MakeCloudCat_GC.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "import pandas as pd\n",
    "import numpy as np\n",
    "import sys, os\n",
    "from glob import glob\n",
    "import xarray as xr\n",
    "import datetime\n",
    "import warnings\n",
    "import gcsfs\n",
    "import datetime, calendar, time\n",
    "import pickle"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### The NEW zarrs are all in gs://cmip6/CMIP6, but there are OLD zarrs in gs://cmip6/DCPP.  \n",
    "So this notebook:\n",
    "- constructs the new catalogs (standard and noQC), saving them in the csv2 directory\n",
    "- concatenates the new csv2/* catalogs with the old (unchanging) csv1/* catalogs\n",
    "- saves the new combined catalogs in csv/"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "initialize = False\n",
    "# only initialize if starting a new updating directory - will regenerate the complete GC listings"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "# Initialize the store listings in GC_exps - should only need to be run once in awhile or if there is a problem\n",
    "# If someone else takes over, this should be re-run\n",
    "\n",
    "fs = gcsfs.GCSFileSystem(token='anon',access='read_only')\n",
    "\n",
    "if initialize:\n",
    "    last_data_update = datetime.datetime.now().strftime('%Y%m%d-%H%M')\n",
    "    \n",
    "    # Make list of all AISE already in GCS\n",
    "    acts = fs.ls(\"gs://cmip6/CMIP6/\")\n",
    "    acts.remove('cmip6/CMIP6/old_catalogs')\n",
    "\n",
    "    new_exps = []\n",
    "    for act in acts:\n",
    "        insts = fs.ls(f\"gs://{act}\")\n",
    "        for inst in insts:\n",
    "            mods = fs.ls(f\"gs://{inst}\")\n",
    "            for mod in mods:\n",
    "                exps = fs.ls(f\"gs://{mod}\")\n",
    "                for exp in exps:\n",
    "                    #print(exp)\n",
    "                    new_exps += ['_'.join(exp.split('/')[2:6])]\n",
    "\n",
    "    new_exps = sorted(list(set(new_exps))) \n",
    "\n",
    "    # Make list of all stores in each AISE\n",
    "    for AISE in new_exps:\n",
    "        GCfile = f'GC_exps/stores-{AISE}.txt'\n",
    "        #if os.path.exists(GCfile):\n",
    "        #    continue\n",
    "        aname = AISE.replace('_','/')\n",
    "        \n",
    "        command = f'gsutil -m ls gs://cmip6/CMIP6/{aname}/**/.zmetadata >& {GCfile} '\n",
    "        os.system(command)\n",
    "\n",
    "        # THE following works, but is too slow\n",
    "        #try:\n",
    "        #    flist = fs.glob(f'gs://cmip6/CMIP6/{aname}/**/.zmetadata')\n",
    "        #    #print(AISE, len(flist))\n",
    "        #    with open(GCfile, \"w\") as file:\n",
    "        #        file.write('\\n'.join(flist))    \n",
    "        #except:\n",
    "        #    print(f'skipping {AISE}')\n",
    "        #    continue\n",
    "else:\n",
    "    with open('MakeCloudCat.pickle', 'rb') as f:\n",
    "        last_data_update  = pickle.load(f)\n",
    "\n",
    "last_time = calendar.timegm(time.strptime(last_data_update, '%Y%m%d-%H%M'))\n",
    "print(last_data_update, last_time)    "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "# list all recent success logs to find updated datasets\n",
    "\n",
    "logs = glob('logs*/*success*.log')\n",
    "recent_logs = []\n",
    "for log in logs:\n",
    "    if os.path.getmtime(log) >= last_time:\n",
    "        recent_logs += [log]\n",
    "print(recent_logs)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "# list AISE for all new files in the logs\n",
    "from_date = int(last_data_update[:8])\n",
    "new_exps = []\n",
    "for logfile in recent_logs:\n",
    "    with open(logfile, \"r\") as file:\n",
    "        print(logfile)\n",
    "        lines = file.read().split('\\n')\n",
    "        for line in lines:\n",
    "            if 'saved to' in line: \n",
    "                if int(line[:8]) >= from_date:\n",
    "                    new_exps += ['_'.join(line.split('gs://cmip6/CMIP6/')[-1].split('/')[:4])]\n",
    "        \n",
    "new_exps = sorted(list(set(new_exps)))\n",
    "len(new_exps)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "# Make list of all stores in each AISE for the newly added datasets\n",
    "\n",
    "for AISE in new_exps:\n",
    "    GCfile = f'GC_exps/stores-{AISE}.txt'\n",
    "    aname = AISE.replace('_','/')\n",
    "\n",
    "    command = f'gsutil -m ls gs://cmip6/CMIP6/{aname}/**/.zmetadata >& {GCfile} '\n",
    "    os.system(command)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Detailed Recipe Here:\n",
    "\n",
    "<details>\n",
    "  <summary>Click to expand!</summary>\n",
    "  \n",
    "A. Make new noQC catalog\n",
    "    1. Collect listings of all files in GC to make dataframe 'dz_GC'\n",
    "       a. figure out which file listings need to be updated, update and concatenate\n",
    "       b. read in list of zarr stores and turn into df with 8-tuple dataset id\n",
    "    2. read dz_exclude from errata files\n",
    "    3. read in dz_old from old noQC\n",
    "    4. make dz_new with version column from old noQC or finding from tracking_ids\n",
    "    5. using vstore=zstore+version, update dz_new with status, severity and url columns\n",
    "    6. save new noQC catalog and then upload to GC\n",
    "B. Make new standard catalog\n",
    "    1. eliminate harmless issues from dz_exclude\n",
    "    2. use this (smaller) list of issues to remove datasets with more serious issues (?) from standard catalog\n",
    "    3. save new standard catalog and then upload to GC\n",
    "</details>\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "# A. Make new noQC catalog\n",
    "#    1. Collect listings of all files in GC to make dataframe 'dz_GC'\n",
    "#       b. read in list of zarr stores and turn into df with 8-tuple dataset id\n",
    "\n",
    "GCfiles = sorted(glob('GC_exps/stores-*.txt'))\n",
    "files = []\n",
    "for GCfile in GCfiles:\n",
    "    with open(GCfile, \"r\") as file:\n",
    "        files += file.read().split('\\n')\n",
    "        \n",
    "print('total number of exps:',len(GCfiles),'total number of datasets:',len(files))\n",
    "\n",
    "ddict = {}\n",
    "for item, tdir in enumerate(files):\n",
    "    if len(tdir) == 0:\n",
    "        continue\n",
    "    store = tdir.split('.zmetadata')[0]\n",
    "        \n",
    "    vlist = tdir.split('/')[-10:-1]\n",
    "    if vlist[-2] == vlist[-1]:   # unknown bug puts another zstore inside existing - e.g., 'v20210318/v20210318'\n",
    "        print('must fix:',tdir)\n",
    "        assert False\n",
    "        \n",
    "    vlist += [store]\n",
    "    ddict[item] = vlist\n",
    "\n",
    "dz_GC = pd.DataFrame.from_dict(ddict, orient='index')\n",
    "dz_GC = dz_GC.rename(columns={0: \"activity_id\", 1: \"institution_id\", 2:\"source_id\",\n",
    "                        3:\"experiment_id\",4:\"member_id\",5:\"table_id\",6:\"variable_id\",\n",
    "                        7:\"grid_label\",8:\"version\",9:\"zstore\"}) \n",
    "print('sanity check: grid_labels =',dz_GC.grid_label.unique())\n",
    "dz_GC[\"dcpp_init_year\"] = dz_GC.member_id.map(lambda x: float(x.split(\"-\")[0][1:] if x.startswith(\"s\") else np.nan))\n",
    "dz_GC[\"member_id\"] = dz_GC[\"member_id\"].map(lambda x: x.split(\"-\")[-1] if x.startswith(\"s\") else x)\n",
    "dz_GC[\"version\"] = dz_GC[\"version\"].map(lambda x: x[1:])\n",
    "\n",
    "len(dz_GC)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "# A. Make new noQC catalog\n",
    "#    2. read dz_exclude from errata files\n",
    "\n",
    "dz_exclude = pd.read_csv('ESDOC/csv/errata-files.csv')\n",
    "dz_exclude['zstore'] = ['gs://cmip6/' + s.replace('#','/v').replace('.','/')+'/'  for s in dz_exclude.file_id]\n",
    "#dz_exclude[dz_exclude.zstore == 'gs://cmip6/CMIP6/DAMIP/NASA-GISS/GISS-E2-1-G/hist-nat/r2i1p1f1/AERmon/bldep/gn/v20180906/']"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "# A. Make new noQC catalog\n",
    "#    5. using vstore=zstore+version, update dz_new with status, severity and url columns\n",
    "\n",
    "# this can be made much more efficient - with merge, etc\n",
    "\n",
    "# Find vstores (= zstore+version) in dz_GC which have issues at ES-DOC\n",
    "set_A = set(sorted(list(dz_GC.zstore.values))) \n",
    "set_B = set(sorted(list(dz_exclude.zstore.values)))\n",
    "\n",
    "in_both = sorted(list(set_A.intersection(set_B)))\n",
    "print(len(set_A),len(set_B),len(in_both))\n",
    "\n",
    "status = []\n",
    "severity = []\n",
    "url = []\n",
    "for index, row in dz_GC.iterrows():\n",
    "    zstore = row.zstore\n",
    "    if zstore in in_both:\n",
    "        dze = dz_exclude[dz_exclude.zstore==zstore]\n",
    "        status += [dze.status.values[0]]\n",
    "        severity += [dze.severity.values[0]]\n",
    "        url += [dze.issue_url.values[0]]\n",
    "    else:\n",
    "        status += ['good']\n",
    "        severity += ['none']\n",
    "        url += ['none']\n",
    "\n",
    "dz_GC['status'] = status\n",
    "dz_GC['severity'] = severity\n",
    "dz_GC['issue_url'] = url"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "dz_GC['ds_dir']=[s.split('gs://cmip6/CMIP6/')[-1].split('/v20')[0] for s in dz_GC.zstore]\n",
    "\n",
    "dz_GC = dz_GC.sort_values(by=['version'])\n",
    "dz_GC = dz_GC.drop_duplicates(subset =[\"ds_dir\"],keep='last')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "len(dz_GC)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "# MAKE SURE NEW CATALOG IS LARGER THAN OLD\n",
    "dz_old = pd.read_csv('csv2/pangeo-cmip6-noQC.csv', dtype='unicode')\n",
    "\n",
    "print(len(dz_GC),len(dz_old))\n",
    "assert len(dz_GC) >= len(dz_old)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "dz_GC = dz_GC[['activity_id', 'institution_id', 'source_id', 'experiment_id',\n",
    "       'member_id', 'table_id', 'variable_id', 'grid_label', \n",
    "       'zstore', 'dcpp_init_year', 'version', 'status', 'severity', 'issue_url']]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "#    6b. save new noQC catalog and then upload to GC\n",
    "dz_GC.to_csv('csv2/pangeo-cmip6-noQC.csv', mode='w+', index=False)"
   ]
  },
  {
   "cell_type": "raw",
   "metadata": {},
   "source": [
    "# B. Make new standard catalog\n",
    "#    1. eliminate harmless issues from dz_exclude\n",
    "#    2. use this (smaller) version to eliminate the more serious issues from standard catalog\n",
    "#    3. save new standard catalog and then upload to GC"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "# B. Make new standard catalog\n",
    "#    1. eliminate harmless issues from dz_exclude\n",
    "#       these should all be properly evaluated - I just made a first guess\n",
    "\n",
    "dz_exclude = dz_exclude[dz_exclude.status != 'resolved']\n",
    "dz_exclude = dz_exclude[dz_exclude.severity != 'low']\n",
    "dz_exclude = dz_exclude[dz_exclude.issue_uid != 'b6302400-3620-c8f1-999b-d192c0349084']\n",
    "dz_exclude = dz_exclude[dz_exclude.issue_uid != '45f9e7b9-1844-7a92-8b54-10d954e621db']\n",
    "dz_exclude = dz_exclude[dz_exclude.issue_uid != '4aa40e49-b2d4-0b29-a6b1-c80ee8dce11a']\n",
    "dz_exclude = dz_exclude[dz_exclude.issue_uid != '2f6b5963-f87e-b2df-a5b0-2f12b6b68d32']\n",
    "dz_exclude = dz_exclude[dz_exclude.issue_uid != '61fb170e-91bb-4c64-8f1d-6f5e342ee421']\n",
    "dz_exclude = dz_exclude[dz_exclude.issue_uid != '90cac29b-eaff-c450-8621-ea31e305a40e']\n",
    "dz_exclude = dz_exclude[dz_exclude.issue_uid != '8fbd8df5-c349-315b-9ec3-5a2f4ec4ec63']\n",
    "dz_exclude = dz_exclude[dz_exclude.issue_uid != 'ad5ca671-39d0-39ed-bf4f-6c8fb1a06047']"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "# B. Make new standard catalog\n",
    "#    2. use this (smaller) list of issues to eliminate the more serious issues from standard catalog\n",
    "\n",
    "# Find zstores in both:\n",
    "set_A = set(sorted(list(dz_GC.zstore.values))) \n",
    "set_B = set(sorted(list(dz_exclude.zstore.values)))\n",
    "\n",
    "in_both = sorted(list(set_A.intersection(set_B)))\n",
    "print(len(set_A),len(set_B),len(in_both))\n",
    "\n",
    "dfz = dz_GC.copy()\n",
    "dfz['issue'] = [value in in_both for value in dfz.zstore.values]\n",
    "dz_issues = dfz[dfz.issue]\n",
    "dz_clean  = dfz[dfz.issue==False]\n",
    "dz_orig = pd.concat([dfz, dz_issues, dz_issues]).drop_duplicates(keep=False)\n",
    "dz_orig = dz_orig.drop(['issue'],1)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "# MAKE SURE NEW CATALOG IS LARGER THAN OLD\n",
    "dfcat = pd.read_csv('csv2/pangeo-cmip6.csv')\n",
    "print(len(dz_orig),len(dfcat))\n",
    "assert len(dz_orig) >= len(dfcat)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "# B. Make new standard catalog\n",
    "#    3b. save new standard catalog and then upload to GC\n",
    "\n",
    "dz_orig.drop(['status','severity','issue_url'],1).to_csv('csv2/pangeo-cmip6.csv', mode='w+', index=False)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "# Now for the real catalogs"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "date = str(datetime.datetime.now().strftime(\"%Y%m%d\"))\n",
    "old_cat = f'old_catalogs/pangeo-cmip6-{date}-noQC.csv'\n",
    "os.system(f'cp csv/pangeo-cmip6-noQC.csv {old_cat}')\n",
    "os.system(f'gzip {old_cat}')\n",
    "os.system(f'rm {old_cat}')\n",
    "ret = os.system(f'/usr/bin/gsutil -m cp {old_cat}.gz gs://cmip6/CMIP6/{old_cat}.gz')\n",
    "\n",
    "old_cat = f'old_catalogs/pangeo-cmip6-{date}.csv'\n",
    "os.system(f'cp csv/pangeo-cmip6.csv {old_cat}')\n",
    "os.system(f'gzip {old_cat}')\n",
    "ret = os.system(f'/usr/bin/gsutil -m cp {old_cat}.gz gs://cmip6/CMIP6/{old_cat}.gz')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "# Combine the two catalogs - dropping the old url even if it still exists  \n",
    "#   - put in MakeCloudCat.ipynb just before saving new '-noQC' catalog and then again just before saving standard catalog\n",
    "\n",
    "df_type1 = pd.read_csv('csv1/pangeo-cmip6-noQC.csv', dtype='unicode')\n",
    "df_type1['vstore'] = df_type1.apply(lambda row: row.zstore + 'v' + str(row.version) + '/', axis = 1)\n",
    "#print(len(df_type1[df_type1.version.str.contains('/')]))\n",
    "df_type2 = pd.read_csv('csv2/pangeo-cmip6-noQC.csv', dtype='unicode')\n",
    "df_type2['vstore'] = df_type2.apply(lambda row: row.zstore.replace('/CMIP6/','/'), axis = 1)\n",
    "#print(len(df_type2[df_type2.version.str.contains('/')]))\n",
    "\n",
    "df_both = pd.concat([df_type1,df_type2])\n",
    "df_both = df_both.drop_duplicates(subset =[\"vstore\"],keep='last').drop('vstore',1)\n",
    "\n",
    "# ONLY WANT THE LATEST VERSION IN THE CATALOG\n",
    "df_both['cstore'] = df_both.apply(lambda row: row.zstore.split('gs://cmip6/')[-1].split('CMIP6/')[-1].split('v20')[0], axis = 1)\n",
    "df_both = df_both.sort_values(by=['version'])\n",
    "df_both = df_both.drop_duplicates(subset =[\"cstore\"],keep='last').drop('cstore',1)\n",
    "df_both = df_both[df_both.version != 'unknown']\n",
    "\n",
    "df_both.to_csv('csv/pangeo-cmip6-noQC.csv', mode='w+', index=False)\n",
    "\n",
    "print(len(df_type1),len(df_type2),len(df_both))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "# Combine the two catalogs - dropping the old url even if it still exists  \n",
    "#   - put in MakeCloudCat.ipynb just before saving new '-noQC' catalog and then again just before saving standard catalog\n",
    "\n",
    "df_type1 = pd.read_csv('csv1/pangeo-cmip6.csv', dtype='unicode')\n",
    "df_type1['vstore'] = df_type1.apply(lambda row: row.zstore + 'v' + str(row.version) + '/', axis = 1)\n",
    "df_type2 = pd.read_csv('csv2/pangeo-cmip6.csv', dtype='unicode')\n",
    "df_type2['vstore'] = df_type2.apply(lambda row: row.zstore.replace('/CMIP6/','/'), axis = 1)\n",
    "\n",
    "df_both = pd.concat([df_type1,df_type2])\n",
    "df_both = df_both.drop_duplicates(subset =[\"vstore\"],keep='last').drop('vstore',1)\n",
    "\n",
    "# ONLY WANT THE LATEST VERSION IN THE CATALOG\n",
    "df_both['cstore'] = df_both.apply(lambda row: row.zstore.split('gs://cmip6/')[-1].split('CMIP6/')[-1].split('v20')[0], axis = 1)\n",
    "df_both = df_both.sort_values(by=['version'])\n",
    "df_both = df_both.drop_duplicates(subset =[\"cstore\"],keep='last').drop('cstore',1)\n",
    "df_both = df_both[df_both.version != 'unknown']\n",
    "\n",
    "df_both.to_csv('csv/pangeo-cmip6.csv', mode='w+', index=False)\n",
    "\n",
    "print(len(df_type1),len(df_type2),len(df_both))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "ret = os.system('/usr/bin/gsutil -m cp csv/pangeo-cmip6-noQC.csv gs://cmip6/pangeo-cmip6-noQC.csv')\n",
    "if ret != 0:\n",
    "    print('noQC upload not working')\n",
    "\n",
    "ret = os.system('/usr/bin/gsutil -m cp csv/pangeo-cmip6-noQC.csv gs://cmip6/cmip6-zarr-consolidated-stores-noQC.csv')\n",
    "if ret != 0:\n",
    "    print('noQC upload not working')\n",
    "    \n",
    "ret = os.system('/usr/bin/gsutil -m cp csv/pangeo-cmip6.csv gs://cmip6/pangeo-cmip6.csv')\n",
    "if ret != 0:\n",
    "    print('noQC upload not working')\n",
    "\n",
    "ret = os.system('/usr/bin/gsutil -m cp csv/pangeo-cmip6.csv gs://cmip6/cmip6-zarr-consolidated-stores.csv')\n",
    "if ret != 0:\n",
    "    print('noQC upload not working')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "last_data_update = datetime.datetime.now().strftime('%Y%m%d-%H%M')\n",
    "with open('MakeCloudCat.pickle', 'wb') as f:\n",
    "    pickle.dump(last_data_update, f)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "last_data_update"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
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