updates to paper

Author: ialbert

docs/paper.md

@@ -139,7 +139,7 @@ genescape tree -m lipid --micov 2 genes2.txt -o output.pdf
 
 The filtering process will result in a smaller tree with 18 nodes and 29 edges, focused on the functions that contain the word "lipid":
 
-![Filtering a large graph for a specific term \label{fig:filter}][img_filter]{height="216pt"}
+![Filtering a large graph for a specific term \label{fig:filter}][img_filter]
 
 [img_filter]: images/gs_output_3.png
 

src/genescape/main.py

@@ -179,7 +179,6 @@ def build(idx_fname=None, obo_fname=None, gaf_fname=None, stats=False, dump=Fals
     fnames = [
         ('obo', obo_fname),
         ('gaf', gaf_fname),
-        ('idx', idx_fname),
     ]
 
     check_files(fnames)
@@ -198,7 +197,7 @@ def build(idx_fname=None, obo_fname=None, gaf_fname=None, stats=False, dump=Fals
 
 
 @run.command()
-@click.option("-i", "--index", "idx_fname", default="", help="Index file")
+@click.option("-i", "--idx", "idx_fname", default="", help="Index file")
 @click.option("--host", "host", default="127.0.0.1", help="Hostname to bind to")
 @click.option("--port", "port", default=8000, type=int, help="Port number")
 @click.option("-r", "--reload", "reload", is_flag=True, help="Reload the webserver on changes")
@@ -225,45 +224,6 @@ def web(idx_fname='', host='localhost', port=8000, reload=False, test=False):
     shiny.run_app("genescape.shiny.tree.app:app", host=host, port=port, reload=reload)
 
 
-@run.command()
-@click.argument("words", default=None, nargs=-1)
-@click.option("-i", "--index", "idx_fname", default="", help="Index file (genescape.json.gz)")
-@click.help_option("-h", "--help")
-def show(words, idx_fname=''):
-    res = resources.init()
-    idx_fname = idx_fname or res.INDEX_FILE
-
-    utils.info(f"index: {idx_fname}")
-
-    idx = nexus.load_index(idx_fname)
-    obo = idx[nexus.OBO_KEY]
-    go2sym = idx[nexus.GO2SYM]
-    name2sym = idx[nexus.NAME2SYM]
-
-    obo = idx[nexus.OBO_KEY]
-
-    graph = nexus.build_graph(idx)
-
-    valid = list(filter(lambda x: x in obo, words))
-    missing = set(words) - set(valid)
-
-    if missing:
-        utils.error(f"Words not found: {missing}")
-
-    # The database info
-    info = idx[nexus.INFO_KEY]
-
-    for word in valid:
-        data = graph.nodes[word]
-        vals = go2sym[word]
-        # data['symbols'] = vals
-        data['parents'] = list(graph.predecessors(word))
-        data['children'] = list(graph.successors(word))
-        data['info'] = info
-        text = json.dumps(data, indent=4)
-        print(text)
-
-
 if __name__ == '__main__':
     # sys.argv.extend( ("build", "--stats"))
 

src/genescape/resources.py

@@ -11,6 +11,7 @@
 import toml
 
 from genescape import utils
+from pprint import pprint
 
 CURR_DIR = Path(os.path.dirname(__file__))
 
@@ -90,6 +91,7 @@ def pieces(elem):
     def find_index(self, code=None):
         code = code or self.DEFAULT_CODE
         if code not in self.INDEX_MAP:
+            pprint(self.INDEX_MAP)
             raise Exception(f"Code not found: {code}")
         return self.INDEX_MAP[code][2]
 
@@ -103,7 +105,7 @@ def update_from_env(self, key="GENESCAPE_INDEX"):
         """
         value = os.environ.get(key, None)
         if value:
-
+            utils.info(f"Environment: {value}")
             code, label, path = value.split(":")
 
             path = Path(path)
@@ -118,6 +120,7 @@ def update_from_env(self, key="GENESCAPE_INDEX"):
             # Recreate the index map
             self.INDEX_MAP = dict(map(lambda x: (x[0], x), current))
 
+
 # Reset the resource directory
 def reset_dir(cnf=None):
     """

src/genescape/shiny/tree/app.py

@@ -14,7 +14,6 @@
 # Load the default resources.
 res = resources.init()
 
-
 def random_gene_list(res, N=50):
     """
     Returns a random gene list.
@@ -24,6 +23,9 @@ def random_gene_list(res, N=50):
     return "\n".join(sym)
 
 
+# Update the index location from environment
+res.update_from_env()
+
 # This is the global database choices
 DATABASE_CHOICES = dict()
 
@@ -291,6 +293,8 @@ async def submit():
         await create_tree()
 
     async def create_tree():
+        global res
+
         limit = 10
         # Emulate some sort of progress bar
         with ui.Progress(min=1, max=limit) as p:
@@ -311,8 +315,6 @@ async def create_tree():
         pattern = input.pattern()
         root = input.root()
 
-        # Initialize the resources.
-        res = resources.init()
 
         # Locate the database from the index.
         idx_fname = res.find_index(db_code)