diff --git a/automated-issue-ref.ipynb b/automated-issue-ref.ipynb index ab495c62..67a64928 100755 --- a/automated-issue-ref.ipynb +++ b/automated-issue-ref.ipynb @@ -2,7 +2,7 @@ "cells": [ { "cell_type": "code", - "execution_count": 1, + "execution_count": 7, "id": "f64573a2", "metadata": {}, "outputs": [], @@ -15,6 +15,8 @@ "# the number of milestone we start to read\n", "start_milestone=1\n", "start_sub_milestone=1\n", + "end_milestone=795\n", + "end_sub_milestone=13\n", "def read_milestone(num,di='cov-lineages/pango-designation'):\n", " # or sars-cov-2 proj if it starts to add milestones\n", " url=\"https://github.com/\"+di+\"/milestone/\"+str(num)\n", @@ -38,21 +40,12 @@ }, { "cell_type": "code", - "execution_count": 3, + "execution_count": 8, "id": "769f2d32", "metadata": { "scrolled": false }, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "796 HTTP Error 404: Not Found\n", - "8 HTTP Error 404: Not Found\n" - ] - } - ], + "outputs": [], "source": [ "# read milestones \n", "milestone_end=False\n", @@ -63,6 +56,7 @@ "import os \n", "listd=os.listdir()\n", "\n", + "\n", "if not(\"autoref\" in listd):\n", " os.mkdir(\"autoref\")\n", "lista=os.listdir(\"autoref\")\n", @@ -80,7 +74,7 @@ " milestone_list.append([linsp[0],linsp[1]])\n", " # don't read twice for old milestones\n", " if issue>=milestone:\n", - " milestone=issue+1 \n", + " milestone=issue+1\n", " w.close()\n", "\n", "if (\"milestone_sub.txt\" in lista):\n", @@ -104,7 +98,7 @@ " print(item[0],item[1],file=w)\n", "\n", "\n", - "while not(milestone_end):\n", + "while (milestone<=end_milestone):\n", " try:\n", " title=read_milestone(milestone)\n", " for item in title:\n", @@ -112,7 +106,7 @@ " print(milestone,item,file=w)\n", " except Exception as e:\n", " print(milestone,e)\n", - " milestone_end=True\n", + " \n", " milestone+=1\n", " if milestone%10==0:\n", " print(\"Reading Milestone\",milestone)\n", @@ -124,7 +118,7 @@ " print(item[0],item[1],file=w)\n", "\n", "milestone_end=False\n", - "while not(milestone_end):\n", + "while (milestone_sub<=end_sub_milestone):\n", " try:\n", " title=read_milestone(milestone_sub,di=\"sars-cov-2-variants/lineage-proposals\")\n", " for item in title:\n", @@ -132,9 +126,9 @@ " print(milestone_sub,item,file=w)\n", " except Exception as e:\n", " print(milestone_sub,e)\n", - " milestone_end=True\n", + " \n", " milestone_sub+=1\n", - " if milestone%10==0:\n", + " if milestone_sub%10==0:\n", " print(\"Reading Milestone in sars-cov-2-variants \",milestone)\n", "\n", "w.close()\n", @@ -146,7 +140,7 @@ }, { "cell_type": "code", - "execution_count": 12, + "execution_count": 9, "id": "88a367db", "metadata": {}, "outputs": [], @@ -175,49 +169,10 @@ }, { "cell_type": "code", - "execution_count": 13, + "execution_count": null, "id": "a56544a8", "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "['BA.2.75.9', '#1098']\n", - "['CB.1', '#1098']\n", - "['CK.2', '#1190']\n", - "['CK.2.1.1', '#1190']\n", - "['BA.5.2.36', '#1203']\n", - "['CT.1', '#1203']\n", - "['BA.5.2.38', '#1254']\n", - "['DA.1', '#1254']\n", - "['AY.13', '#198']\n", - "['AY.14', '#198']\n", - "['AY.15', '#198']\n", - "['AY.16', '#198']\n", - "['AY.17', '#198']\n", - "['AY.18', '#198']\n", - "['AY.19', '#198']\n", - "['AY.20', '#198']\n", - "['AY.21', '#198']\n", - "['AY.22', '#198']\n", - "['AY.34.1.1', '#255']\n", - "['AY.58', '#286']\n", - "['AY.63', '#286']\n", - "['AY.99', '#258']\n", - "['AY.99.1', '#258']\n", - "['AY.99.2', '#258']\n", - "['AY.112.1', '#283']\n", - "['AY.121.1', '#344']\n", - "['AY.122', '#320']\n", - "['EG.4.2', 'sars-cov-2-variants/lineage-proposals/#46']\n", - "['GY.6', 'sars-cov-2-variants/lineage-proposals/#308']\n", - "['XBB.1.32', '#1827']\n", - "['XBB.1.37', '#1929']\n", - "['XBF.1.1', '#1651']\n" - ] - } - ], + "outputs": [], "source": [ "# read lineage_notes.txt\n", "\n", @@ -239,7 +194,7 @@ " item_to_milestone[to_add]=item[1]\n", " \n", "for item in milestone_list_sub:\n", - " to_add='sars-cov-2-variants/lineage-proposals/#'+str(item[0])\n", + " to_add='sars-cov-2-variants/lineage-proposals#'+str(item[0])\n", " all_milestones[item[1]]=to_add\n", " if to_add in item_to_milestone:\n", " item_to_milestone[to_add]+='+'+item[1]\n", @@ -260,7 +215,7 @@ " if 'sars' in all_milestones[title]:\n", " issue_num=read_milestone_issues(title,di='sars-cov-2-variants/lineage-proposals')\n", " if issue_num!=0:\n", - " missing_milestones.append([title,'sars-cov-2-variants/lineage-proposals/#'+str(issue_num)])\n", + " missing_milestones.append([title,'sars-cov-2-variants/lineage-proposals#'+str(issue_num)])\n", " print(missing_milestones[-1])\n", " else:\n", " issue_num=read_milestone_issues(title)\n", diff --git a/autoref/milestone_sub.txt b/autoref/milestone_sub.txt index ed2b392c..a31c0afd 100755 --- a/autoref/milestone_sub.txt +++ b/autoref/milestone_sub.txt @@ -4,3 +4,8 @@ 4 CM.7.1.1 5 EG.4.2 7 GY.6 +8 GK.1.3 +9 XBB.1.41.1 +11 FL.4.3 +12 GJ.1.1 +13 GW.1 diff --git a/autoref/missing_refs.txt b/autoref/missing_refs.txt index e262b4c9..ec8c5134 100755 --- a/autoref/missing_refs.txt +++ b/autoref/missing_refs.txt @@ -1,32 +1,4 @@ -BA.2.75.9 #1098 -CB.1 #1098 -CK.2 #1190 -CK.2.1.1 #1190 -BA.5.2.36 #1203 -CT.1 #1203 -BA.5.2.38 #1254 -DA.1 #1254 -AY.13 #198 -AY.14 #198 -AY.15 #198 -AY.16 #198 -AY.17 #198 -AY.18 #198 -AY.19 #198 -AY.20 #198 -AY.21 #198 -AY.22 #198 -AY.34.1.1 #255 -AY.58 #286 -AY.63 #286 -AY.99 #258 -AY.99.1 #258 -AY.99.2 #258 -AY.112.1 #283 -AY.121.1 #344 -AY.122 #320 -EG.4.2 sars-cov-2-variants/lineage-proposals/#46 -GY.6 sars-cov-2-variants/lineage-proposals/#308 -XBB.1.32 #1827 -XBB.1.37 #1929 -XBF.1.1 #1651 +GK.1.3 sars-cov-2-variants/lineage-proposals#179 +FL.4.3 sars-cov-2-variants/lineage-proposals#153 +XBB.1.41.1 sars-cov-2-variants/lineage-proposals#150 +GJ.1.1 sars-cov-2-variants/lineage-proposals#109