mm-dev--api

Consume JSON-LD metadata from a paged API

configs/template/README_Configure_Template.md

@@ -75,7 +75,7 @@ hack,SourceType,Active,Name,ProperName,URL,Headless,Domain,PID,Logo
 
 Fields: 
 1. hack:a hack to make the fields are properly read.
-2. SourceType : [sitemap, sitegraph, googledrive] type of source
+2. SourceType : [sitemap, sitegraph, googledrive, api] type of source
 3. Active: [TRUE,FALSE] is source active. 
 4. Name: short name of source. It should be one word (no space) and be lower case.
 5. ProperName: Long name of source that will be added to organization record for provenance

docs/GleanerConfig.md

@@ -76,7 +76,7 @@ The miller and summon sections are true and we will leave them that way.  It mea
 Now look at the "miller:"  section when lets of pick what milling to do.   Currently it is set with only graph set to true.  Let's leave it that way for now.  This means Gleaner will only attempt to make graph and not also run validation or generate prov reports for the process.  
 
 The final section we need to look at is the "sources:" section.   
-Here is where the fun is.  While there are two types, sitegraph and sitemaps we will normally use sitemap type. 
+Here is where the fun is.  While there multiple types, sitegraph, sitemaps, googledrive and api, we will normally use sitemap type.
 
 
 A standard [sitemap](./SourceSitemap.md) is below:
@@ -122,6 +122,19 @@ sources:
   credentialsfile: configs/credentials/gleaner-331805-030e15e1d9c4.json
   other: {}
 ```
+
+An [API endpoint](./SourceAPI.md)
+```yaml
+sources:
+- sourcetype: api
+  name: example
+  url: http://test-metadata-api.com?query=something&page=%d
+  properName: Example JSON-LD API Source
+  domain: http://test-metadata-api.com
+  active: true
+  apipagelimit: 200
+```
+
 These are the sources we wish to pull and process. 
 Each source has a type, and 8 entries though at this time we no longer use the "logo" value. 
 It was used in the past to provide a page showing all the sources and 

docs/SourceAPI.md

@@ -0,0 +1,16 @@
+## Using a paged API endpoint as a Gleaner source
+
+Sometimes, instead of crawling webpages using a list in a sitemap, we have the opportunity to query an API that will let us directly ingest JSON-LD. To do so, we can specify a `sourcetype: api` in our Gleaner config yaml, and Gleaner will iterate through a paged API, using the given `url` as a template. For example, let's say that you want to use the API endpoint at `http://test-api.com`, and that you can page through it by using a url like `http://test/api.com/page/4`. You would put this in your config:
+
+```yaml
+url: http://test-api.com/page/%d
+```
+
+Notice the `%d` where the page number goes. Gleaner will then increment that number (starting from 0) until it gets an error back from the API.
+
+Optionally, you can set a limit on the number of pages to iterate through, using `apipagelimit`. This means that Gleaner will page through the API until it gets an error back *or* until it reaches the limit you set. That looks like the example below:
+
+```yaml
+url: http://test-api.com/page/%d
+apipagelimit: 200
+```

internal/config/minio.go

@@ -43,7 +43,7 @@ func ReadMinioConfig(minioSubtress *viper.Viper) (Minio, error) {
 	// config already read. substree passed
 	err := minioSubtress.Unmarshal(&minioCfg)
 	if err != nil {
-		log.Fatal("error when parsing minio config: %v", err)
+		log.Fatal("error when parsing minio config: ", err)
 	}
 	return minioCfg, err
 }

internal/config/sources.go

@@ -15,7 +15,7 @@ import (
 
 // as read from csv
 type Sources struct {
-	// Valid values for SourceType: sitemap, sitegraph, csv, googledrive, and robots
+	// Valid values for SourceType: sitemap, sitegraph, csv, googledrive, api, and robots
 	SourceType      string `default:"sitemap"`
 	Name            string
 	Logo            string
@@ -31,6 +31,7 @@ type Sources struct {
 	// Active        bool
 	HeadlessWait int   // if loading is slow, wait
 	Delay        int64 // A domain-specific crawl delay value
+	ApiPageLimit int
 }
 
 // add needed for file
@@ -124,7 +125,7 @@ func GetSources(g1 *viper.Viper) ([]Sources, error) {
 	// config already read. substree passed
 	err := g1.UnmarshalKey(subtreeKey, &cfg)
 	if err != nil {
-		log.Fatal("error when parsing %v config: %v", subtreeKey, err)
+		log.Fatal("error when parsing ", subtreeKey, " config: ", err)
 		//No sources, so nothing to run
 	}
 	for i, s := range cfg {

internal/objects/sourcesAndGraphs.go

@@ -7,17 +7,17 @@ import (
 	"github.com/spf13/viper"
 )
 
-//type Sources struct {
-//	Name       string
-//	Logo       string
-//	URL        string
-//	Headless   bool
-//	PID        string
-//	ProperName string
-//	Domain     string
-//	// SitemapFormat string
-//	// Active        bool
-//}
+//	type Sources struct {
+//		Name       string
+//		Logo       string
+//		URL        string
+//		Headless   bool
+//		PID        string
+//		ProperName string
+//		Domain     string
+//		// SitemapFormat string
+//		// Active        bool
+//	}
 type Sources = configTypes.Sources
 
 // Return all sources and sitegraph domains

internal/summoner/acquire/acquire.go

@@ -21,6 +21,7 @@ import (
 )
 
 const EarthCubeAgent = "EarthCube_DataBot/1.0"
+const JSONContentType = "application/ld+json"
 
 // ResRetrieve is a function to pull down the data graphs at resources
 func ResRetrieve(v1 *viper.Viper, mc *minio.Client, m map[string][]string, db *bolt.DB, runStats *common.RunStats) {
@@ -157,7 +158,8 @@ func getDomain(v1 *viper.Viper, mc *minio.Client, urls []string, sourceName stri
 			}
 			defer resp.Body.Close()
 
-			doc, err := goquery.NewDocumentFromResponse(resp)
+			jsonlds, err := FindJSONInResponse(v1, urlloc, repologger, resp)
+
 			if err != nil {
 				log.Error("#", i, " error on ", urlloc, err) // print an message containing the index (won't keep order)
 				repoStats.Inc(common.Issues)
@@ -166,34 +168,6 @@ func getDomain(v1 *viper.Viper, mc *minio.Client, urls []string, sourceName stri
 				return
 			}
 
-			var jsonlds []string
-			var contentTypeHeader = resp.Header["Content-Type"]
-
-			// if
-			// The URL is sending back JSON-LD correctly as application/ld+json
-			// this should not be here IMHO, but need to support people not setting proper header value
-			// The URL is sending back JSON-LD but incorrectly sending as application/json
-			if contains(contentTypeHeader, "application/ld+json") || contains(contentTypeHeader, "application/json") || fileExtensionIsJson(urlloc) {
-				repologger.WithFields(log.Fields{"url": urlloc, "contentType": "json or ld_json"}).Debug()
-				log.WithFields(log.Fields{"url": urlloc, "contentType": "json or ld_json"}).Debug(urlloc, " as ", contentTypeHeader)
-
-				jsonlds, err = addToJsonListIfValid(v1, jsonlds, doc.Text())
-				if err != nil {
-					log.WithFields(log.Fields{"url": urlloc, "contentType": "json or ld_json"}).Error("Error processing json response from ", urlloc, err)
-					repologger.WithFields(log.Fields{"url": urlloc, "contentType": "json or ld_json"}).Error(err)
-				}
-				// look in the HTML page for <script type=application/ld+json>
-			} else {
-				doc.Find("script[type='application/ld+json']").Each(func(i int, s *goquery.Selection) {
-					jsonlds, err = addToJsonListIfValid(v1, jsonlds, s.Text())
-					repologger.WithFields(log.Fields{"url": urlloc, "contentType": "script[type='application/ld+json']"}).Info()
-					if err != nil {
-						log.WithFields(log.Fields{"url": urlloc, "contentType": "script[type='application/ld+json']"}).Error("Error processing script tag in ", urlloc, err)
-						repologger.WithFields(log.Fields{"url": urlloc, "contentType": "script[type='application/ld+json']"}).Error(err)
-					}
-				})
-			}
-
 			// For incremental indexing I want to know every URL I visit regardless
 			// if there is a valid JSON-LD document or not.   For "full" indexing we
 			// visit ALL URLs.  However, many will not have JSON-LD, so let's also record
@@ -225,43 +199,7 @@ func getDomain(v1 *viper.Viper, mc *minio.Client, urls []string, sourceName stri
 				repoStats.Inc(common.Summoned)
 			}
 
-			for i, jsonld := range jsonlds {
-				if jsonld != "" { // traps out the root domain...   should do this different
-					log.WithFields(log.Fields{"url": urlloc, "issue": "Uploading"}).Trace("#", i, "Uploading ")
-					repologger.WithFields(log.Fields{"url": urlloc, "issue": "Uploading"}).Trace()
-					sha, err := Upload(v1, mc, bucketName, sourceName, urlloc, jsonld)
-					if err != nil {
-						log.WithFields(log.Fields{"url": urlloc, "sha": sha, "issue": "Error uploading jsonld to object store"}).Error("Error uploading jsonld to object store: ", urlloc, err)
-						repologger.WithFields(log.Fields{"url": urlloc, "sha": sha, "issue": "Error uploading jsonld to object store"}).Error(err)
-						repoStats.Inc(common.StoreError)
-					} else {
-						repologger.WithFields(log.Fields{"url": urlloc, "sha": sha, "issue": "Uploaded to object store"}).Trace(err)
-						log.WithFields(log.Fields{"url": urlloc, "sha": sha, "issue": "Uploaded to object store"}).Info("Successfully put ", sha, " in summoned bucket for ", urlloc)
-						repoStats.Inc(common.Stored)
-					}
-					// TODO  Is here where to add an entry to the KV store
-					db.Update(func(tx *bolt.Tx) error {
-						b := tx.Bucket([]byte(sourceName))
-						err := b.Put([]byte(urlloc), []byte(sha))
-						if err != nil {
-							log.Error("Error writing to bolt ", err)
-						}
-						return nil
-					})
-				} else {
-					log.WithFields(log.Fields{"url": urlloc, "issue": "Empty JSON-LD document found "}).Info("Empty JSON-LD document found. Continuing.")
-					repologger.WithFields(log.Fields{"url": urlloc, "issue": "Empty JSON-LD document found "}).Error(err)
-					// TODO  Is here where to add an entry to the KV store
-					db.Update(func(tx *bolt.Tx) error {
-						b := tx.Bucket([]byte(sourceName))
-						err := b.Put([]byte(urlloc), []byte(fmt.Sprintf("NULL: %s", urlloc))) // no JOSN-LD found at this URL
-						if err != nil {
-							log.Error("Error writing to bolt ", err)
-						}
-						return nil
-					})
-				}
-			}
+			UploadWrapper(v1, mc, bucketName, sourceName, urlloc, db, repologger, repoStats, jsonlds)
 
 			bar.Add(1)                                          // bar.Incr()
 			log.Trace("#", i, "thread for", urlloc)             // print an message containing the index (won't keep order)
@@ -275,6 +213,88 @@ func getDomain(v1 *viper.Viper, mc *minio.Client, urls []string, sourceName stri
 	}
 }
 
+func FindJSONInResponse(v1 *viper.Viper, urlloc string, repologger *log.Logger, response *http.Response) ([]string, error) {
+	doc, err := goquery.NewDocumentFromResponse(response)
+	if err != nil {
+		return nil, err
+	}
+
+	contentTypeHeader := response.Header["Content-Type"]
+	var jsonlds []string
+
+	// if the URL is sending back JSON-LD correctly as application/ld+json
+	// this should not be here IMHO, but need to support people not setting proper header value
+	// The URL is sending back JSON-LD but incorrectly sending as application/json
+	if contains(contentTypeHeader, JSONContentType) || contains(contentTypeHeader, "application/json") || fileExtensionIsJson(urlloc) {
+		logFields := log.Fields{"url": urlloc, "contentType": "json or ld_json"}
+		repologger.WithFields(logFields).Debug()
+		log.WithFields(logFields).Debug(urlloc, " as ", contentTypeHeader)
+
+		jsonlds, err = addToJsonListIfValid(v1, jsonlds, doc.Text())
+		if err != nil {
+			log.WithFields(logFields).Error("Error processing json response from ", urlloc, err)
+			repologger.WithFields(logFields).Error(err)
+		}
+		// look in the HTML response for <script type=application/ld+json>
+	} else {
+		doc.Find("script[type='application/ld+json']").Each(func(i int, s *goquery.Selection) {
+			jsonlds, err = addToJsonListIfValid(v1, jsonlds, s.Text())
+			logFields := log.Fields{"url": urlloc, "contentType": "script[type='application/ld+json']"}
+			repologger.WithFields(logFields).Info()
+			if err != nil {
+				log.WithFields(logFields).Error("Error processing script tag in ", urlloc, err)
+				repologger.WithFields(logFields).Error(err)
+			}
+		})
+	}
+
+	return jsonlds, nil
+}
+
+func UploadWrapper(v1 *viper.Viper, mc *minio.Client, bucketName string, sourceName string, urlloc string, db *bolt.DB, repologger *log.Logger, repoStats *common.RepoStats, jsonlds []string) {
+	for i, jsonld := range jsonlds {
+		if jsonld != "" { // traps out the root domain...   should do this different
+			logFields := log.Fields{"url": urlloc, "issue": "Uploading"}
+			log.WithFields(logFields).Trace("#", i, "Uploading ")
+			repologger.WithFields(logFields).Trace()
+			sha, err := Upload(v1, mc, bucketName, sourceName, urlloc, jsonld)
+			if err != nil {
+				logFields = log.Fields{"url": urlloc, "sha": sha, "issue": "Error uploading jsonld to object store"}
+				log.WithFields(logFields).Error("Error uploading jsonld to object store: ", urlloc, err)
+				repologger.WithFields(logFields).Error(err)
+				repoStats.Inc(common.StoreError)
+			} else {
+				logFields = log.Fields{"url": urlloc, "sha": sha, "issue": "Uploaded to object store"}
+				repologger.WithFields(logFields).Trace(err)
+				log.WithFields(logFields).Info("Successfully put ", sha, " in summoned bucket for ", urlloc)
+				repoStats.Inc(common.Stored)
+			}
+			// TODO  Is here where to add an entry to the KV store
+			db.Update(func(tx *bolt.Tx) error {
+				b := tx.Bucket([]byte(sourceName))
+				err := b.Put([]byte(urlloc), []byte(sha))
+				if err != nil {
+					log.Error("Error writing to bolt ", err)
+				}
+				return nil
+			})
+		} else {
+			logFields := log.Fields{"url": urlloc, "issue": "Empty JSON-LD document found "}
+			log.WithFields(logFields).Info("Empty JSON-LD document found. Continuing.")
+			repologger.WithFields(logFields).Error("Empty JSON-LD document found. Continuing.")
+			// TODO  Is here where to add an entry to the KV store
+			db.Update(func(tx *bolt.Tx) error {
+				b := tx.Bucket([]byte(sourceName))
+				err := b.Put([]byte(urlloc), []byte(fmt.Sprintf("NULL: %s", urlloc))) // no JSON-LD found at this URL
+				if err != nil {
+					log.Error("Error writing to bolt ", err)
+				}
+				return nil
+			})
+		}
+	}
+}
+
 func contains(arr []string, str string) bool {
 	for _, a := range arr {