Candelbio namespace, use new multitool, better README

README.md

@@ -1,5 +1,9 @@
 # alzabo
 
+A simple schema management and documentation tool for graph-based systems. [Live example](https://candelbio.github.io/alzabo/).
+
+![Alzabo](resources/public/screenshot.png)
+
 Alzabo does a number of different tasks centered around a simple schema format for graph databases.
 
 - Defines an .edn schema format, with semantics similar to RDF.
@@ -79,14 +83,14 @@ Opens the generated documentation in browser..
 
 ## Use as a library
 
-Add dependency `[org.parkerici/alzabo "1.0.0"]` (or whatever the lastest version is)
+Add dependency `[org.candelbio/alzabo "1.0.0"]` (or whatever the lastest version is)
 
 ### Example
 
     (ns ...
-	  (:require [org.parkerici.alzabo.schema :as schema]
-                [org.parkerici.alzabo.datomic :as datomic]
-				[org.parkerici.alzabo.html :as html]))
+	  (:require [org.candelbio.alzabo.schema :as schema]
+                [org.candelbio.alzabo.datomic :as datomic]
+				[org.candelbio.alzabo.html :as html]))
 
 	;; read in a schema file
 	(let [schema (schema/read-schema <schema.edn>)]

project.clj

@@ -1,15 +1,15 @@
-(defproject org.parkerici/alzabo "1.0.0"
+(defproject org.candelbio/alzabo "1.1.0"
   :description "Semantic schema format and tools, for Datomic and other uses."
-  :url "http://github.com/ParkerICI/alzabo"
-  :license {:name "GPLv3"
-            :url "https://www.gnu.org/licenses/gpl-3.0.en.html"}
+  :url "http://github.com/candelbio/alzabo"
+  :license {:name "Apache 2 License"
+             :url "https://opensource.org/licenses/Apache-2.0"}
   :dependencies [;; Clojure 
-                 [org.clojure/clojure "1.10.0"]
+                 [org.clojure/clojure "1.11.1"]
                  [hiccup "1.0.5"]
                  [me.raynes/fs "1.4.6"]
                  ;; Clojurescript
                  [org.clojure/clojurescript "1.10.520"]
-                 [org.parkerici/multitool "0.0.15"]
+                 [org.candelbio/multitool "0.1.0"]
                  [reagent  "0.8.1"]
                  [re-frame "0.10.6"]
                  ]
@@ -24,7 +24,7 @@
                       ["cljsbuild" "once"]
                       ["run" "resources/candel-config.edn" "server" ]
                       ]}
-  :main org.parkerici.alzabo.core
+  :main org.candelbio.alzabo.core
   :target-path "target/%s"
   :profiles {:uberjar {:aot :all
                        }
@@ -33,8 +33,8 @@
                                   [figwheel-sidecar "0.5.16"]
                                   ]
                    :cljsbuild
-                   {:builds {:client {:figwheel     {:on-jsload "org.parkerici.alzabo.search.core/run"}
-                                      :compiler     {:main "org.parkerici.alzabo.search.core"
+                   {:builds {:client {:figwheel     {:on-jsload "org.candelbio.alzabo.search.core/run"}
+                                      :compiler     {:main "org.candelbio.alzabo.search.core"
                                                      :asset-path "js"
                                                      ;; for 10x debugger
                                                      :closure-defines {"re_frame.trace.trace_enabled_QMARK_" true}
@@ -53,7 +53,7 @@
              {:dependencies [[day8.re-frame/tracing-stubs "0.5.1"]]
               :cljsbuild
               {:builds {:client {
-                                 :compiler     {:main "org.parkerici.alzabo.search.core"
+                                 :compiler     {:main "org.candelbio.alzabo.search.core"
                                                 :asset-path "js"
                                                 :closure-defines {goog.DEBUG false}
                                                 :output-dir "resources/public/js"

src/clj/org/parkerici/alzabo/candel.clj → src/clj/org/candelbio/alzabo/candel.clj

@@ -1,10 +1,10 @@
-(ns org.parkerici.alzabo.candel
+(ns org.candelbio.alzabo.candel
   (:require [clojure.set :as set]
             [clojure.string :as str]
             [clojure.java.shell :as shell]
-            [org.parkerici.alzabo.config :as config]
-            [org.parkerici.alzabo.schema :as schema]
-            [org.parkerici.multitool.core :as u]))
+            [org.candelbio.alzabo.config :as config]
+            [org.candelbio.alzabo.schema :as schema]
+            [org.candelbio.multitool.core :as u]))
 
 ;;; Converts CANDEL [meta]schema into an Alzabo schema
 
@@ -114,8 +114,8 @@
         kind-defs (map (fn [em]
                          {:parent (:kind/parent em)
                           ;; TODO I think this will have to change to allow metamodel to be derived...maybe
-                          :unique-id (u/dens (or (:kind/need-uid em) (:kind/context-id em)))
-                          :label (u/dens (:kind/context-id em))
+                          :unique-id (u/de-ns (or (:kind/need-uid em) (:kind/context-id em)))
+                          :label (u/de-ns (:kind/context-id em))
                           :reference? (:kind/ref-data em)})
                        entity-meta)
         [enums version] (read-enums)

src/clj/org/parkerici/alzabo/config.clj → src/clj/org/candelbio/alzabo/config.clj

@@ -1,6 +1,6 @@
-(ns org.parkerici.alzabo.config
+(ns org.candelbio.alzabo.config
   (:require [clojure.edn :as edn]
-            [org.parkerici.multitool.core :as u])
+            [org.candelbio.multitool.core :as u])
   )
 
 (def the-config (atom nil))
@@ -20,22 +20,22 @@
   ([key] (get @the-config key))
   ([] @the-config ))
 
-;;; TODO document or default config vars here
-
 ;;; → multitool – change to deal with keyword bindings
 (defn expand-template-string
   "Template is a string containing {foo} elements, which get replaced by corresponding values from bindings"
   [template bindings]
-  (let [matches (->> (re-seq u/template-regex template) 
+  (let [matches (->> (re-seq u/param-regex template) 
                      (map (fn [[match key]]
                             [match (or (bindings key) (bindings (keyword key)) "")])))]
     (reduce (fn [s [match key]]
               (clojure.string/replace s (u/re-pattern-literal match) (str key)))
             template matches)))
 
+;;; TODO document or default config vars here
+
 (defn output-path
   [filename]
-  (str (expand-template-string (config :output-path) config)
+  (str (expand-template-string (config :output-path) (config))
        filename))
 
 

src/clj/org/parkerici/alzabo/core.clj → src/clj/org/candelbio/alzabo/core.clj

@@ -1,11 +1,11 @@
-(ns org.parkerici.alzabo.core
-  (:require [org.parkerici.alzabo.candel :as candel]
-            [org.parkerici.alzabo.schema :as schema]
-            [org.parkerici.alzabo.config :as config]
-            [org.parkerici.alzabo.html :as html]
-            [org.parkerici.alzabo.output :as output]
-            [org.parkerici.alzabo.datomic :as datomic]
-            [org.parkerici.multitool.core :as u])
+(ns org.candelbio.alzabo.core
+  (:require [org.candelbio.alzabo.candel :as candel]
+            [org.candelbio.alzabo.schema :as schema]
+            [org.candelbio.alzabo.config :as config]
+            [org.candelbio.alzabo.html :as html]
+            [org.candelbio.alzabo.output :as output]
+            [org.candelbio.alzabo.datomic :as datomic]
+            [org.candelbio.multitool.core :as u])
   (:gen-class))
 
 ;;; Note: CLI use is somewhat deprecated; it's expected that Alzabo will be used

src/clj/org/parkerici/alzabo/datomic.clj → src/clj/org/candelbio/alzabo/datomic.clj

@@ -1,6 +1,6 @@
-(ns org.parkerici.alzabo.datomic
-  (:require [org.parkerici.multitool.core :as u]
-            [org.parkerici.alzabo.schema :as alzs]
+(ns org.candelbio.alzabo.datomic
+  (:require [org.candelbio.multitool.core :as u]
+            [org.candelbio.alzabo.schema :as alzs]
             ))
 
 ;;; Write out a Datomic schema from Alzabo schema

src/clj/org/parkerici/alzabo/html.clj → src/clj/org/candelbio/alzabo/html.clj

@@ -1,7 +1,7 @@
-(ns org.parkerici.alzabo.html
-  (:require [org.parkerici.alzabo.schema :as schema]
-            [org.parkerici.alzabo.config :as config]
-            [org.parkerici.multitool.core :as u]
+(ns org.candelbio.alzabo.html
+  (:require [org.candelbio.alzabo.schema :as schema]
+            [org.candelbio.alzabo.config :as config]
+            [org.candelbio.multitool.core :as u]
             [clojure.string :as s]
             [clojure.pprint :as pp]
             [me.raynes.fs :as fs]
@@ -177,11 +177,11 @@
          (for [enum (sort (keys enums))]
            (html [:li (kind-html enum)]))]]
        ;; Pass the schema to clojurescript widget inside an invisible div
-       ;; See org.parkerici.alzabo.search.core/get-schema
+       ;; See org.candelbio.alzabo.search.core/get-schema
        [:div#aschema {:style (style-arg {:display "none"})}
         (str schema)]
        [:script {:src "js/client.js"}]
-       [:script "window.onload = function() { org.parkerici.alzabo.search.core.run(); }"]
+       [:script "window.onload = function() { org.candelbio.alzabo.search.core.run(); }"]
        ]]
      )))
 
@@ -206,7 +206,7 @@
     res))
 
 ;;; To use this, do 'brew install graphviz' first (on Mac)
-(def dot-command "dot")
+(def dot-command "/usr/local/bin/dot")
 
 ;;; Font should be available in Docker build image
 (def graph-font "Helvetica")

src/clj/org/parkerici/alzabo/output.clj → src/clj/org/candelbio/alzabo/output.clj

@@ -1,4 +1,4 @@
-(ns org.parkerici.alzabo.output
+(ns org.candelbio.alzabo.output
   (:require [clojure.pprint :as pprint]
             [clojure.java.io :as io]
             [me.raynes.fs :as fs]

src/cljc/org/parkerici/alzabo/schema.cljc → src/cljc/org/candelbio/alzabo/schema.cljc

@@ -1,4 +1,4 @@
-(ns org.parkerici.alzabo.schema
+(ns org.candelbio.alzabo.schema
   (:require [clojure.spec.alpha :as s]))
 
 (def primitives #{:long :float :string :boolean :instant :keyword})
@@ -21,7 +21,9 @@
 (s/def ::fields (s/map-of keyword? ::field))
 
 (s/def ::kind (s/keys :req-un [::fields] ;::inherits, but CANDEL not using that.
-                      :opt-un [::doc ::reference?]))
+                      :opt-un [::doc
+                               ::uri
+                               ::reference?])) ;TODO reference is too CANDEL-specific, replace with a kind-labels or tags or something
 
 (s/def ::kinds (s/map-of keyword? ::kind :conform-keys? true))
 
@@ -35,6 +37,8 @@
 
 (s/def ::version string?)
 
+(s/def ::uri (s/or :string string? :key keyword?))
+
 (s/def ::schema (s/keys :req-un [::kinds]
                         :opt-un [::enums ::version ::title]))
 

src/cljc/org/parkerici/alzabo/search/lexicon.cljc → src/cljc/org/candelbio/alzabo/search/lexicon.cljc

@@ -1,6 +1,6 @@
-(ns org.parkerici.alzabo.search.lexicon
+(ns org.candelbio.alzabo.search.lexicon
   (:require [clojure.string :as str]
-            [org.parkerici.multitool.nlp :as nlp]))
+            [org.candelbio.multitool.nlp :as nlp]))
 
 (defn add-def-word [dict word def]
   (let [word (str/lower-case word)]

src/cljs/org/parkerici/alzabo/search/core.cljs → src/cljs/org/candelbio/alzabo/search/core.cljs

@@ -1,8 +1,8 @@
-(ns org.parkerici.alzabo.search.core
+(ns org.candelbio.alzabo.search.core
   (:require [reagent.core :as reagent]
             [re-frame.core :as rf]
             [clojure.reader :as reader]
-            [org.parkerici.alzabo.search.lexicon :as lex]
+            [org.candelbio.alzabo.search.lexicon :as lex]
             ))
 
 ;; Get the schema from an invisible div on the page

test/clj/org/parkerici/alzabo/core_test.clj → test/clj/org/candelbio/alzabo/core_test.clj

@@ -1,5 +1,5 @@
-(ns org.parkerici.alzabo.core-test
-  (:require [org.parkerici.alzabo.core :as sut]
+(ns org.candelbio.alzabo.core-test
+  (:require [org.candelbio.alzabo.core :as sut]
             [me.raynes.fs :as fs]
             [clojure.test :refer :all]))
 

test/clj/org/parkerici/alzabo/datomic_test.clj → test/clj/org/candelbio/alzabo/datomic_test.clj

@@ -1,6 +1,6 @@
-(ns org.parkerici.alzabo.datomic-test
-  (:require [org.parkerici.alzabo.datomic :refer :all]
-            [org.parkerici.alzabo.schema :as schema]
+(ns org.candelbio.alzabo.datomic-test
+  (:require [org.candelbio.alzabo.datomic :refer :all]
+            [org.candelbio.alzabo.schema :as schema]
             [clojure.test :refer :all]
             ))
 

test/clj/org/parkerici/alzabo/html_test.clj → test/clj/org/candelbio/alzabo/html_test.clj

@@ -1,9 +1,9 @@
-(ns org.parkerici.alzabo.html-test
+(ns org.candelbio.alzabo.html-test
   (:require [clojure.test :refer :all]
-            [org.parkerici.alzabo.schema :as schema]
-            [org.parkerici.alzabo.config :as config]
+            [org.candelbio.alzabo.schema :as schema]
+            [org.candelbio.alzabo.config :as config]
             [me.raynes.fs :as fs]
-            [org.parkerici.alzabo.html :refer :all]))
+            [org.candelbio.alzabo.html :refer :all]))
 
 ;;; TODO this machinery should be for all tests
 (def test-config "test/resources/test-config.edn")

test/clj/org/parkerici/alzabo/roundtrip.clj → test/clj/org/candelbio/alzabo/roundtrip.clj

@@ -1,11 +1,11 @@
-(ns org.parkerici.alzabo.roundtrip
+(ns org.candelbio.alzabo.roundtrip
   (:require [clojure.data :as data]
             [clojure.pprint :refer [pprint]]
-            [org.parkerici.alzabo.output :as output]
-            [org.parkerici.alzabo.candel :as candel]
-            [org.parkerici.alzabo.config :as config]
-            [org.parkerici.alzabo.datomic :as datomic]
-            [org.parkerici.multitool.core :as u]))
+            [org.candelbio.alzabo.output :as output]
+            [org.candelbio.alzabo.candel :as candel]
+            [org.candelbio.alzabo.config :as config]
+            [org.candelbio.alzabo.datomic :as datomic]
+            [org.candelbio.multitool.core :as u]))
 
 ;;; TODO finish?
 ;;; Experiments in roundtripping.