Support for debug option, etc.

- "debug" option passed to CovSpectrum code in cooc_cojac
- debug also shows urls and arguments
- [bugfix] lintype wasn't properly passed to cooc_cojac
- also update REAMDE.md

README.md

@@ -144,8 +144,8 @@ Options:
 $ cojac cooc-curate --help
 Usage: cojac cooc-curate [OPTIONS] [VOC]...
 
-  Helps determining specific mutations and cooccurrences by querying CoV-
-  Spectrum
+  Helps determining specific mutations and cooccurrences by querying
+  covSPECTRUM
 
 Options:
   -u, --url URL               url to use when querying covspectrum (e.g.
@@ -166,7 +166,8 @@ Options:
                               assessing signatures of old variants that have
                               branched out by now.
   --colour / --no-colour      use coloured output
-  --help                      Show this message and exit.
+  --debug / --no-debug        show API calls details (urls and arguments)
+  -h, --help                  Show this message and exit.
 
   This tool queries LAPIS, see https://lapis-docs.readthedocs.io/en/latest/
 ```
@@ -187,7 +188,7 @@ Options:
 
 ```console
 $ cojac sig-generate --help
-Usage: cojac  sig-generate [OPTIONS]
+Usage: cojac sig-generate [OPTIONS]
 
   Helps generating a list of mutations frequently found in a variant by
   querying covSPECTRUM
@@ -206,18 +207,18 @@ Options:
   -f, --minfreq FREQ      Minimum frequency for inclusion in list
   -d, --mindelfreq FREQ   Use a different minimum frequency for deletions
                           (useful early on when there are few sequences and
-                          some of those were produced by pipeline that don't
+                          some of those were produced by pipelines that don't
                           handle deletions)
   -s, --minseqs NUM       Minimum number of sequence supporting for inclusion
                           in list
   --covariants TSV        import from a covariants.org TSV file instead of
                           covSpectrum. (See: https://github.com/hodcroftlab/co
                           variants/blob/master/defining_mutations/)
-  --debug / --no-debug
-  --help                  Show this message and exit.
+  --debug / --no-debug    show 'extra' query content, show API details (urls
+                          and arguments)
+  -h, --help              Show this message and exit.
 
   This tool queries LAPIS, see https://lapis-docs.readthedocs.io/en/latest/
-
 ```
 
 ## Howto

cojac/cooc_curate.py

@@ -23,6 +23,7 @@
 
 server = "https://lapis.cov-spectrum.org/open/v1"
 lintype = "nextcladePangoLineage"
+debug = False
 
 
 def setURL(url):
@@ -42,9 +43,19 @@ def setLinType(lin):
     - nextcladePangoLineage : as found by nextclade
     - pangoLineage : as provided by GISAID
     """
+    global lintype
     lintype = lin
 
 
+def setDebug(d):
+    """
+    Switch debug on or off
+    - this will show urlparse
+    """
+    global debug
+    debug = d
+
+
 def getAccessKey():
     # TODO proper global handling
 
@@ -92,13 +103,20 @@ def nucmutations(**kwargs):
     - list of mutation, frequencies and sample counts (for all frequencies > 0.05 )
     """
     kwargs["accessKey"] = getAccessKey()
+    url = (
+        f"{server}/sample/nuc-mutations"
+        if server[-2:] == "v1" or server[-3:] == "v1/"
+        else f"{server}/sample/nucleotideMutations"
+    )
+
+    if debug:
+        print(
+            f"url: {url}\nargs:\n{kwargs}\n",
+            file=sys.stderr,
+        )
     reply = json.loads(
         requests.get(
-            (
-                f"{server}/sample/nuc-mutations"
-                if server[-2:] == "v1" or server[-3:] == "v1/"
-                else f"{server}/sample/nucleotideMutations"
-            ),
+            url,
             params=kwargs,
         ).text
     )
@@ -122,7 +140,15 @@ def aggregated(**kwargs):
     - count of samples that fit criteria (the other parameters)
     """
     kwargs["accessKey"] = getAccessKey()
-    reply = json.loads(requests.get(f"{server}/sample/aggregated", params=kwargs).text)
+    url = f"{server}/sample/aggregated"
+
+    if debug:
+        print(
+            f"url: {url}\nargs:\n{kwargs}\n",
+            file=sys.stderr,
+        )
+
+    reply = json.loads(requests.get(url, params=kwargs).text)
 
     checkerror(reply)
 
@@ -354,12 +380,20 @@ def curate_muts(
     default=True,
     help="use coloured output",
 )
+@click.option(
+    "--debug/--no-debug",
+    "debug",
+    default=False,
+    help="show API calls details (urls and arguments)",
+)
 @click.argument("voc", nargs=-1)
-def cooc_curate(url, lintype, amp, domuts, high, low, collapse, colour, voc):
+def cooc_curate(url, lintype, amp, domuts, high, low, collapse, colour, voc, debug):
     if url:
         setURL(url)
     if lintype:
         setLinType(lintype)
+    if debug:
+        setDebug(debug)
     amplicons = None
     if amp:
         with open(amp, "r") as yf:

cojac/sig_generate.py

@@ -7,7 +7,7 @@
 import yaml
 import csv
 
-from .cooc_curate import listfilteredmutations, setURL, setLinType
+from .cooc_curate import listfilteredmutations, setURL, setLinType, setDebug
 
 
 # regex
@@ -95,6 +95,7 @@
     "--debug/--no-debug",
     "debug",
     default=False,
+    help="show 'extra' query content, show API details (urls and arguments)",
 )
 def sig_generate(
     url, lintype, var, minfreq, mindelfreq, minseqs, extras, covariants, debug
@@ -105,10 +106,16 @@ def sig_generate(
         setLinType(lintype)
 
     if debug:
+        setDebug(debug)
         import sys
 
         print(
-            "extra:\n", yaml.load(extras, Loader=yaml.FullLoader), "\n", file=sys.stderr
+            (
+                "extra:\n",
+                yaml.load(extras, Loader=yaml.FullLoader) if extras else "extra: None",
+            ),
+            "\n",
+            file=sys.stderr,
         )
 
     # get initial list