Merge pull request #279 from bacpop/i273

Allow overwrite if forced
bacpop · Oct 13, 2023 · 14bcd2b · 14bcd2b
2 parents eaad3db + 54ffc03
commit 14bcd2b
Show file tree

Hide file tree

Showing 3 changed files with 22 additions and 11 deletions.
diff --git a/.github/workflows/azure_ci.yml b/.github/workflows/azure_ci.yml
@@ -21,12 +21,17 @@ jobs:
       uses: actions/setup-python@v2
       with:
         python-version: ${{ matrix.python-version }}
+    - name: Get current date
+      id: date
+      run: echo "date=$(date +%Y-%m-%d)" >> "${GITHUB_OUTPUT}"
     - name: Install Conda environment from environment.yml
       uses: mamba-org/setup-micromamba@v1
       with:
         micromamba-version: '1.4.6-0'
         environment-file: environment.yml
-        cache-environment: true
+        # persist on the same day.
+        cache-environment-key: environment-${{ steps.date.outputs.date }}
+        cache-downloads-key: downloads-${{ steps.date.outputs.date }}
     - name: Install and run_test.py
       shell: bash -l {0}
       run: |

diff --git a/PopPUNK/assign.py b/PopPUNK/assign.py
@@ -271,8 +271,8 @@ def assign_query(dbFuncs,
     constructDatabase = dbFuncs['constructDatabase']
     readDBParams = dbFuncs['readDBParams']
 
-    if ref_db == output:
-        sys.stderr.write("--output and --ref-db must be different to "
+    if ref_db == output and overwrite == False:
+        sys.stderr.write("--output and --db must be different to "
                          "prevent overwrite.\n")
         sys.exit(1)
 
@@ -386,8 +386,8 @@ def assign_query_hdf5(dbFuncs,
     readDBParams = dbFuncs['readDBParams']
     getSeqsInDb = dbFuncs['getSeqsInDb']
 
-    if ref_db == output:
-        sys.stderr.write("--output and --ref-db must be different to "
+    if ref_db == output and overwrite == False:
+        sys.stderr.write("--output and --db must be different to "
                          "prevent overwrite.\n")
         sys.exit(1)
     if (update_db and not distances):
@@ -509,8 +509,9 @@ def assign_query_hdf5(dbFuncs,
 
             n_vertices = len(get_vertex_list(genomeNetwork, use_gpu = gpu_graph))
             if n_vertices != len(rNames):
-                sys.stderr.write(f"There are {n_vertices}  vertices in the network but {len(rNames)} reference names supplied; " + \
+                sys.stderr.write(f"ERROR: There are {n_vertices} vertices in the network but {len(rNames)} reference names supplied; " + \
                                  "please check the '--model-dir' variable is pointing to the correct directory\n")
+                sys.exit(1)
 
         if model.type == 'lineage':
             # Assign lineages by calculating query-query information

diff --git a/PopPUNK/network.py b/PopPUNK/network.py
@@ -536,11 +536,16 @@ def network_to_edges(prev_G_fn, rlist, adding_qq_dists = False,
         source_ids = old_source_ids
         target_ids = old_target_ids
     else:
-        # Update IDs to new versions
-        old_id_indices = [rlist.index(x) for x in old_ids]
-        # translate to indices
-        source_ids = [old_id_indices[x] for x in old_source_ids]
-        target_ids = [old_id_indices[x] for x in old_target_ids]
+        try:
+            # Update IDs to new versions
+            old_id_indices = [rlist.index(x) for x in old_ids]
+            # translate to indices
+            source_ids = [old_id_indices[x] for x in old_source_ids]
+            target_ids = [old_id_indices[x] for x in old_target_ids]
+        except ValueError:
+            sys.stderr.write(f"Network size mismatch. Previous network nodes: {max(old_id_indices)}."
+                             f"New network nodes: {max(old_source_ids.a)}/{max(old_target_ids.a)}\n")
+            sys.exit(1)
 
     # return values
     if weights: