miga-base 0.7.19.0 → 0.7.20.0

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: bc5df224531c2f5e902304b478aabe0ba18c02b836c5bab66a675257a3739a08
-  data.tar.gz: 438b9f2cefad3ecc3b65e17f81d5708f6a589c8b34f22b63235cf4123a156922
+  metadata.gz: de9486ffe4bff4fd61295c004f36af331ce5a50645f4aa706076a38d3523ee38
+  data.tar.gz: 60ded180b92cfb27729a4844c00713b4e78bf08b6a1f8ebf30f6bdccd24eb769
 SHA512:
-  metadata.gz: 506dd5c19259071abd5cf0a130a70557967833edc520fada73030372d7736f2fe114ce4879bc224e37bcbe407a566bbd3cef39a5bc8ec9669c9c4cd1e63edb74
-  data.tar.gz: 4edb685f9a4adb69339e5ef477d4a0a332da606b402d380e3eab77a055ab94582be3be90f904e9403bc20d3f81c3753ed85df8a43bd9afc3e97b41f88cfd9fb1
+  metadata.gz: 7a5e89cf299d72c2b3fb9a267923caef0ecfc399cabfec71011e9ebc3c37d874cb8a93e16d169db7c3bbda1f54d3ab5863ba889341295339b69673d3457edef7
+  data.tar.gz: 4ac7cf2785e42afd17f19749632e1deda80cecfa10103f64d4bc366a29e4a8acf9ead5e8a412ae1b11ba966c6dc9501017cb7dbee2572ebcbc835e9db0341a7b

data/lib/miga/version.rb

@@ -8,7 +8,7 @@ module MiGA
   # - Float representing the major.minor version.
   # - Integer representing gem releases of the current version.
   # - Integer representing minor changes that require new version number.
-  VERSION = [0.7, 19, 0]
+  VERSION = [0.7, 20, 0]
 
   ##
   # Nickname for the current major.minor version.
@@ -16,7 +16,7 @@ module MiGA
 
   ##
   # Date of the current gem release.
-  VERSION_DATE = Date.new(2021, 1, 2)
+  VERSION_DATE = Date.new(2021, 1, 7)
 
   ##
   # Reference of MiGA.

data/scripts/aai_distances.bash

@@ -4,10 +4,10 @@ set -e
 SCRIPT="aai_distances"
 # shellcheck source=scripts/miga.bash
 . "$MIGA/scripts/miga.bash" || exit 1
-cd "$PROJECT/data/09.distances/02.aai"
+DIR="$PROJECT/data/09.distances/02.aai"
 
 # Initialize
-miga date > "miga-project.start"
+miga_start_project_step "$DIR"
 
 echo -n "" > miga-project.log
 DS=$(miga ls -P "$PROJECT" --ref --no-multi --active)
@@ -39,5 +39,4 @@ if(sum(aai[,'a'] != aai[,'b']) > 0){
 " | R --vanilla
 
 # Finalize
-miga date > "miga-project.done"
-miga add_result -P "$PROJECT" -r "$SCRIPT" -f
+miga_end_project_step "$DIR"

data/scripts/ani_distances.bash

@@ -4,10 +4,10 @@ set -e
 SCRIPT="ani_distances"
 # shellcheck source=scripts/miga.bash
 . "$MIGA/scripts/miga.bash" || exit 1
-cd "$PROJECT/data/09.distances/03.ani"
+DIR="$PROJECT/data/09.distances/03.ani"
 
 # Initialize
-miga date > "miga-project.start"
+miga_start_project_step "$DIR"
 
 echo -n "" > miga-project.log
 DS=$(miga ls -P "$PROJECT" --ref --no-multi --active)
@@ -38,5 +38,4 @@ if(sum(ani[,'a'] != ani[,'b']) > 0){
 " | R --vanilla
 
 # Finalize
-miga date > "miga-project.done"
-miga add_result -P "$PROJECT" -r "$SCRIPT" -f
+miga_end_project_step "$DIR"

data/scripts/clade_finding.bash

@@ -4,14 +4,13 @@ set -e
 SCRIPT="clade_finding"
 # shellcheck source=scripts/miga.bash
 . "$MIGA/scripts/miga.bash" || exit 1
-cd "$PROJECT/data/10.clades/01.find"
+DIR="$PROJECT/data/10.clades/01.find"
 
 # Initialize
-miga date > "miga-project.start"
+miga_start_project_step "$DIR"
 
 # Run
 ruby -I "$MIGA/lib" "$MIGA/utils/subclades.rb" "$PROJECT" "$SCRIPT"
 
 # Finalize
-miga date > "miga-project.done"
-miga add_result -P "$PROJECT" -r "$SCRIPT" -f
+miga_end_project_step "$DIR"

data/scripts/haai_distances.bash

@@ -4,10 +4,10 @@ set -e
 SCRIPT="haai_distances"
 # shellcheck source=scripts/miga.bash
 . "$MIGA/scripts/miga.bash" || exit 1
-cd "$PROJECT/data/09.distances/01.haai"
+DIR="$PROJECT/data/09.distances/01.haai"
 
 # Initialize
-miga date > "miga-project.start"
+miga_start_project_step "$DIR"
 
 # Cleanup databases
 ruby -I "$MIGA/lib" "$MIGA/utils/cleanup-databases.rb" "$PROJECT" "$CORES"
@@ -42,5 +42,4 @@ if(sum(haai[,'a'] != haai[,'b']) > 0){
 " | R --vanilla
 
 # Finalize
-miga date > "miga-project.done"
-miga add_result -P "$PROJECT" -r "$SCRIPT" -f
+miga_end_project_step "$DIR"

data/scripts/miga.bash

@@ -9,6 +9,24 @@ SCRIPT=${SCRIPT:-$(basename "$0" .bash)}
 
 function exists { [[ -e "$1" ]] ; }
 function fx_exists { [[ $(type -t "$1") == "function" ]] ; }
+function miga_start_project_step {
+  local dir="$1"
+  local dir_r="${dir}.running"
+  mkdir -p "$dir"
+  mkdir -p "$dir_r"
+  cd "$dir_r"
+  miga date > "miga-project.start"
+}
+function miga_end_project_step {
+  local dir="$1"
+  local dir_r="${dir}.running"
+  cd "$dir"
+  rm -rf miga-project.*
+  mv "$dir_r"/miga-project.* .
+  rmdir "$dir_r" &>/dev/null || true
+  miga date > "miga-project.done"
+  miga add_result -P "$PROJECT" -r "$SCRIPT" -f
+}
 
 if [[ "$SCRIPT" != "d" && "$SCRIPT" != "p" ]] ; then
   echo ""

data/scripts/ogs.bash

@@ -4,10 +4,10 @@ set -e
 SCRIPT="ogs"
 # shellcheck source=scripts/miga.bash
 . "$MIGA/scripts/miga.bash" || exit 1
-cd "$PROJECT/data/10.clades/03.ogs"
+DIR="$PROJECT/data/10.clades/03.ogs"
 
 # Initialize
-miga date > "miga-project.start"
+miga_start_project_step "$DIR"
 
 DS=$(miga ls -P "$PROJECT" --ref --no-multi)
 
@@ -51,5 +51,4 @@ else
 fi
 
 # Finalize
-miga date > "miga-project.done"
-miga add_result -P "$PROJECT" -r "$SCRIPT" -f
+miga_end_project_step "$DIR"

data/scripts/p.bash

@@ -13,7 +13,7 @@ while true ; do
     let k=$k+1
     if [[ $k -gt 10 ]] ; then
       miga new --update -P "$PROJECT" \
-        -m "run_$res=false,warn=Too many failed attempts to run $res."
+        -m "run_$res=false,warn=Too many failed attempts to run $res"
     fi
   else
     k=0

data/scripts/project_stats.bash

@@ -5,11 +5,9 @@ SCRIPT="project_stats"
 # shellcheck source=scripts/miga.bash
 . "$MIGA/scripts/miga.bash" || exit 1
 DIR="$PROJECT/data/90.stats"
-[[ -d "$DIR" ]] || mkdir -p "$DIR"
-cd "$DIR"
 
 # Initialize
-miga date > "miga-project.start"
+miga_start_project_step "$DIR"
 
 # Execute doctor
 echo "# Doctor"
@@ -25,5 +23,4 @@ ruby -I "$MIGA/lib" \
   "$MIGA/utils/index_metadata.rb" "$PROJECT" "miga-project.metadata.db"
 
 # Finalize
-miga date > "miga-project.done"
-miga add_result -P "$PROJECT" -r "$SCRIPT" -f
+miga_end_project_step "$DIR"

data/scripts/subclades.bash

@@ -4,14 +4,13 @@ set -e
 SCRIPT="subclades"
 # shellcheck source=scripts/miga.bash
 . "$MIGA/scripts/miga.bash" || exit 1
-cd "$PROJECT/data/10.clades/02.ani"
+DIR="$PROJECT/data/10.clades/02.ani"
 
 # Initialize
-miga date > "miga-project.start"
+miga_start_project_step "$DIR"
 
-# Run R code
+# Run
 ruby -I "$MIGA/lib" "$MIGA/utils/subclades.rb" "$PROJECT" "$SCRIPT"
 
 # Finalize
-miga date > "miga-project.done"
-miga add_result -P "$PROJECT" -r "$SCRIPT" -f
+miga_end_project_step "$DIR"

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: miga-base
 version: !ruby/object:Gem::Version
-  version: 0.7.19.0
+  version: 0.7.20.0
 platform: ruby
 authors:
 - Luis M. Rodriguez-R
 autorequire:
 bindir: bin
 cert_chain: []
-date: 2021-01-02 00:00:00.000000000 Z
+date: 2021-01-07 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: daemons